Menu
▾
▴
pymol-users — Collaborative support and tips for PyMOL users
You can subscribe to this list here.
| 2001 |
Jan
|
Feb
|
Mar
|
Apr
|
May
|
Jun
|
Jul
|
Aug
|
Sep
|
Oct
(13) |
Nov
(22) |
Dec
(35) |
|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 2002 |
Jan
(33) |
Feb
(46) |
Mar
(56) |
Apr
(29) |
May
(56) |
Jun
(30) |
Jul
(64) |
Aug
(54) |
Sep
(86) |
Oct
(106) |
Nov
(50) |
Dec
(67) |
| 2003 |
Jan
(78) |
Feb
(98) |
Mar
(51) |
Apr
(95) |
May
(53) |
Jun
(103) |
Jul
(93) |
Aug
(64) |
Sep
(87) |
Oct
(93) |
Nov
(78) |
Dec
(86) |
| 2004 |
Jan
(83) |
Feb
(90) |
Mar
(64) |
Apr
(112) |
May
(103) |
Jun
(57) |
Jul
(101) |
Aug
(84) |
Sep
(92) |
Oct
(96) |
Nov
(86) |
Dec
(32) |
| 2005 |
Jan
(88) |
Feb
(108) |
Mar
(111) |
Apr
(107) |
May
(120) |
Jun
(134) |
Jul
(143) |
Aug
(129) |
Sep
(75) |
Oct
(171) |
Nov
(125) |
Dec
(65) |
| 2006 |
Jan
(95) |
Feb
(105) |
Mar
(114) |
Apr
(124) |
May
(87) |
Jun
(66) |
Jul
(88) |
Aug
(65) |
Sep
(71) |
Oct
(92) |
Nov
(94) |
Dec
(60) |
| 2007 |
Jan
(81) |
Feb
(84) |
Mar
(82) |
Apr
(68) |
May
(58) |
Jun
(80) |
Jul
(30) |
Aug
(47) |
Sep
(68) |
Oct
(92) |
Nov
(59) |
Dec
(17) |
| 2008 |
Jan
(69) |
Feb
(81) |
Mar
(60) |
Apr
(34) |
May
(47) |
Jun
(65) |
Jul
(46) |
Aug
(49) |
Sep
(84) |
Oct
(43) |
Nov
(33) |
Dec
(30) |
| 2009 |
Jan
(62) |
Feb
(48) |
Mar
(123) |
Apr
(73) |
May
(72) |
Jun
(69) |
Jul
(78) |
Aug
(72) |
Sep
(99) |
Oct
(82) |
Nov
(70) |
Dec
(53) |
| 2010 |
Jan
(112) |
Feb
(95) |
Mar
(127) |
Apr
(110) |
May
(135) |
Jun
(91) |
Jul
(91) |
Aug
(79) |
Sep
(136) |
Oct
(63) |
Nov
(38) |
Dec
(64) |
| 2011 |
Jan
(59) |
Feb
(109) |
Mar
(191) |
Apr
(130) |
May
(94) |
Jun
(90) |
Jul
(89) |
Aug
(127) |
Sep
(135) |
Oct
(113) |
Nov
(136) |
Dec
(140) |
| 2012 |
Jan
(158) |
Feb
(131) |
Mar
(151) |
Apr
(88) |
May
(121) |
Jun
(85) |
Jul
(82) |
Aug
(56) |
Sep
(55) |
Oct
(125) |
Nov
(87) |
Dec
(65) |
| 2013 |
Jan
(81) |
Feb
(64) |
Mar
(90) |
Apr
(77) |
May
(80) |
Jun
(92) |
Jul
(92) |
Aug
(70) |
Sep
(69) |
Oct
(60) |
Nov
(99) |
Dec
(50) |
| 2014 |
Jan
(89) |
Feb
(66) |
Mar
(52) |
Apr
(70) |
May
(68) |
Jun
(44) |
Jul
(68) |
Aug
(81) |
Sep
(152) |
Oct
(106) |
Nov
(74) |
Dec
(57) |
| 2015 |
Jan
(93) |
Feb
(48) |
Mar
(60) |
Apr
(107) |
May
(82) |
Jun
(64) |
Jul
(74) |
Aug
(38) |
Sep
(49) |
Oct
(99) |
Nov
(105) |
Dec
(51) |
| 2016 |
Jan
(68) |
Feb
(87) |
Mar
(55) |
Apr
(90) |
May
(68) |
Jun
(25) |
Jul
(25) |
Aug
(41) |
Sep
(35) |
Oct
(55) |
Nov
(24) |
Dec
(26) |
| 2017 |
Jan
(59) |
Feb
(49) |
Mar
(24) |
Apr
(50) |
May
(45) |
Jun
(63) |
Jul
(36) |
Aug
(26) |
Sep
(22) |
Oct
(23) |
Nov
(26) |
Dec
(29) |
| 2018 |
Jan
(17) |
Feb
(21) |
Mar
(30) |
Apr
(34) |
May
(24) |
Jun
(47) |
Jul
(65) |
Aug
(30) |
Sep
(24) |
Oct
(52) |
Nov
(21) |
Dec
(17) |
| 2019 |
Jan
(9) |
Feb
(39) |
Mar
(32) |
Apr
(22) |
May
(30) |
Jun
(69) |
Jul
(40) |
Aug
(48) |
Sep
(17) |
Oct
(26) |
Nov
(30) |
Dec
(19) |
| 2020 |
Jan
(32) |
Feb
(26) |
Mar
(16) |
Apr
(34) |
May
(50) |
Jun
(87) |
Jul
(51) |
Aug
(23) |
Sep
(25) |
Oct
(48) |
Nov
(32) |
Dec
(6) |
| 2021 |
Jan
(12) |
Feb
(31) |
Mar
(15) |
Apr
(31) |
May
(13) |
Jun
(13) |
Jul
(24) |
Aug
(9) |
Sep
(11) |
Oct
(28) |
Nov
(26) |
Dec
(25) |
| 2022 |
Jan
(47) |
Feb
(22) |
Mar
(22) |
Apr
(12) |
May
(4) |
Jun
(26) |
Jul
(17) |
Aug
(2) |
Sep
(13) |
Oct
(6) |
Nov
(13) |
Dec
(4) |
| 2023 |
Jan
(7) |
Feb
(6) |
Mar
(13) |
Apr
(2) |
May
(25) |
Jun
(13) |
Jul
(12) |
Aug
(10) |
Sep
(5) |
Oct
(13) |
Nov
(19) |
Dec
(7) |
| 2024 |
Jan
(3) |
Feb
(12) |
Mar
(1) |
Apr
(13) |
May
(11) |
Jun
|
Jul
(20) |
Aug
(4) |
Sep
(4) |
Oct
(5) |
Nov
(4) |
Dec
(6) |
| 2025 |
Jan
(16) |
Feb
(8) |
Mar
(10) |
Apr
(6) |
May
(13) |
Jun
(7) |
Jul
(4) |
Aug
(1) |
Sep
|
Oct
|
Nov
|
Dec
|
|
From: sunyeping <sun...@al...> - 2020-06-17 03:05:40
|
Dear pymol users, I am trying to align two very similar trimeric molecules. I tried different alignment commands including "align", "cealign" and "super", but none of them gives satisfying effect. Athough the backbone conformations and orientations of two two molecules look very similar, there are obvious displacements between them after alignment with these three commands. The rmsd of the two molecules for these three methods are 2.250, 4.682, 2.206 and 2.206, respectively. I wonder whether there is any better alignment command or there are any parameters that can be passed to these three alignment commands to improve the effects. Could you help me check this? The pdb files of these two molecules, the image for the two molecules after using "super" command, and the alignment effect in the publication I mentioned can be found at the following link. https://drive.google.com/file/d/1ff3XgTexgdul-SezUz75dVoCx2cL5YPL/view?usp=sharing With many thanks. |
|
From: Chen, Q. <qi...@pi...> - 2020-06-16 20:38:32
|
This script will have a memory issue. My pymol will stuck if I have more than 3 files be processed.
file_list = [f'{m:02d}' for m in list(range(1,30,1))]
[cmd.do("load model.000."+str(k)+"_minimized.pdb") for k in file_list]
object_list=cmd.get_object_list('(model.000.*_minimized)')
chains=[('A','F'),('B', 'F'),('C','F'),('D','F'),('E','F')]
run C:\Users\user\AppData\Local\Programs\Python\Python38\lib\site-packages\pymol\pymol_path\Pymol-script-repo\list_hb.py
[cmd.do("list_hb chain F, chain A:E, write_distances_file=hb_"+str(file)+".txt") for file in object_list ]
I modified from the sample script here
https://www.pymolwiki.org/index.php/Process_All_Files_In_Directory
Save the following lines in a file named as, eg. multiple_hb.py and make sure list_hb.py in the working directory of searching directory.
Then run multiple_hb.py in the pymol command line.
from pymol import cmd
from glob import glob
for file in glob("model.000.*.pdb"):
print(file)
#file_list = [f'{m:02d}' for m in list(range(0,30,1))]
cmd.load(file)
obj=cmd.get_object_list('all')
print(obj)
#chains=[('A','F'),('B', 'F'),('C','F'),('D','F'),('E','F')]
cmd.do("run list_hb.py")
cmd.do("list_hb chain F, chain A:E, write_distances_file=hb_"+str(obj[0])+".txt")
cmd.delete("all”)
On Jun 16, 2020, at 11:15 AM, pym...@li...<mailto:pym...@li...> wrote:
Send PyMOL-users mailing list submissions to
pym...@li...<mailto:pym...@li...>
To subscribe or unsubscribe via the World Wide Web, visit
https://nam05.safelinks.protection.outlook.com/?url=https%3A%2F%2Flists.sourceforge.net%2Flists%2Flistinfo%2Fpymol-users&data=02%7C01%7Cqic8%40pitt.edu%7C4ec7afdbd857446afad308d812081e49%7C9ef9f489e0a04eeb87cc3a526112fd0d%7C1%7C0%7C637279173371378327&sdata=v28nxT%2ByGrbeZCuvUvBY327R7wDd2z%2FSDo13H8%2BoPwc%3D&reserved=0
or, via email, send a message with subject or body 'help' to
pym...@li...
You can reach the person managing the list at
pym...@li...
When replying, please edit your Subject line so it is more specific
than "Re: Contents of PyMOL-users digest..."
Today's Topics:
1. Re: hydrogen bond list for a series of files
(Mooers, Blaine H.M. (HSC))
2. Re: hydrogen bond list for a series of files (Chen, Qiang)
----------------------------------------------------------------------
Message: 1
Date: Tue, 16 Jun 2020 14:51:38 +0000
From: "Mooers, Blaine H.M. (HSC)" <Bla...@ou...>
To: "Chen, Qiang" <qi...@pi...>, "pym...@li..."
<pym...@li...>
Subject: Re: [PyMOL] hydrogen bond list for a series of files
Message-ID:
<87D...@CO...>
Content-Type: text/plain; charset="Windows-1252"
Hi Charlie,
This will give the desired list.
file_list = [f'{m:02d}' for m in list(range(1,30,1))]
print(file_list)
Best regards,
Blaine
Blaine Mooers, Ph.D.
Associate Professor
Department of Biochemistry and Molecular Biology
College of Medicine
University of Oklahoma Health Sciences Center
S.L. Young Biomedical Research Center (BRC) Rm. 466
975 NE 10th Street, BRC 466
Oklahoma City, OK 73104-5419
________________________________________
From: Chen, Qiang [qi...@pi...]
Sent: Tuesday, June 16, 2020 9:26 AM
To: Mooers, Blaine H.M. (HSC); pym...@li...
Subject: [EXTERNAL] Re: hydrogen bond list for a series of files
Hi, Blaine,
Then the question becomes how to generate a list with 30 or 300 numbers.
Will this work?
file_list=list(range(00, 30))
Thanks!
Charles
________________________________
From: Mooers, Blaine H.M. (HSC) <Bla...@ou...>
Sent: Tuesday, June 16, 2020 9:57 AM
To: Chen, Qiang <qi...@pi...>; pym...@li... <pym...@li...>
Subject: RE: hydrogen bond list for a series of files
Hi Charles,
You are right and I am wrong about the files needing to be loaded.
The object name has the pesky pdb file extension stripped off, so lets use the object name instead of using Python to strip it off for us.
We no longer need to use glob.
We do need to the create a list of strings that encode the indexing of the files.
This code worked for me with two files.
Adapt to your 30 or 300 files.
file_list = ['01','02']
[cmd.do("load model.000."+str(k)+"_minimized.pdb") for k in file_list]
object_list=cmd.get_object_list('(model.000.*_minimized)')
chains=[('A','F'),('B', 'F'),('C','F'),('D','F'),('E','F')]
run C:\Users\user\AppData\Local\Programs\Python\Python38\lib\site-packages\pymol\pymol_path\Pymol-script-repo\list_hb.py
[cmd.do("list_hb chain F, chain A:E, write_distances_file=hb_"+str(file)+".txt") for file in object_list ]
Best regards,
Blaine
Blaine Mooers, Ph.D.
Associate Professor
Department of Biochemistry and Molecular Biology
College of Medicine
University of Oklahoma Health Sciences Center
S.L. Young Biomedical Research Center (BRC) Rm. 466
975 NE 10th Street, BRC 466
Oklahoma City, OK 73104-5419
________________________________________
From: Chen, Qiang [qi...@pi...]
Sent: Monday, June 15, 2020 10:18 PM
To: Mooers, Blaine H.M. (HSC); pym...@li...
Subject: [EXTERNAL] Re: hydrogen bond list for a series of files
Thanks, Dr. Mooers.
I modified a little.
It seems the pdb files need be loaded.
I put all the following lines in a file multifile_hb.pml
run C:\Users\user\AppData\Local\Programs\Python\Python38\lib\site-packages\pymol\pymol_path\Pymol-script-repo\list_hb.py
import glob
load model.000.*_minimized.pdb
#chains=[('A','F'),('B', 'F'),('C','F'),('D','F'),('E','F')]
[cmd.do("list_hb chain F, chain A:E, write_distances_file=hb_"+str(file)+".txt") for file in glob.glob("model.000.??_minimized.pdb")]
A little not so perfect is that the output file,
hb_model.000.??_minimized.pdb.txt
Is is possible to do something like this
write_distances_file=hb_"+basename(file)+".txt"
Then the output will be
hb_model.000.??_minimized.txt
I tried, and this simple thing does not work.
Any suggestion?
Thanks!
Charles
________________________________
From: Mooers, Blaine H.M. (HSC) <Bla...@ou...>
Sent: Monday, June 15, 2020 9:44 PM
To: Chen, Qiang <qi...@pi...>; pym...@li... <pym...@li...>
Subject: RE: hydrogen bond list for a series of files
Hi Charles,
Make sure that PyMOL's present working directory is where the pdb files are stored.
Copy and paste each of the four lines below one at a time on the command line in PyMOL.
run list_hb.py<https://nam05.safelinks.protection.outlook.com/?url=https%3A%2F%2Furldefense.proofpoint.com%2Fv2%2Furl%3Fu%3Dhttp-3A__list-5Fhb.py%26d%3DDwQF-g%26c%3DVjzId-SM5S6aVB_cCGQ0d3uo9UfKByQ3sI6Audoy6dY%26r%3Dk0gMbcsdOcdbPUNV5tW66KQSZfXL0ewVDPVBp7tqbks%26m%3DX2B3s7D21CBjGtOAQJ2noNR7vnKXPiHiT2eLIRiSC18%26s%3DKYQX_tOI8_HnmseLbJRMv7UTirG78evoaztp35Gg74E%26e%3D&data=02%7C01%7Cqic8%40pitt.edu%7C4ec7afdbd857446afad308d812081e49%7C9ef9f489e0a04eeb87cc3a526112fd0d%7C1%7C0%7C637279173371388314&sdata=3P2lfWf2Q00u%2FEXkXRI4PiebkpUWkT%2Fx9vU2Zn2WV60%3D&reserved=0<https://nam05.safelinks.protection.outlook.com/?url=https%3A%2F%2Furldefense.proofpoint.com%2Fv2%2Furl%3Fu%3Dhttps-3A__nam05.safelinks.protection.outlook.com_-3Furl-3Dhttps-253A-252F-252Furldefense.proofpoint.com-252Fv2-252Furl-253Fu-253Dhttp-2D3A-5F-5Flist-2D5Fhb.py-2526d-253DDwQF-2Dg-2526c-253DVjzId-2DSM5S6aVB-5FcCGQ0d3uo9UfKByQ3sI6Audoy6dY-2526r-253Dk0gMbcsdOcdbPUNV5tW66KQSZfXL0ewVDPVBp7tqbks-2526m-253DX2B3s7D21CBjGtOAQJ2noNR7vnKXPiHiT2eLIRiSC18-2526s-253DKYQX-5FtOI8-5FHnmseLbJRMv7UTirG78evoaztp35Gg74E-2526e-253D-26amp-3Bdata-3D02-257C01-257Cqic8-2540pitt.edu-257C2ea32a0b061443a37f1908d811fd40fd-257C9ef9f489e0a04eeb87cc3a526112fd0d-257C1-257C0-257C637279126707606574-26amp-3Bsdata-3D8VnRodmeEUrqQfFm7fe0gqd02cYPsKv8VxPcb09RIkQ-253D-26amp-3Breserved-3D0%26d%3DDwMF-g%26c%3DVjzId-SM5S6aVB_cCGQ0d3uo9UfKByQ3sI6Audoy6dY%26r%3Dk0gMbcsdOcdbPUNV5tW66KQSZfXL0ewVDPVBp7tqbks%26m%3DQ6LxvA7WaglxixxzDsbpjU7pbOFqJPXxmweHw0k_x7I%26s%3D6cyeevFFP1ip0quoSgRLS9fqrvVtj8JlnLJWMpJWqFg%26e%3D&data=02%7C01%7Cqic8%40pitt.edu%7C4ec7afdbd857446afad308d812081e49%7C9ef9f489e0a04eeb87cc3a526112fd0d%7C1%7C0%7C637279173371388314&sdata=UAhgDbT%2BFe4seXKcS%2FKeKAdARmT8pHxKdUB3yyz2rk4%3D&reserved=0>>
import glob
chains = [('A','B'), ('A','C'), ('A','D'), ('A','E'), ('B','C'), ('B','D'), ('B','E'), ('C','D'), ('C','E'), ('D','E') ]
[[cmd.do("list_hb chain "+ str(i) +", chain " +str(j) + ", write_distances_file=hb_"+ str(file) + "_" + str(i) + "_" +str( j) + "_001.txt") for i, j in chains] for file in glob.glob("model.??.pdb")]
Note that you do not have to load the pdb files into PyMOL.
If you want to analyze more than 99 files and less than 999 files, add a third question mark to the argument of glob.glob().
Best regards,
Blaine
Blaine Mooers, Ph.D.
Associate Professor
Department of Biochemistry and Molecular Biology
College of Medicine
University of Oklahoma Health Sciences Center
S.L. Young Biomedical Research Center (BRC) Rm. 466
975 NE 10th Street, BRC 466
Oklahoma City, OK 73104-5419
________________________________________
From: Chen, Qiang [qi...@pi...]
Sent: Monday, June 15, 2020 2:53 PM
To: pym...@li...
Subject: [EXTERNAL] [PyMOL] hydrogen bond list for a series of files
Hi, Pymol users
Could you help me do this in an efficient way?
Let me describe the task I try to do.
I have a series of numerically ordered files, say model00.pdb model.01.pdb ?? model.30.pdb
All the pdb have the same protein composition, chain A, B, C, D, and E. Their relative position is different in each file.
I would like to check the hydrogen bonds between, say, chain A and B.
Thanks to Prof. Robert L. Campbell, I can list the hydrogen bonds in one pdb and print the list as the follows
list_hb chain A, chain B, write_distances_file=hb_A_B_01.txt
How can I process the 30 files in an efficient way? what if I have 300 pdb files?
Shell script, python, or anything else?
Thanks!
Charles Chen
_______________________________________________
PyMOL-users mailing list
Archives: https://nam05.safelinks.protection.outlook.com/?url=https%3A%2F%2Furldefense.proofpoint.com%2Fv2%2Furl%3Fu%3Dhttp-3A__www.mail-2Darchive.com_pymol-2Dusers-40lists.sourceforge.net%26d%3DDwIGaQ%26c%3DVjzId-SM5S6aVB_cCGQ0d3uo9UfKByQ3sI6Audoy6dY%26r%3Dk0gMbcsdOcdbPUNV5tW66KQSZfXL0ewVDPVBp7tqbks%26m%3DxyAmhZRZYDjhbBLdiMRRk6wCJ14kA5UeQYC4urBFvQw%26s%3DaOpeSOw9Gqop8KF8Xf_lkPoBC_MSbb5i0cKlRaIAulI%26e%3D&data=02%7C01%7Cqic8%40pitt.edu%7C4ec7afdbd857446afad308d812081e49%7C9ef9f489e0a04eeb87cc3a526112fd0d%7C1%7C0%7C637279173371388314&sdata=Nj27saqQ0NO7f2sQ2B5tJdKbpCaabdaPk6YKhpfXvrs%3D&reserved=0<https://nam05.safelinks.protection.outlook.com/?url=https%3A%2F%2Furldefense.proofpoint.com%2Fv2%2Furl%3Fu%3Dhttps-3A__nam05.safelinks.protection.outlook.com_-3Furl-3Dhttps-253A-252F-252Furldefense.proofpoint.com-252Fv2-252Furl-253Fu-253Dhttp-2D3A-5F-5Fwww.mail-2D2Darchive.com-5Fpymol-2D2Dusers-2D40lists.sourceforge.net-2526d-253DDwIGaQ-2526c-253DVjzId-2DSM5S6aVB-5FcCGQ0d3uo9UfKByQ3sI6Audoy6dY-2526r-253Dk0gMbcsdOcdbPUNV5tW66KQSZfXL0ewVDPVBp7tqbks-2526m-253DxyAmhZRZYDjhbBLdiMRRk6wCJ14kA5UeQYC4urBFvQw-2526s-253DaOpeSOw9Gqop8KF8Xf-5FlkPoBC-5FMSbb5i0cKlRaIAulI-2526e-253D-26amp-3Bdata-3D02-257C01-257Cqic8-2540pitt.edu-257C01a30e93a2ca4a40b37308d81196d7ba-257C9ef9f489e0a04eeb87cc3a526112fd0d-257C1-257C0-257C637278686852886299-26amp-3Bsdata-3DH-252BbXZ7ylGnf8aHeqS8UfkWyeYYuKCLZv1GikWVh2gAM-253D-26amp-3Breserved-3D0%26d%3DDwMF-g%26c%3DVjzId-SM5S6aVB_cCGQ0d3uo9UfKByQ3sI6Audoy6dY%26r%3Dk0gMbcsdOcdbPUNV5tW66KQSZfXL0ewVDPVBp7tqbks%26m%3DX2B3s7D21CBjGtOAQJ2noNR7vnKXPiHiT2eLIRiSC18%26s%3DUml8pWJGL1VV1FRsRqY0A8xQ-ZVcOqvXJIUCvJgGjSY%26e%3D&data=02%7C01%7Cqic8%40pitt.edu%7C4ec7afdbd857446afad308d812081e49%7C9ef9f489e0a04eeb87cc3a526112fd0d%7C1%7C0%7C637279173371388314&sdata=KMnRP7MISFydbuZGP3Lv7%2BhFnl13MEF1WEQ%2BPDuF494%3D&reserved=0>
Unsubscribe: https://nam05.safelinks.protection.outlook.com/?url=https%3A%2F%2Furldefense.proofpoint.com%2Fv2%2Furl%3Fu%3Dhttps-3A__sourceforge.net_projects_pymol_lists_pymol-2Dusers_unsubscribe%26d%3DDwIGaQ%26c%3DVjzId-SM5S6aVB_cCGQ0d3uo9UfKByQ3sI6Audoy6dY%26r%3Dk0gMbcsdOcdbPUNV5tW66KQSZfXL0ewVDPVBp7tqbks%26m%3DxyAmhZRZYDjhbBLdiMRRk6wCJ14kA5UeQYC4urBFvQw%26s%3DPY-g0XYMB9DqXC06Iixbjxfqf8jB9Pb_GFu8zClx3oY%26e%3D&data=02%7C01%7Cqic8%40pitt.edu%7C4ec7afdbd857446afad308d812081e49%7C9ef9f489e0a04eeb87cc3a526112fd0d%7C1%7C0%7C637279173371388314&sdata=J7iovKUIEHJ28eMxPcjWJ1ukh6hunV8eq4Sf4Rq1c4U%3D&reserved=0<https://nam05.safelinks.protection.outlook.com/?url=https%3A%2F%2Furldefense.proofpoint.com%2Fv2%2Furl%3Fu%3Dhttps-3A__nam05.safelinks.protection.outlook.com_-3Furl-3Dhttps-253A-252F-252Furldefense.proofpoint.com-252Fv2-252Furl-253Fu-253Dhttps-2D3A-5F-5Fsourceforge.net-5Fprojects-5Fpymol-5Flists-5Fpymol-2D2Dusers-5Funsubscribe-2526d-253DDwIGaQ-2526c-253DVjzId-2DSM5S6aVB-5FcCGQ0d3uo9UfKByQ3sI6Audoy6dY-2526r-253Dk0gMbcsdOcdbPUNV5tW66KQSZfXL0ewVDPVBp7tqbks-2526m-253DxyAmhZRZYDjhbBLdiMRRk6wCJ14kA5UeQYC4urBFvQw-2526s-253DPY-2Dg0XYMB9DqXC06Iixbjxfqf8jB9Pb-5FGFu8zClx3oY-2526e-253D-26amp-3Bdata-3D02-257C01-257Cqic8-2540pitt.edu-257C01a30e93a2ca4a40b37308d81196d7ba-257C9ef9f489e0a04eeb87cc3a526112fd0d-257C1-257C0-257C637278686852886299-26amp-3Bsdata-3Do1asKPIbwdAFwN-252FCJSTCXDg-252BndmmLXC8VJW8z48Y-252BAA-253D-26amp-3Breserved-3D0%26d%3DDwMF-g%26c%3DVjzId-SM5S6aVB_cCGQ0d3uo9UfKByQ3sI6Audoy6dY%26r%3Dk0gMbcsdOcdbPUNV5tW66KQSZfXL0ewVDPVBp7tqbks%26m%3DX2B3s7D21CBjGtOAQJ2noNR7vnKXPiHiT2eLIRiSC18%26s%3D52GYpWEgXcbl5EqO1gYdzX31C41KuEUPECZU1zDR_TU%26e%3D&data=02%7C01%7Cqic8%40pitt.edu%7C4ec7afdbd857446afad308d812081e49%7C9ef9f489e0a04eeb87cc3a526112fd0d%7C1%7C0%7C637279173371398312&sdata=MNwexB0N5N91cfjWjfFxuJUG6UwzjwxfRQdclayPPQQ%3D&reserved=0>
------------------------------
Message: 2
Date: Tue, 16 Jun 2020 15:15:11 +0000
From: "Chen, Qiang" <qi...@pi...>
To: "Mooers, Blaine H.M. (HSC)" <Bla...@ou...>,
"pym...@li..."
<pym...@li...>
Subject: Re: [PyMOL] hydrogen bond list for a series of files
Message-ID:
<BL0...@BL...>
Content-Type: text/plain; charset="windows-1252"
Great, thanks!
Really appreciate your help!
Charles
________________________________
From: Mooers, Blaine H.M. (HSC) <Bla...@ou...>
Sent: Tuesday, June 16, 2020 10:51 AM
To: Chen, Qiang <qi...@pi...>; pym...@li... <pym...@li...>
Subject: RE: hydrogen bond list for a series of files
Hi Charlie,
This will give the desired list.
file_list = [f'{m:02d}' for m in list(range(1,30,1))]
print(file_list)
Best regards,
Blaine
Blaine Mooers, Ph.D.
Associate Professor
Department of Biochemistry and Molecular Biology
College of Medicine
University of Oklahoma Health Sciences Center
S.L. Young Biomedical Research Center (BRC) Rm. 466
975 NE 10th Street, BRC 466
Oklahoma City, OK 73104-5419
________________________________________
From: Chen, Qiang [qi...@pi...]
Sent: Tuesday, June 16, 2020 9:26 AM
To: Mooers, Blaine H.M. (HSC); pym...@li...
Subject: [EXTERNAL] Re: hydrogen bond list for a series of files
Hi, Blaine,
Then the question becomes how to generate a list with 30 or 300 numbers.
Will this work?
file_list=list(range(00, 30))
Thanks!
Charles
________________________________
From: Mooers, Blaine H.M. (HSC) <Bla...@ou...>
Sent: Tuesday, June 16, 2020 9:57 AM
To: Chen, Qiang <qi...@pi...>; pym...@li... <pym...@li...>
Subject: RE: hydrogen bond list for a series of files
Hi Charles,
You are right and I am wrong about the files needing to be loaded.
The object name has the pesky pdb file extension stripped off, so lets use the object name instead of using Python to strip it off for us.
We no longer need to use glob.
We do need to the create a list of strings that encode the indexing of the files.
This code worked for me with two files.
Adapt to your 30 or 300 files.
file_list = ['01','02']
[cmd.do("load model.000."+str(k)+"_minimized.pdb") for k in file_list]
object_list=cmd.get_object_list('(model.000.*_minimized)')
chains=[('A','F'),('B', 'F'),('C','F'),('D','F'),('E','F')]
run C:\Users\user\AppData\Local\Programs\Python\Python38\lib\site-packages\pymol\pymol_path\Pymol-script-repo\list_hb.py
[cmd.do("list_hb chain F, chain A:E, write_distances_file=hb_"+str(file)+".txt") for file in object_list ]
Best regards,
Blaine
Blaine Mooers, Ph.D.
Associate Professor
Department of Biochemistry and Molecular Biology
College of Medicine
University of Oklahoma Health Sciences Center
S.L. Young Biomedical Research Center (BRC) Rm. 466
975 NE 10th Street, BRC 466
Oklahoma City, OK 73104-5419
________________________________________
From: Chen, Qiang [qi...@pi...]
Sent: Monday, June 15, 2020 10:18 PM
To: Mooers, Blaine H.M. (HSC); pym...@li...
Subject: [EXTERNAL] Re: hydrogen bond list for a series of files
Thanks, Dr. Mooers.
I modified a little.
It seems the pdb files need be loaded.
I put all the following lines in a file multifile_hb.pml
run C:\Users\user\AppData\Local\Programs\Python\Python38\lib\site-packages\pymol\pymol_path\Pymol-script-repo\list_hb.py
import glob
load model.000.*_minimized.pdb
#chains=[('A','F'),('B', 'F'),('C','F'),('D','F'),('E','F')]
[cmd.do("list_hb chain F, chain A:E, write_distances_file=hb_"+str(file)+".txt") for file in glob.glob("model.000.??_minimized.pdb")]
A little not so perfect is that the output file,
hb_model.000.??_minimized.pdb.txt
Is is possible to do something like this
write_distances_file=hb_"+basename(file)+".txt"
Then the output will be
hb_model.000.??_minimized.txt
I tried, and this simple thing does not work.
Any suggestion?
Thanks!
Charles
________________________________
From: Mooers, Blaine H.M. (HSC) <Bla...@ou...>
Sent: Monday, June 15, 2020 9:44 PM
To: Chen, Qiang <qi...@pi...>; pym...@li... <pym...@li...>
Subject: RE: hydrogen bond list for a series of files
Hi Charles,
Make sure that PyMOL's present working directory is where the pdb files are stored.
Copy and paste each of the four lines below one at a time on the command line in PyMOL.
run list_hb.py<https://nam05.safelinks.protection.outlook.com/?url=https%3A%2F%2Furldefense.proofpoint.com%2Fv2%2Furl%3Fu%3Dhttp-3A__list-5Fhb.py%26d%3DDwQF-g%26c%3DVjzId-SM5S6aVB_cCGQ0d3uo9UfKByQ3sI6Audoy6dY%26r%3Dk0gMbcsdOcdbPUNV5tW66KQSZfXL0ewVDPVBp7tqbks%26m%3DX2B3s7D21CBjGtOAQJ2noNR7vnKXPiHiT2eLIRiSC18%26s%3DKYQX_tOI8_HnmseLbJRMv7UTirG78evoaztp35Gg74E%26e%3D&data=02%7C01%7Cqic8%40pitt.edu%7C4ec7afdbd857446afad308d812081e49%7C9ef9f489e0a04eeb87cc3a526112fd0d%7C1%7C0%7C637279173371398312&sdata=ilvH%2BGXKjFH7emRi360ey7DCVVXcuWaR0cNmrcs%2BCZs%3D&reserved=0<https://nam05.safelinks.protection.outlook.com/?url=https%3A%2F%2Furldefense.proofpoint.com%2Fv2%2Furl%3Fu%3Dhttps-3A__nam05.safelinks.protection.outlook.com_-3Furl-3Dhttps-253A-252F-252Furldefense.proofpoint.com-252Fv2-252Furl-253Fu-253Dhttp-2D3A-5F-5Flist-2D5Fhb.py-2526d-253DDwQF-2Dg-2526c-253DVjzId-2DSM5S6aVB-5FcCGQ0d3uo9UfKByQ3sI6Audoy6dY-2526r-253Dk0gMbcsdOcdbPUNV5tW66KQSZfXL0ewVDPVBp7tqbks-2526m-253DX2B3s7D21CBjGtOAQJ2noNR7vnKXPiHiT2eLIRiSC18-2526s-253DKYQX-5FtOI8-5FHnmseLbJRMv7UTirG78evoaztp35Gg74E-2526e-253D-26amp-3Bdata-3D02-257C01-257Cqic8-2540pitt.edu-257C2ea32a0b061443a37f1908d811fd40fd-257C9ef9f489e0a04eeb87cc3a526112fd0d-257C1-257C0-257C637279126707606574-26amp-3Bsdata-3D8VnRodmeEUrqQfFm7fe0gqd02cYPsKv8VxPcb09RIkQ-253D-26amp-3Breserved-3D0%26d%3DDwMF-g%26c%3DVjzId-SM5S6aVB_cCGQ0d3uo9UfKByQ3sI6Audoy6dY%26r%3Dk0gMbcsdOcdbPUNV5tW66KQSZfXL0ewVDPVBp7tqbks%26m%3DQ6LxvA7WaglxixxzDsbpjU7pbOFqJPXxmweHw0k_x7I%26s%3D6cyeevFFP1ip0quoSgRLS9fqrvVtj8JlnLJWMpJWqFg%26e%3D&data=02%7C01%7Cqic8%40pitt.edu%7C4ec7afdbd857446afad308d812081e49%7C9ef9f489e0a04eeb87cc3a526112fd0d%7C1%7C0%7C637279173371398312&sdata=0rqBcuqgLy243MKuKcWJnqKh8kL5JPs24Ya4hRWvW0M%3D&reserved=0>>
import glob
chains = [('A','B'), ('A','C'), ('A','D'), ('A','E'), ('B','C'), ('B','D'), ('B','E'), ('C','D'), ('C','E'), ('D','E') ]
[[cmd.do("list_hb chain "+ str(i) +", chain " +str(j) + ", write_distances_file=hb_"+ str(file) + "_" + str(i) + "_" +str( j) + "_001.txt") for i, j in chains] for file in glob.glob("model.??.pdb")]
Note that you do not have to load the pdb files into PyMOL.
If you want to analyze more than 99 files and less than 999 files, add a third question mark to the argument of glob.glob().
Best regards,
Blaine
Blaine Mooers, Ph.D.
Associate Professor
Department of Biochemistry and Molecular Biology
College of Medicine
University of Oklahoma Health Sciences Center
S.L. Young Biomedical Research Center (BRC) Rm. 466
975 NE 10th Street, BRC 466
Oklahoma City, OK 73104-5419
________________________________________
From: Chen, Qiang [qi...@pi...]
Sent: Monday, June 15, 2020 2:53 PM
To: pym...@li...
Subject: [EXTERNAL] [PyMOL] hydrogen bond list for a series of files
Hi, Pymol users
Could you help me do this in an efficient way?
Let me describe the task I try to do.
I have a series of numerically ordered files, say model00.pdb model.01.pdb ?? model.30.pdb
All the pdb have the same protein composition, chain A, B, C, D, and E. Their relative position is different in each file.
I would like to check the hydrogen bonds between, say, chain A and B.
Thanks to Prof. Robert L. Campbell, I can list the hydrogen bonds in one pdb and print the list as the follows
list_hb chain A, chain B, write_distances_file=hb_A_B_01.txt
How can I process the 30 files in an efficient way? what if I have 300 pdb files?
Shell script, python, or anything else?
Thanks!
Charles Chen
_______________________________________________
PyMOL-users mailing list
Archives: https://nam05.safelinks.protection.outlook.com/?url=https%3A%2F%2Furldefense.proofpoint.com%2Fv2%2Furl%3Fu%3Dhttp-3A__www.mail-2Darchive.com_pymol-2Dusers-40lists.sourceforge.net%26d%3DDwIGaQ%26c%3DVjzId-SM5S6aVB_cCGQ0d3uo9UfKByQ3sI6Audoy6dY%26r%3Dk0gMbcsdOcdbPUNV5tW66KQSZfXL0ewVDPVBp7tqbks%26m%3DxyAmhZRZYDjhbBLdiMRRk6wCJ14kA5UeQYC4urBFvQw%26s%3DaOpeSOw9Gqop8KF8Xf_lkPoBC_MSbb5i0cKlRaIAulI%26e%3D&data=02%7C01%7Cqic8%40pitt.edu%7C4ec7afdbd857446afad308d812081e49%7C9ef9f489e0a04eeb87cc3a526112fd0d%7C1%7C0%7C637279173371398312&sdata=dA2FsS4JYlgy%2BzEDUf7Ym7ZjxZpt67MzbjQLcqhLZtA%3D&reserved=0<https://nam05.safelinks.protection.outlook.com/?url=https%3A%2F%2Furldefense.proofpoint.com%2Fv2%2Furl%3Fu%3Dhttps-3A__nam05.safelinks.protection.outlook.com_-3Furl-3Dhttps-253A-252F-252Furldefense.proofpoint.com-252Fv2-252Furl-253Fu-253Dhttp-2D3A-5F-5Fwww.mail-2D2Darchive.com-5Fpymol-2D2Dusers-2D40lists.sourceforge.net-2526d-253DDwIGaQ-2526c-253DVjzId-2DSM5S6aVB-5FcCGQ0d3uo9UfKByQ3sI6Audoy6dY-2526r-253Dk0gMbcsdOcdbPUNV5tW66KQSZfXL0ewVDPVBp7tqbks-2526m-253DxyAmhZRZYDjhbBLdiMRRk6wCJ14kA5UeQYC4urBFvQw-2526s-253DaOpeSOw9Gqop8KF8Xf-5FlkPoBC-5FMSbb5i0cKlRaIAulI-2526e-253D-26amp-3Bdata-3D02-257C01-257Cqic8-2540pitt.edu-257C01a30e93a2ca4a40b37308d81196d7ba-257C9ef9f489e0a04eeb87cc3a526112fd0d-257C1-257C0-257C637278686852886299-26amp-3Bsdata-3DH-252BbXZ7ylGnf8aHeqS8UfkWyeYYuKCLZv1GikWVh2gAM-253D-26amp-3Breserved-3D0%26d%3DDwMF-g%26c%3DVjzId-SM5S6aVB_cCGQ0d3uo9UfKByQ3sI6Audoy6dY%26r%3Dk0gMbcsdOcdbPUNV5tW66KQSZfXL0ewVDPVBp7tqbks%26m%3DX2B3s7D21CBjGtOAQJ2noNR7vnKXPiHiT2eLIRiSC18%26s%3DUml8pWJGL1VV1FRsRqY0A8xQ-ZVcOqvXJIUCvJgGjSY%26e%3D&data=02%7C01%7Cqic8%40pitt.edu%7C4ec7afdbd857446afad308d812081e49%7C9ef9f489e0a04eeb87cc3a526112fd0d%7C1%7C0%7C637279173371408309&sdata=ntuExgK7Jy5fzjZKQkolAYAbTFp9JcAAVtTJpaBO52E%3D&reserved=0>
Unsubscribe: https://nam05.safelinks.protection.outlook.com/?url=https%3A%2F%2Furldefense.proofpoint.com%2Fv2%2Furl%3Fu%3Dhttps-3A__sourceforge.net_projects_pymol_lists_pymol-2Dusers_unsubscribe%26d%3DDwIGaQ%26c%3DVjzId-SM5S6aVB_cCGQ0d3uo9UfKByQ3sI6Audoy6dY%26r%3Dk0gMbcsdOcdbPUNV5tW66KQSZfXL0ewVDPVBp7tqbks%26m%3DxyAmhZRZYDjhbBLdiMRRk6wCJ14kA5UeQYC4urBFvQw%26s%3DPY-g0XYMB9DqXC06Iixbjxfqf8jB9Pb_GFu8zClx3oY%26e%3D&data=02%7C01%7Cqic8%40pitt.edu%7C4ec7afdbd857446afad308d812081e49%7C9ef9f489e0a04eeb87cc3a526112fd0d%7C1%7C0%7C637279173371408309&sdata=xulJjUVGYDp4FlQS%2F2cOaj%2BesmBZ2mKHFbBhghAW%2Fek%3D&reserved=0<https://nam05.safelinks.protection.outlook.com/?url=https%3A%2F%2Furldefense.proofpoint.com%2Fv2%2Furl%3Fu%3Dhttps-3A__nam05.safelinks.protection.outlook.com_-3Furl-3Dhttps-253A-252F-252Furldefense.proofpoint.com-252Fv2-252Furl-253Fu-253Dhttps-2D3A-5F-5Fsourceforge.net-5Fprojects-5Fpymol-5Flists-5Fpymol-2D2Dusers-5Funsubscribe-2526d-253DDwIGaQ-2526c-253DVjzId-2DSM5S6aVB-5FcCGQ0d3uo9UfKByQ3sI6Audoy6dY-2526r-253Dk0gMbcsdOcdbPUNV5tW66KQSZfXL0ewVDPVBp7tqbks-2526m-253DxyAmhZRZYDjhbBLdiMRRk6wCJ14kA5UeQYC4urBFvQw-2526s-253DPY-2Dg0XYMB9DqXC06Iixbjxfqf8jB9Pb-5FGFu8zClx3oY-2526e-253D-26amp-3Bdata-3D02-257C01-257Cqic8-2540pitt.edu-257C01a30e93a2ca4a40b37308d81196d7ba-257C9ef9f489e0a04eeb87cc3a526112fd0d-257C1-257C0-257C637278686852886299-26amp-3Bsdata-3Do1asKPIbwdAFwN-252FCJSTCXDg-252BndmmLXC8VJW8z48Y-252BAA-253D-26amp-3Breserved-3D0%26d%3DDwMF-g%26c%3DVjzId-SM5S6aVB_cCGQ0d3uo9UfKByQ3sI6Audoy6dY%26r%3Dk0gMbcsdOcdbPUNV5tW66KQSZfXL0ewVDPVBp7tqbks%26m%3DX2B3s7D21CBjGtOAQJ2noNR7vnKXPiHiT2eLIRiSC18%26s%3D52GYpWEgXcbl5EqO1gYdzX31C41KuEUPECZU1zDR_TU%26e%3D&data=02%7C01%7Cqic8%40pitt.edu%7C4ec7afdbd857446afad308d812081e49%7C9ef9f489e0a04eeb87cc3a526112fd0d%7C1%7C0%7C637279173371408309&sdata=CsHgBohQtDcnbhYGJ6IWPNjZzpGLkPYSIR4ys%2Fy2wC0%3D&reserved=0>
-------------- next part --------------
An HTML attachment was scrubbed...
------------------------------
------------------------------
Subject: Digest Footer
_______________________________________________
PyMOL-users mailing list
PyM...@li...
https://nam05.safelinks.protection.outlook.com/?url=https%3A%2F%2Flists.sourceforge.net%2Flists%2Flistinfo%2Fpymol-users&data=02%7C01%7Cqic8%40pitt.edu%7C4ec7afdbd857446afad308d812081e49%7C9ef9f489e0a04eeb87cc3a526112fd0d%7C1%7C0%7C637279173371408309&sdata=xWJOyonGPnYfhmNOqZP3SPZxA75whMdLZfZVGNyAtUU%3D&reserved=0
Unsubscribe: https://nam05.safelinks.protection.outlook.com/?url=https%3A%2F%2Fsourceforge.net%2Fprojects%2Fpymol%2Flists%2Fpymol-users%2Funsubscribe&data=02%7C01%7Cqic8%40pitt.edu%7C4ec7afdbd857446afad308d812081e49%7C9ef9f489e0a04eeb87cc3a526112fd0d%7C1%7C0%7C637279173371408309&sdata=6I5fj6RgavUMUFysgpciHBNIzIeZGS74y%2FIMLD3xp9Y%3D&reserved=0
------------------------------
End of PyMOL-users Digest, Vol 169, Issue 26
********************************************
|
|
From: Chen, Q. <qi...@pi...> - 2020-06-16 15:15:23
|
Great, thanks!
Really appreciate your help!
Charles
________________________________
From: Mooers, Blaine H.M. (HSC) <Bla...@ou...>
Sent: Tuesday, June 16, 2020 10:51 AM
To: Chen, Qiang <qi...@pi...>; pym...@li... <pym...@li...>
Subject: RE: hydrogen bond list for a series of files
Hi Charlie,
This will give the desired list.
file_list = [f'{m:02d}' for m in list(range(1,30,1))]
print(file_list)
Best regards,
Blaine
Blaine Mooers, Ph.D.
Associate Professor
Department of Biochemistry and Molecular Biology
College of Medicine
University of Oklahoma Health Sciences Center
S.L. Young Biomedical Research Center (BRC) Rm. 466
975 NE 10th Street, BRC 466
Oklahoma City, OK 73104-5419
________________________________________
From: Chen, Qiang [qi...@pi...]
Sent: Tuesday, June 16, 2020 9:26 AM
To: Mooers, Blaine H.M. (HSC); pym...@li...
Subject: [EXTERNAL] Re: hydrogen bond list for a series of files
Hi, Blaine,
Then the question becomes how to generate a list with 30 or 300 numbers.
Will this work?
file_list=list(range(00, 30))
Thanks!
Charles
________________________________
From: Mooers, Blaine H.M. (HSC) <Bla...@ou...>
Sent: Tuesday, June 16, 2020 9:57 AM
To: Chen, Qiang <qi...@pi...>; pym...@li... <pym...@li...>
Subject: RE: hydrogen bond list for a series of files
Hi Charles,
You are right and I am wrong about the files needing to be loaded.
The object name has the pesky pdb file extension stripped off, so lets use the object name instead of using Python to strip it off for us.
We no longer need to use glob.
We do need to the create a list of strings that encode the indexing of the files.
This code worked for me with two files.
Adapt to your 30 or 300 files.
file_list = ['01','02']
[cmd.do("load model.000."+str(k)+"_minimized.pdb") for k in file_list]
object_list=cmd.get_object_list('(model.000.*_minimized)')
chains=[('A','F'),('B', 'F'),('C','F'),('D','F'),('E','F')]
run C:\Users\user\AppData\Local\Programs\Python\Python38\lib\site-packages\pymol\pymol_path\Pymol-script-repo\list_hb.py
[cmd.do("list_hb chain F, chain A:E, write_distances_file=hb_"+str(file)+".txt") for file in object_list ]
Best regards,
Blaine
Blaine Mooers, Ph.D.
Associate Professor
Department of Biochemistry and Molecular Biology
College of Medicine
University of Oklahoma Health Sciences Center
S.L. Young Biomedical Research Center (BRC) Rm. 466
975 NE 10th Street, BRC 466
Oklahoma City, OK 73104-5419
________________________________________
From: Chen, Qiang [qi...@pi...]
Sent: Monday, June 15, 2020 10:18 PM
To: Mooers, Blaine H.M. (HSC); pym...@li...
Subject: [EXTERNAL] Re: hydrogen bond list for a series of files
Thanks, Dr. Mooers.
I modified a little.
It seems the pdb files need be loaded.
I put all the following lines in a file multifile_hb.pml
run C:\Users\user\AppData\Local\Programs\Python\Python38\lib\site-packages\pymol\pymol_path\Pymol-script-repo\list_hb.py
import glob
load model.000.*_minimized.pdb
#chains=[('A','F'),('B', 'F'),('C','F'),('D','F'),('E','F')]
[cmd.do("list_hb chain F, chain A:E, write_distances_file=hb_"+str(file)+".txt") for file in glob.glob("model.000.??_minimized.pdb")]
A little not so perfect is that the output file,
hb_model.000.??_minimized.pdb.txt
Is is possible to do something like this
write_distances_file=hb_"+basename(file)+".txt"
Then the output will be
hb_model.000.??_minimized.txt
I tried, and this simple thing does not work.
Any suggestion?
Thanks!
Charles
________________________________
From: Mooers, Blaine H.M. (HSC) <Bla...@ou...>
Sent: Monday, June 15, 2020 9:44 PM
To: Chen, Qiang <qi...@pi...>; pym...@li... <pym...@li...>
Subject: RE: hydrogen bond list for a series of files
Hi Charles,
Make sure that PyMOL's present working directory is where the pdb files are stored.
Copy and paste each of the four lines below one at a time on the command line in PyMOL.
run list_hb.py<https://nam05.safelinks.protection.outlook.com/?url=https%3A%2F%2Furldefense.proofpoint.com%2Fv2%2Furl%3Fu%3Dhttp-3A__list-5Fhb.py%26d%3DDwQF-g%26c%3DVjzId-SM5S6aVB_cCGQ0d3uo9UfKByQ3sI6Audoy6dY%26r%3Dk0gMbcsdOcdbPUNV5tW66KQSZfXL0ewVDPVBp7tqbks%26m%3DX2B3s7D21CBjGtOAQJ2noNR7vnKXPiHiT2eLIRiSC18%26s%3DKYQX_tOI8_HnmseLbJRMv7UTirG78evoaztp35Gg74E%26e%3D&data=02%7C01%7Cqic8%40pitt.edu%7C912defbc336647dae60f08d81204d365%7C9ef9f489e0a04eeb87cc3a526112fd0d%7C1%7C0%7C637279159230377514&sdata=TmlSgLQRAHpH6y8B3uBrgkFCoe5%2B%2BDxlB5ELDeXPBWc%3D&reserved=0<https://nam05.safelinks.protection.outlook.com/?url=https%3A%2F%2Furldefense.proofpoint.com%2Fv2%2Furl%3Fu%3Dhttps-3A__nam05.safelinks.protection.outlook.com_-3Furl-3Dhttps-253A-252F-252Furldefense.proofpoint.com-252Fv2-252Furl-253Fu-253Dhttp-2D3A-5F-5Flist-2D5Fhb.py-2526d-253DDwQF-2Dg-2526c-253DVjzId-2DSM5S6aVB-5FcCGQ0d3uo9UfKByQ3sI6Audoy6dY-2526r-253Dk0gMbcsdOcdbPUNV5tW66KQSZfXL0ewVDPVBp7tqbks-2526m-253DX2B3s7D21CBjGtOAQJ2noNR7vnKXPiHiT2eLIRiSC18-2526s-253DKYQX-5FtOI8-5FHnmseLbJRMv7UTirG78evoaztp35Gg74E-2526e-253D-26amp-3Bdata-3D02-257C01-257Cqic8-2540pitt.edu-257C2ea32a0b061443a37f1908d811fd40fd-257C9ef9f489e0a04eeb87cc3a526112fd0d-257C1-257C0-257C637279126707606574-26amp-3Bsdata-3D8VnRodmeEUrqQfFm7fe0gqd02cYPsKv8VxPcb09RIkQ-253D-26amp-3Breserved-3D0%26d%3DDwMF-g%26c%3DVjzId-SM5S6aVB_cCGQ0d3uo9UfKByQ3sI6Audoy6dY%26r%3Dk0gMbcsdOcdbPUNV5tW66KQSZfXL0ewVDPVBp7tqbks%26m%3DQ6LxvA7WaglxixxzDsbpjU7pbOFqJPXxmweHw0k_x7I%26s%3D6cyeevFFP1ip0quoSgRLS9fqrvVtj8JlnLJWMpJWqFg%26e%3D&data=02%7C01%7Cqic8%40pitt.edu%7C912defbc336647dae60f08d81204d365%7C9ef9f489e0a04eeb87cc3a526112fd0d%7C1%7C0%7C637279159230377514&sdata=WwpxXonai3NKa2289uyyZSaX%2BiogfaMUstB4PvumZzM%3D&reserved=0>>
import glob
chains = [('A','B'), ('A','C'), ('A','D'), ('A','E'), ('B','C'), ('B','D'), ('B','E'), ('C','D'), ('C','E'), ('D','E') ]
[[cmd.do("list_hb chain "+ str(i) +", chain " +str(j) + ", write_distances_file=hb_"+ str(file) + "_" + str(i) + "_" +str( j) + "_001.txt") for i, j in chains] for file in glob.glob("model.??.pdb")]
Note that you do not have to load the pdb files into PyMOL.
If you want to analyze more than 99 files and less than 999 files, add a third question mark to the argument of glob.glob().
Best regards,
Blaine
Blaine Mooers, Ph.D.
Associate Professor
Department of Biochemistry and Molecular Biology
College of Medicine
University of Oklahoma Health Sciences Center
S.L. Young Biomedical Research Center (BRC) Rm. 466
975 NE 10th Street, BRC 466
Oklahoma City, OK 73104-5419
________________________________________
From: Chen, Qiang [qi...@pi...]
Sent: Monday, June 15, 2020 2:53 PM
To: pym...@li...
Subject: [EXTERNAL] [PyMOL] hydrogen bond list for a series of files
Hi, Pymol users
Could you help me do this in an efficient way?
Let me describe the task I try to do.
I have a series of numerically ordered files, say model00.pdb model.01.pdb …… model.30.pdb
All the pdb have the same protein composition, chain A, B, C, D, and E. Their relative position is different in each file.
I would like to check the hydrogen bonds between, say, chain A and B.
Thanks to Prof. Robert L. Campbell, I can list the hydrogen bonds in one pdb and print the list as the follows
list_hb chain A, chain B, write_distances_file=hb_A_B_01.txt
How can I process the 30 files in an efficient way? what if I have 300 pdb files?
Shell script, python, or anything else?
Thanks!
Charles Chen
_______________________________________________
PyMOL-users mailing list
Archives: https://nam05.safelinks.protection.outlook.com/?url=https%3A%2F%2Furldefense.proofpoint.com%2Fv2%2Furl%3Fu%3Dhttp-3A__www.mail-2Darchive.com_pymol-2Dusers-40lists.sourceforge.net%26d%3DDwIGaQ%26c%3DVjzId-SM5S6aVB_cCGQ0d3uo9UfKByQ3sI6Audoy6dY%26r%3Dk0gMbcsdOcdbPUNV5tW66KQSZfXL0ewVDPVBp7tqbks%26m%3DxyAmhZRZYDjhbBLdiMRRk6wCJ14kA5UeQYC4urBFvQw%26s%3DaOpeSOw9Gqop8KF8Xf_lkPoBC_MSbb5i0cKlRaIAulI%26e%3D&data=02%7C01%7Cqic8%40pitt.edu%7C912defbc336647dae60f08d81204d365%7C9ef9f489e0a04eeb87cc3a526112fd0d%7C1%7C0%7C637279159230387509&sdata=yNeKzDtF62jtKbwlABRSdk9Z2YsifFaBdbfDw0GAQ6k%3D&reserved=0<https://nam05.safelinks.protection.outlook.com/?url=https%3A%2F%2Furldefense.proofpoint.com%2Fv2%2Furl%3Fu%3Dhttps-3A__nam05.safelinks.protection.outlook.com_-3Furl-3Dhttps-253A-252F-252Furldefense.proofpoint.com-252Fv2-252Furl-253Fu-253Dhttp-2D3A-5F-5Fwww.mail-2D2Darchive.com-5Fpymol-2D2Dusers-2D40lists.sourceforge.net-2526d-253DDwIGaQ-2526c-253DVjzId-2DSM5S6aVB-5FcCGQ0d3uo9UfKByQ3sI6Audoy6dY-2526r-253Dk0gMbcsdOcdbPUNV5tW66KQSZfXL0ewVDPVBp7tqbks-2526m-253DxyAmhZRZYDjhbBLdiMRRk6wCJ14kA5UeQYC4urBFvQw-2526s-253DaOpeSOw9Gqop8KF8Xf-5FlkPoBC-5FMSbb5i0cKlRaIAulI-2526e-253D-26amp-3Bdata-3D02-257C01-257Cqic8-2540pitt.edu-257C01a30e93a2ca4a40b37308d81196d7ba-257C9ef9f489e0a04eeb87cc3a526112fd0d-257C1-257C0-257C637278686852886299-26amp-3Bsdata-3DH-252BbXZ7ylGnf8aHeqS8UfkWyeYYuKCLZv1GikWVh2gAM-253D-26amp-3Breserved-3D0%26d%3DDwMF-g%26c%3DVjzId-SM5S6aVB_cCGQ0d3uo9UfKByQ3sI6Audoy6dY%26r%3Dk0gMbcsdOcdbPUNV5tW66KQSZfXL0ewVDPVBp7tqbks%26m%3DX2B3s7D21CBjGtOAQJ2noNR7vnKXPiHiT2eLIRiSC18%26s%3DUml8pWJGL1VV1FRsRqY0A8xQ-ZVcOqvXJIUCvJgGjSY%26e%3D&data=02%7C01%7Cqic8%40pitt.edu%7C912defbc336647dae60f08d81204d365%7C9ef9f489e0a04eeb87cc3a526112fd0d%7C1%7C0%7C637279159230387509&sdata=dCkeeyUd5TGKmYILIOqxanCGsFaADZTnLWnnq%2BxQrXQ%3D&reserved=0>
Unsubscribe: https://nam05.safelinks.protection.outlook.com/?url=https%3A%2F%2Furldefense.proofpoint.com%2Fv2%2Furl%3Fu%3Dhttps-3A__sourceforge.net_projects_pymol_lists_pymol-2Dusers_unsubscribe%26d%3DDwIGaQ%26c%3DVjzId-SM5S6aVB_cCGQ0d3uo9UfKByQ3sI6Audoy6dY%26r%3Dk0gMbcsdOcdbPUNV5tW66KQSZfXL0ewVDPVBp7tqbks%26m%3DxyAmhZRZYDjhbBLdiMRRk6wCJ14kA5UeQYC4urBFvQw%26s%3DPY-g0XYMB9DqXC06Iixbjxfqf8jB9Pb_GFu8zClx3oY%26e%3D&data=02%7C01%7Cqic8%40pitt.edu%7C912defbc336647dae60f08d81204d365%7C9ef9f489e0a04eeb87cc3a526112fd0d%7C1%7C0%7C637279159230387509&sdata=RtHkAW6zuhZ83R5twJasizwy%2BqyMlMD6ZKl%2F6V3Eiqs%3D&reserved=0<https://nam05.safelinks.protection.outlook.com/?url=https%3A%2F%2Furldefense.proofpoint.com%2Fv2%2Furl%3Fu%3Dhttps-3A__nam05.safelinks.protection.outlook.com_-3Furl-3Dhttps-253A-252F-252Furldefense.proofpoint.com-252Fv2-252Furl-253Fu-253Dhttps-2D3A-5F-5Fsourceforge.net-5Fprojects-5Fpymol-5Flists-5Fpymol-2D2Dusers-5Funsubscribe-2526d-253DDwIGaQ-2526c-253DVjzId-2DSM5S6aVB-5FcCGQ0d3uo9UfKByQ3sI6Audoy6dY-2526r-253Dk0gMbcsdOcdbPUNV5tW66KQSZfXL0ewVDPVBp7tqbks-2526m-253DxyAmhZRZYDjhbBLdiMRRk6wCJ14kA5UeQYC4urBFvQw-2526s-253DPY-2Dg0XYMB9DqXC06Iixbjxfqf8jB9Pb-5FGFu8zClx3oY-2526e-253D-26amp-3Bdata-3D02-257C01-257Cqic8-2540pitt.edu-257C01a30e93a2ca4a40b37308d81196d7ba-257C9ef9f489e0a04eeb87cc3a526112fd0d-257C1-257C0-257C637278686852886299-26amp-3Bsdata-3Do1asKPIbwdAFwN-252FCJSTCXDg-252BndmmLXC8VJW8z48Y-252BAA-253D-26amp-3Breserved-3D0%26d%3DDwMF-g%26c%3DVjzId-SM5S6aVB_cCGQ0d3uo9UfKByQ3sI6Audoy6dY%26r%3Dk0gMbcsdOcdbPUNV5tW66KQSZfXL0ewVDPVBp7tqbks%26m%3DX2B3s7D21CBjGtOAQJ2noNR7vnKXPiHiT2eLIRiSC18%26s%3D52GYpWEgXcbl5EqO1gYdzX31C41KuEUPECZU1zDR_TU%26e%3D&data=02%7C01%7Cqic8%40pitt.edu%7C912defbc336647dae60f08d81204d365%7C9ef9f489e0a04eeb87cc3a526112fd0d%7C1%7C0%7C637279159230387509&sdata=UDQRLlo6MjA8oDalXJJkEVFPBPyxSqZbr9e8HH4fxyU%3D&reserved=0>
|
|
From: Mooers, B. H.M. (HSC) <Bla...@ou...> - 2020-06-16 14:52:00
|
Hi Charlie,
This will give the desired list.
file_list = [f'{m:02d}' for m in list(range(1,30,1))]
print(file_list)
Best regards,
Blaine
Blaine Mooers, Ph.D.
Associate Professor
Department of Biochemistry and Molecular Biology
College of Medicine
University of Oklahoma Health Sciences Center
S.L. Young Biomedical Research Center (BRC) Rm. 466
975 NE 10th Street, BRC 466
Oklahoma City, OK 73104-5419
________________________________________
From: Chen, Qiang [qi...@pi...]
Sent: Tuesday, June 16, 2020 9:26 AM
To: Mooers, Blaine H.M. (HSC); pym...@li...
Subject: [EXTERNAL] Re: hydrogen bond list for a series of files
Hi, Blaine,
Then the question becomes how to generate a list with 30 or 300 numbers.
Will this work?
file_list=list(range(00, 30))
Thanks!
Charles
________________________________
From: Mooers, Blaine H.M. (HSC) <Bla...@ou...>
Sent: Tuesday, June 16, 2020 9:57 AM
To: Chen, Qiang <qi...@pi...>; pym...@li... <pym...@li...>
Subject: RE: hydrogen bond list for a series of files
Hi Charles,
You are right and I am wrong about the files needing to be loaded.
The object name has the pesky pdb file extension stripped off, so lets use the object name instead of using Python to strip it off for us.
We no longer need to use glob.
We do need to the create a list of strings that encode the indexing of the files.
This code worked for me with two files.
Adapt to your 30 or 300 files.
file_list = ['01','02']
[cmd.do("load model.000."+str(k)+"_minimized.pdb") for k in file_list]
object_list=cmd.get_object_list('(model.000.*_minimized)')
chains=[('A','F'),('B', 'F'),('C','F'),('D','F'),('E','F')]
run C:\Users\user\AppData\Local\Programs\Python\Python38\lib\site-packages\pymol\pymol_path\Pymol-script-repo\list_hb.py
[cmd.do("list_hb chain F, chain A:E, write_distances_file=hb_"+str(file)+".txt") for file in object_list ]
Best regards,
Blaine
Blaine Mooers, Ph.D.
Associate Professor
Department of Biochemistry and Molecular Biology
College of Medicine
University of Oklahoma Health Sciences Center
S.L. Young Biomedical Research Center (BRC) Rm. 466
975 NE 10th Street, BRC 466
Oklahoma City, OK 73104-5419
________________________________________
From: Chen, Qiang [qi...@pi...]
Sent: Monday, June 15, 2020 10:18 PM
To: Mooers, Blaine H.M. (HSC); pym...@li...
Subject: [EXTERNAL] Re: hydrogen bond list for a series of files
Thanks, Dr. Mooers.
I modified a little.
It seems the pdb files need be loaded.
I put all the following lines in a file multifile_hb.pml
run C:\Users\user\AppData\Local\Programs\Python\Python38\lib\site-packages\pymol\pymol_path\Pymol-script-repo\list_hb.py
import glob
load model.000.*_minimized.pdb
#chains=[('A','F'),('B', 'F'),('C','F'),('D','F'),('E','F')]
[cmd.do("list_hb chain F, chain A:E, write_distances_file=hb_"+str(file)+".txt") for file in glob.glob("model.000.??_minimized.pdb")]
A little not so perfect is that the output file,
hb_model.000.??_minimized.pdb.txt
Is is possible to do something like this
write_distances_file=hb_"+basename(file)+".txt"
Then the output will be
hb_model.000.??_minimized.txt
I tried, and this simple thing does not work.
Any suggestion?
Thanks!
Charles
________________________________
From: Mooers, Blaine H.M. (HSC) <Bla...@ou...>
Sent: Monday, June 15, 2020 9:44 PM
To: Chen, Qiang <qi...@pi...>; pym...@li... <pym...@li...>
Subject: RE: hydrogen bond list for a series of files
Hi Charles,
Make sure that PyMOL's present working directory is where the pdb files are stored.
Copy and paste each of the four lines below one at a time on the command line in PyMOL.
run list_hb.py<https://nam05.safelinks.protection.outlook.com/?url=https%3A%2F%2Furldefense.proofpoint.com%2Fv2%2Furl%3Fu%3Dhttp-3A__list-5Fhb.py%26d%3DDwQF-g%26c%3DVjzId-SM5S6aVB_cCGQ0d3uo9UfKByQ3sI6Audoy6dY%26r%3Dk0gMbcsdOcdbPUNV5tW66KQSZfXL0ewVDPVBp7tqbks%26m%3DX2B3s7D21CBjGtOAQJ2noNR7vnKXPiHiT2eLIRiSC18%26s%3DKYQX_tOI8_HnmseLbJRMv7UTirG78evoaztp35Gg74E%26e%3D&data=02%7C01%7Cqic8%40pitt.edu%7C2ea32a0b061443a37f1908d811fd40fd%7C9ef9f489e0a04eeb87cc3a526112fd0d%7C1%7C0%7C637279126707606574&sdata=8VnRodmeEUrqQfFm7fe0gqd02cYPsKv8VxPcb09RIkQ%3D&reserved=0<https://urldefense.proofpoint.com/v2/url?u=https-3A__nam05.safelinks.protection.outlook.com_-3Furl-3Dhttps-253A-252F-252Furldefense.proofpoint.com-252Fv2-252Furl-253Fu-253Dhttp-2D3A-5F-5Flist-2D5Fhb.py-2526d-253DDwQF-2Dg-2526c-253DVjzId-2DSM5S6aVB-5FcCGQ0d3uo9UfKByQ3sI6Audoy6dY-2526r-253Dk0gMbcsdOcdbPUNV5tW66KQSZfXL0ewVDPVBp7tqbks-2526m-253DX2B3s7D21CBjGtOAQJ2noNR7vnKXPiHiT2eLIRiSC18-2526s-253DKYQX-5FtOI8-5FHnmseLbJRMv7UTirG78evoaztp35Gg74E-2526e-253D-26amp-3Bdata-3D02-257C01-257Cqic8-2540pitt.edu-257C2ea32a0b061443a37f1908d811fd40fd-257C9ef9f489e0a04eeb87cc3a526112fd0d-257C1-257C0-257C637279126707606574-26amp-3Bsdata-3D8VnRodmeEUrqQfFm7fe0gqd02cYPsKv8VxPcb09RIkQ-253D-26amp-3Breserved-3D0&d=DwMF-g&c=VjzId-SM5S6aVB_cCGQ0d3uo9UfKByQ3sI6Audoy6dY&r=k0gMbcsdOcdbPUNV5tW66KQSZfXL0ewVDPVBp7tqbks&m=Q6LxvA7WaglxixxzDsbpjU7pbOFqJPXxmweHw0k_x7I&s=6cyeevFFP1ip0quoSgRLS9fqrvVtj8JlnLJWMpJWqFg&e=>>
import glob
chains = [('A','B'), ('A','C'), ('A','D'), ('A','E'), ('B','C'), ('B','D'), ('B','E'), ('C','D'), ('C','E'), ('D','E') ]
[[cmd.do("list_hb chain "+ str(i) +", chain " +str(j) + ", write_distances_file=hb_"+ str(file) + "_" + str(i) + "_" +str( j) + "_001.txt") for i, j in chains] for file in glob.glob("model.??.pdb")]
Note that you do not have to load the pdb files into PyMOL.
If you want to analyze more than 99 files and less than 999 files, add a third question mark to the argument of glob.glob().
Best regards,
Blaine
Blaine Mooers, Ph.D.
Associate Professor
Department of Biochemistry and Molecular Biology
College of Medicine
University of Oklahoma Health Sciences Center
S.L. Young Biomedical Research Center (BRC) Rm. 466
975 NE 10th Street, BRC 466
Oklahoma City, OK 73104-5419
________________________________________
From: Chen, Qiang [qi...@pi...]
Sent: Monday, June 15, 2020 2:53 PM
To: pym...@li...
Subject: [EXTERNAL] [PyMOL] hydrogen bond list for a series of files
Hi, Pymol users
Could you help me do this in an efficient way?
Let me describe the task I try to do.
I have a series of numerically ordered files, say model00.pdb model.01.pdb …… model.30.pdb
All the pdb have the same protein composition, chain A, B, C, D, and E. Their relative position is different in each file.
I would like to check the hydrogen bonds between, say, chain A and B.
Thanks to Prof. Robert L. Campbell, I can list the hydrogen bonds in one pdb and print the list as the follows
list_hb chain A, chain B, write_distances_file=hb_A_B_01.txt
How can I process the 30 files in an efficient way? what if I have 300 pdb files?
Shell script, python, or anything else?
Thanks!
Charles Chen
_______________________________________________
PyMOL-users mailing list
Archives: https://nam05.safelinks.protection.outlook.com/?url=https%3A%2F%2Furldefense.proofpoint.com%2Fv2%2Furl%3Fu%3Dhttp-3A__www.mail-2Darchive.com_pymol-2Dusers-40lists.sourceforge.net%26d%3DDwIGaQ%26c%3DVjzId-SM5S6aVB_cCGQ0d3uo9UfKByQ3sI6Audoy6dY%26r%3Dk0gMbcsdOcdbPUNV5tW66KQSZfXL0ewVDPVBp7tqbks%26m%3DxyAmhZRZYDjhbBLdiMRRk6wCJ14kA5UeQYC4urBFvQw%26s%3DaOpeSOw9Gqop8KF8Xf_lkPoBC_MSbb5i0cKlRaIAulI%26e%3D&data=02%7C01%7Cqic8%40pitt.edu%7C2ea32a0b061443a37f1908d811fd40fd%7C9ef9f489e0a04eeb87cc3a526112fd0d%7C1%7C0%7C637279126707606574&sdata=hv3wxBB9OoMRAwCeb44ok4suuSPP47IGl771qqDqaFs%3D&reserved=0<https://nam05.safelinks.protection.outlook.com/?url=https%3A%2F%2Furldefense.proofpoint.com%2Fv2%2Furl%3Fu%3Dhttps-3A__nam05.safelinks.protection.outlook.com_-3Furl-3Dhttps-253A-252F-252Furldefense.proofpoint.com-252Fv2-252Furl-253Fu-253Dhttp-2D3A-5F-5Fwww.mail-2D2Darchive.com-5Fpymol-2D2Dusers-2D40lists.sourceforge.net-2526d-253DDwIGaQ-2526c-253DVjzId-2DSM5S6aVB-5FcCGQ0d3uo9UfKByQ3sI6Audoy6dY-2526r-253Dk0gMbcsdOcdbPUNV5tW66KQSZfXL0ewVDPVBp7tqbks-2526m-253DxyAmhZRZYDjhbBLdiMRRk6wCJ14kA5UeQYC4urBFvQw-2526s-253DaOpeSOw9Gqop8KF8Xf-5FlkPoBC-5FMSbb5i0cKlRaIAulI-2526e-253D-26amp-3Bdata-3D02-257C01-257Cqic8-2540pitt.edu-257C01a30e93a2ca4a40b37308d81196d7ba-257C9ef9f489e0a04eeb87cc3a526112fd0d-257C1-257C0-257C637278686852886299-26amp-3Bsdata-3DH-252BbXZ7ylGnf8aHeqS8UfkWyeYYuKCLZv1GikWVh2gAM-253D-26amp-3Breserved-3D0%26d%3DDwMF-g%26c%3DVjzId-SM5S6aVB_cCGQ0d3uo9UfKByQ3sI6Audoy6dY%26r%3Dk0gMbcsdOcdbPUNV5tW66KQSZfXL0ewVDPVBp7tqbks%26m%3DX2B3s7D21CBjGtOAQJ2noNR7vnKXPiHiT2eLIRiSC18%26s%3DUml8pWJGL1VV1FRsRqY0A8xQ-ZVcOqvXJIUCvJgGjSY%26e%3D&data=02%7C01%7Cqic8%40pitt.edu%7C2ea32a0b061443a37f1908d811fd40fd%7C9ef9f489e0a04eeb87cc3a526112fd0d%7C1%7C0%7C637279126707606574&sdata=Ro1JrjplPPP%2BnpS29PnQTnnIqNWCdpOJCoViVArOBkE%3D&reserved=0>
Unsubscribe: https://nam05.safelinks.protection.outlook.com/?url=https%3A%2F%2Furldefense.proofpoint.com%2Fv2%2Furl%3Fu%3Dhttps-3A__sourceforge.net_projects_pymol_lists_pymol-2Dusers_unsubscribe%26d%3DDwIGaQ%26c%3DVjzId-SM5S6aVB_cCGQ0d3uo9UfKByQ3sI6Audoy6dY%26r%3Dk0gMbcsdOcdbPUNV5tW66KQSZfXL0ewVDPVBp7tqbks%26m%3DxyAmhZRZYDjhbBLdiMRRk6wCJ14kA5UeQYC4urBFvQw%26s%3DPY-g0XYMB9DqXC06Iixbjxfqf8jB9Pb_GFu8zClx3oY%26e%3D&data=02%7C01%7Cqic8%40pitt.edu%7C2ea32a0b061443a37f1908d811fd40fd%7C9ef9f489e0a04eeb87cc3a526112fd0d%7C1%7C0%7C637279126707606574&sdata=WPFSb8UDLcACThM4ujjxACYr%2FbNL8OtX9oPrQ%2F9ipsA%3D&reserved=0<https://nam05.safelinks.protection.outlook.com/?url=https%3A%2F%2Furldefense.proofpoint.com%2Fv2%2Furl%3Fu%3Dhttps-3A__nam05.safelinks.protection.outlook.com_-3Furl-3Dhttps-253A-252F-252Furldefense.proofpoint.com-252Fv2-252Furl-253Fu-253Dhttps-2D3A-5F-5Fsourceforge.net-5Fprojects-5Fpymol-5Flists-5Fpymol-2D2Dusers-5Funsubscribe-2526d-253DDwIGaQ-2526c-253DVjzId-2DSM5S6aVB-5FcCGQ0d3uo9UfKByQ3sI6Audoy6dY-2526r-253Dk0gMbcsdOcdbPUNV5tW66KQSZfXL0ewVDPVBp7tqbks-2526m-253DxyAmhZRZYDjhbBLdiMRRk6wCJ14kA5UeQYC4urBFvQw-2526s-253DPY-2Dg0XYMB9DqXC06Iixbjxfqf8jB9Pb-5FGFu8zClx3oY-2526e-253D-26amp-3Bdata-3D02-257C01-257Cqic8-2540pitt.edu-257C01a30e93a2ca4a40b37308d81196d7ba-257C9ef9f489e0a04eeb87cc3a526112fd0d-257C1-257C0-257C637278686852886299-26amp-3Bsdata-3Do1asKPIbwdAFwN-252FCJSTCXDg-252BndmmLXC8VJW8z48Y-252BAA-253D-26amp-3Breserved-3D0%26d%3DDwMF-g%26c%3DVjzId-SM5S6aVB_cCGQ0d3uo9UfKByQ3sI6Audoy6dY%26r%3Dk0gMbcsdOcdbPUNV5tW66KQSZfXL0ewVDPVBp7tqbks%26m%3DX2B3s7D21CBjGtOAQJ2noNR7vnKXPiHiT2eLIRiSC18%26s%3D52GYpWEgXcbl5EqO1gYdzX31C41KuEUPECZU1zDR_TU%26e%3D&data=02%7C01%7Cqic8%40pitt.edu%7C2ea32a0b061443a37f1908d811fd40fd%7C9ef9f489e0a04eeb87cc3a526112fd0d%7C1%7C0%7C637279126707606574&sdata=BE4anajstdDJuzCvU74%2B5qsAwIOsOuGCtYme8aV3OVc%3D&reserved=0>
|
|
From: Oganesyan, V. <vah...@as...> - 2020-06-16 14:38:54
|
Hi Annemarie, Thank you for the offer. I was specifically interested in doing it PyMOL. It was my longtime firmly held belief and I still do think that most of the PyMOL users are the biochemists that do not solve x-ray or EM structures. Hence the need to manipulate molecules, domains, numbering etc. Regards, Vaheh Oganesyan, Ph.D. [cid:image001.png@01D643CA.48E859D0] R&D | Antibody Discovery and Protein Engineering One Medimmune Way, Gaithersburg, MD 20878 T: 301-398-5851 Vah...@as...<mailto:Oga...@me...> From: hon...@bi... <hon...@bi...> Sent: Tuesday, June 16, 2020 1:42 AM To: pym...@li... Subject: Re: [PyMOL] Renumber Hello Vaheh Antibody structures are a mess to renumber, both due to the many different numbering schemes used in different structures, and to some older files not even adhering to pub standards, using the alternative localisation columns for the insertion letters specified by Kabat or Chothia nomenclature. That's why I titled my own contribution to the mess "Yet another numbering scheme ..." https://www.researchgate.net/publication/2530255_Yet_Another_Numbering_Scheme_for_Immunoglobulin_Variable_Domains_An_Automatic_Modeling_and_Analysis_Tool/stats<https://www.researchgate.net/publication/2530255_Yet_Another_Numbering_Scheme_for_Immunoglobulin_Variable_Domains_An_Automatic_Modeling_and_Analysis_Tool/stats> For mass renumbering of antibody variable domains, I actually use some homemade EXCEL Visual Basic macros that extract the sequences from the coordinates into a sequence alignment, and then renumber the pub files from the alignment. If I had to do it in PyMOL, I would do it in multiple steps process: I would first change the numbering to sequential numbering, allowing me to then clear the insertion letters (resv or alt), then change the numbering to my own (AHo) scheme by shifting the numbering of each segment by adding the appropriate constant, starting with the most C-terminal segment to avoid problems due to duplicate residue numbers. I would offer to send you my macro collection, but right now I am in the middle of fixing a number of things that broke due to the update to EXCEL 2019, so I have to ask you for patience. best regards Annemarie Honegger Hi Vaheh, I susoect that your issue is an edge case for PyMOL. The resi variable is limited to integers (see https://pymolwiki.org/index.php/Property_Selectors<https://pymolwiki.org/index.php/Property_Selectors>). Atoms with letters in the resi field are invisible to PyMOL. You could write a python script to preprocess the coordinates, run the script from within PyMOL, and then reload the modified coordinates into PyMOL. It might be more expedient to use pdb_set from ccp4, antibody_numbering_converter.macosclangrelease in rosetta, or biopython. Best regards, Blaine PS Half of our students work in OMRF labs. Our interactions with OMRF are as close as ever. Blaine Mooers, Ph.D. Associate Professor Department of Biochemistry and Molecular Biology College of Medicine University of Oklahoma Health Sciences Center S.L. Young Biomedical Research Center (BRC) Rm. 466 975 NE 10th Street, BRC 466 Oklahoma City, OK 73104-5419 |
|
From: Chen, Q. <qi...@pi...> - 2020-06-16 14:26:23
|
Hi, Blaine,
Then the question becomes how to generate a list with 30 or 300 numbers.
Will this work?
file_list=list(range(00, 30))
Thanks!
Charles
________________________________
From: Mooers, Blaine H.M. (HSC) <Bla...@ou...>
Sent: Tuesday, June 16, 2020 9:57 AM
To: Chen, Qiang <qi...@pi...>; pym...@li... <pym...@li...>
Subject: RE: hydrogen bond list for a series of files
Hi Charles,
You are right and I am wrong about the files needing to be loaded.
The object name has the pesky pdb file extension stripped off, so lets use the object name instead of using Python to strip it off for us.
We no longer need to use glob.
We do need to the create a list of strings that encode the indexing of the files.
This code worked for me with two files.
Adapt to your 30 or 300 files.
file_list = ['01','02']
[cmd.do("load model.000."+str(k)+"_minimized.pdb") for k in file_list]
object_list=cmd.get_object_list('(model.000.*_minimized)')
chains=[('A','F'),('B', 'F'),('C','F'),('D','F'),('E','F')]
run C:\Users\user\AppData\Local\Programs\Python\Python38\lib\site-packages\pymol\pymol_path\Pymol-script-repo\list_hb.py
[cmd.do("list_hb chain F, chain A:E, write_distances_file=hb_"+str(file)+".txt") for file in object_list ]
Best regards,
Blaine
Blaine Mooers, Ph.D.
Associate Professor
Department of Biochemistry and Molecular Biology
College of Medicine
University of Oklahoma Health Sciences Center
S.L. Young Biomedical Research Center (BRC) Rm. 466
975 NE 10th Street, BRC 466
Oklahoma City, OK 73104-5419
________________________________________
From: Chen, Qiang [qi...@pi...]
Sent: Monday, June 15, 2020 10:18 PM
To: Mooers, Blaine H.M. (HSC); pym...@li...
Subject: [EXTERNAL] Re: hydrogen bond list for a series of files
Thanks, Dr. Mooers.
I modified a little.
It seems the pdb files need be loaded.
I put all the following lines in a file multifile_hb.pml
run C:\Users\user\AppData\Local\Programs\Python\Python38\lib\site-packages\pymol\pymol_path\Pymol-script-repo\list_hb.py
import glob
load model.000.*_minimized.pdb
#chains=[('A','F'),('B', 'F'),('C','F'),('D','F'),('E','F')]
[cmd.do("list_hb chain F, chain A:E, write_distances_file=hb_"+str(file)+".txt") for file in glob.glob("model.000.??_minimized.pdb")]
A little not so perfect is that the output file,
hb_model.000.??_minimized.pdb.txt
Is is possible to do something like this
write_distances_file=hb_"+basename(file)+".txt"
Then the output will be
hb_model.000.??_minimized.txt
I tried, and this simple thing does not work.
Any suggestion?
Thanks!
Charles
________________________________
From: Mooers, Blaine H.M. (HSC) <Bla...@ou...>
Sent: Monday, June 15, 2020 9:44 PM
To: Chen, Qiang <qi...@pi...>; pym...@li... <pym...@li...>
Subject: RE: hydrogen bond list for a series of files
Hi Charles,
Make sure that PyMOL's present working directory is where the pdb files are stored.
Copy and paste each of the four lines below one at a time on the command line in PyMOL.
run list_hb.py<https://nam05.safelinks.protection.outlook.com/?url=https%3A%2F%2Furldefense.proofpoint.com%2Fv2%2Furl%3Fu%3Dhttp-3A__list-5Fhb.py%26d%3DDwQF-g%26c%3DVjzId-SM5S6aVB_cCGQ0d3uo9UfKByQ3sI6Audoy6dY%26r%3Dk0gMbcsdOcdbPUNV5tW66KQSZfXL0ewVDPVBp7tqbks%26m%3DX2B3s7D21CBjGtOAQJ2noNR7vnKXPiHiT2eLIRiSC18%26s%3DKYQX_tOI8_HnmseLbJRMv7UTirG78evoaztp35Gg74E%26e%3D&data=02%7C01%7Cqic8%40pitt.edu%7C2ea32a0b061443a37f1908d811fd40fd%7C9ef9f489e0a04eeb87cc3a526112fd0d%7C1%7C0%7C637279126707606574&sdata=8VnRodmeEUrqQfFm7fe0gqd02cYPsKv8VxPcb09RIkQ%3D&reserved=0>
import glob
chains = [('A','B'), ('A','C'), ('A','D'), ('A','E'), ('B','C'), ('B','D'), ('B','E'), ('C','D'), ('C','E'), ('D','E') ]
[[cmd.do("list_hb chain "+ str(i) +", chain " +str(j) + ", write_distances_file=hb_"+ str(file) + "_" + str(i) + "_" +str( j) + "_001.txt") for i, j in chains] for file in glob.glob("model.??.pdb")]
Note that you do not have to load the pdb files into PyMOL.
If you want to analyze more than 99 files and less than 999 files, add a third question mark to the argument of glob.glob().
Best regards,
Blaine
Blaine Mooers, Ph.D.
Associate Professor
Department of Biochemistry and Molecular Biology
College of Medicine
University of Oklahoma Health Sciences Center
S.L. Young Biomedical Research Center (BRC) Rm. 466
975 NE 10th Street, BRC 466
Oklahoma City, OK 73104-5419
________________________________________
From: Chen, Qiang [qi...@pi...]
Sent: Monday, June 15, 2020 2:53 PM
To: pym...@li...
Subject: [EXTERNAL] [PyMOL] hydrogen bond list for a series of files
Hi, Pymol users
Could you help me do this in an efficient way?
Let me describe the task I try to do.
I have a series of numerically ordered files, say model00.pdb model.01.pdb …… model.30.pdb
All the pdb have the same protein composition, chain A, B, C, D, and E. Their relative position is different in each file.
I would like to check the hydrogen bonds between, say, chain A and B.
Thanks to Prof. Robert L. Campbell, I can list the hydrogen bonds in one pdb and print the list as the follows
list_hb chain A, chain B, write_distances_file=hb_A_B_01.txt
How can I process the 30 files in an efficient way? what if I have 300 pdb files?
Shell script, python, or anything else?
Thanks!
Charles Chen
_______________________________________________
PyMOL-users mailing list
Archives: https://nam05.safelinks.protection.outlook.com/?url=https%3A%2F%2Furldefense.proofpoint.com%2Fv2%2Furl%3Fu%3Dhttp-3A__www.mail-2Darchive.com_pymol-2Dusers-40lists.sourceforge.net%26d%3DDwIGaQ%26c%3DVjzId-SM5S6aVB_cCGQ0d3uo9UfKByQ3sI6Audoy6dY%26r%3Dk0gMbcsdOcdbPUNV5tW66KQSZfXL0ewVDPVBp7tqbks%26m%3DxyAmhZRZYDjhbBLdiMRRk6wCJ14kA5UeQYC4urBFvQw%26s%3DaOpeSOw9Gqop8KF8Xf_lkPoBC_MSbb5i0cKlRaIAulI%26e%3D&data=02%7C01%7Cqic8%40pitt.edu%7C2ea32a0b061443a37f1908d811fd40fd%7C9ef9f489e0a04eeb87cc3a526112fd0d%7C1%7C0%7C637279126707606574&sdata=hv3wxBB9OoMRAwCeb44ok4suuSPP47IGl771qqDqaFs%3D&reserved=0<https://nam05.safelinks.protection.outlook.com/?url=https%3A%2F%2Furldefense.proofpoint.com%2Fv2%2Furl%3Fu%3Dhttps-3A__nam05.safelinks.protection.outlook.com_-3Furl-3Dhttps-253A-252F-252Furldefense.proofpoint.com-252Fv2-252Furl-253Fu-253Dhttp-2D3A-5F-5Fwww.mail-2D2Darchive.com-5Fpymol-2D2Dusers-2D40lists.sourceforge.net-2526d-253DDwIGaQ-2526c-253DVjzId-2DSM5S6aVB-5FcCGQ0d3uo9UfKByQ3sI6Audoy6dY-2526r-253Dk0gMbcsdOcdbPUNV5tW66KQSZfXL0ewVDPVBp7tqbks-2526m-253DxyAmhZRZYDjhbBLdiMRRk6wCJ14kA5UeQYC4urBFvQw-2526s-253DaOpeSOw9Gqop8KF8Xf-5FlkPoBC-5FMSbb5i0cKlRaIAulI-2526e-253D-26amp-3Bdata-3D02-257C01-257Cqic8-2540pitt.edu-257C01a30e93a2ca4a40b37308d81196d7ba-257C9ef9f489e0a04eeb87cc3a526112fd0d-257C1-257C0-257C637278686852886299-26amp-3Bsdata-3DH-252BbXZ7ylGnf8aHeqS8UfkWyeYYuKCLZv1GikWVh2gAM-253D-26amp-3Breserved-3D0%26d%3DDwMF-g%26c%3DVjzId-SM5S6aVB_cCGQ0d3uo9UfKByQ3sI6Audoy6dY%26r%3Dk0gMbcsdOcdbPUNV5tW66KQSZfXL0ewVDPVBp7tqbks%26m%3DX2B3s7D21CBjGtOAQJ2noNR7vnKXPiHiT2eLIRiSC18%26s%3DUml8pWJGL1VV1FRsRqY0A8xQ-ZVcOqvXJIUCvJgGjSY%26e%3D&data=02%7C01%7Cqic8%40pitt.edu%7C2ea32a0b061443a37f1908d811fd40fd%7C9ef9f489e0a04eeb87cc3a526112fd0d%7C1%7C0%7C637279126707606574&sdata=Ro1JrjplPPP%2BnpS29PnQTnnIqNWCdpOJCoViVArOBkE%3D&reserved=0>
Unsubscribe: https://nam05.safelinks.protection.outlook.com/?url=https%3A%2F%2Furldefense.proofpoint.com%2Fv2%2Furl%3Fu%3Dhttps-3A__sourceforge.net_projects_pymol_lists_pymol-2Dusers_unsubscribe%26d%3DDwIGaQ%26c%3DVjzId-SM5S6aVB_cCGQ0d3uo9UfKByQ3sI6Audoy6dY%26r%3Dk0gMbcsdOcdbPUNV5tW66KQSZfXL0ewVDPVBp7tqbks%26m%3DxyAmhZRZYDjhbBLdiMRRk6wCJ14kA5UeQYC4urBFvQw%26s%3DPY-g0XYMB9DqXC06Iixbjxfqf8jB9Pb_GFu8zClx3oY%26e%3D&data=02%7C01%7Cqic8%40pitt.edu%7C2ea32a0b061443a37f1908d811fd40fd%7C9ef9f489e0a04eeb87cc3a526112fd0d%7C1%7C0%7C637279126707606574&sdata=WPFSb8UDLcACThM4ujjxACYr%2FbNL8OtX9oPrQ%2F9ipsA%3D&reserved=0<https://nam05.safelinks.protection.outlook.com/?url=https%3A%2F%2Furldefense.proofpoint.com%2Fv2%2Furl%3Fu%3Dhttps-3A__nam05.safelinks.protection.outlook.com_-3Furl-3Dhttps-253A-252F-252Furldefense.proofpoint.com-252Fv2-252Furl-253Fu-253Dhttps-2D3A-5F-5Fsourceforge.net-5Fprojects-5Fpymol-5Flists-5Fpymol-2D2Dusers-5Funsubscribe-2526d-253DDwIGaQ-2526c-253DVjzId-2DSM5S6aVB-5FcCGQ0d3uo9UfKByQ3sI6Audoy6dY-2526r-253Dk0gMbcsdOcdbPUNV5tW66KQSZfXL0ewVDPVBp7tqbks-2526m-253DxyAmhZRZYDjhbBLdiMRRk6wCJ14kA5UeQYC4urBFvQw-2526s-253DPY-2Dg0XYMB9DqXC06Iixbjxfqf8jB9Pb-5FGFu8zClx3oY-2526e-253D-26amp-3Bdata-3D02-257C01-257Cqic8-2540pitt.edu-257C01a30e93a2ca4a40b37308d81196d7ba-257C9ef9f489e0a04eeb87cc3a526112fd0d-257C1-257C0-257C637278686852886299-26amp-3Bsdata-3Do1asKPIbwdAFwN-252FCJSTCXDg-252BndmmLXC8VJW8z48Y-252BAA-253D-26amp-3Breserved-3D0%26d%3DDwMF-g%26c%3DVjzId-SM5S6aVB_cCGQ0d3uo9UfKByQ3sI6Audoy6dY%26r%3Dk0gMbcsdOcdbPUNV5tW66KQSZfXL0ewVDPVBp7tqbks%26m%3DX2B3s7D21CBjGtOAQJ2noNR7vnKXPiHiT2eLIRiSC18%26s%3D52GYpWEgXcbl5EqO1gYdzX31C41KuEUPECZU1zDR_TU%26e%3D&data=02%7C01%7Cqic8%40pitt.edu%7C2ea32a0b061443a37f1908d811fd40fd%7C9ef9f489e0a04eeb87cc3a526112fd0d%7C1%7C0%7C637279126707606574&sdata=BE4anajstdDJuzCvU74%2B5qsAwIOsOuGCtYme8aV3OVc%3D&reserved=0>
|
|
From: Mooers, B. H.M. (HSC) <Bla...@ou...> - 2020-06-16 13:57:47
|
Hi Charles,
You are right and I am wrong about the files needing to be loaded.
The object name has the pesky pdb file extension stripped off, so lets use the object name instead of using Python to strip it off for us.
We no longer need to use glob.
We do need to the create a list of strings that encode the indexing of the files.
This code worked for me with two files.
Adapt to your 30 or 300 files.
file_list = ['01','02']
[cmd.do("load model.000."+str(k)+"_minimized.pdb") for k in file_list]
object_list=cmd.get_object_list('(model.000.*_minimized)')
chains=[('A','F'),('B', 'F'),('C','F'),('D','F'),('E','F')]
run C:\Users\user\AppData\Local\Programs\Python\Python38\lib\site-packages\pymol\pymol_path\Pymol-script-repo\list_hb.py
[cmd.do("list_hb chain F, chain A:E, write_distances_file=hb_"+str(file)+".txt") for file in object_list ]
Best regards,
Blaine
Blaine Mooers, Ph.D.
Associate Professor
Department of Biochemistry and Molecular Biology
College of Medicine
University of Oklahoma Health Sciences Center
S.L. Young Biomedical Research Center (BRC) Rm. 466
975 NE 10th Street, BRC 466
Oklahoma City, OK 73104-5419
________________________________________
From: Chen, Qiang [qi...@pi...]
Sent: Monday, June 15, 2020 10:18 PM
To: Mooers, Blaine H.M. (HSC); pym...@li...
Subject: [EXTERNAL] Re: hydrogen bond list for a series of files
Thanks, Dr. Mooers.
I modified a little.
It seems the pdb files need be loaded.
I put all the following lines in a file multifile_hb.pml
run C:\Users\user\AppData\Local\Programs\Python\Python38\lib\site-packages\pymol\pymol_path\Pymol-script-repo\list_hb.py
import glob
load model.000.*_minimized.pdb
#chains=[('A','F'),('B', 'F'),('C','F'),('D','F'),('E','F')]
[cmd.do("list_hb chain F, chain A:E, write_distances_file=hb_"+str(file)+".txt") for file in glob.glob("model.000.??_minimized.pdb")]
A little not so perfect is that the output file,
hb_model.000.??_minimized.pdb.txt
Is is possible to do something like this
write_distances_file=hb_"+basename(file)+".txt"
Then the output will be
hb_model.000.??_minimized.txt
I tried, and this simple thing does not work.
Any suggestion?
Thanks!
Charles
________________________________
From: Mooers, Blaine H.M. (HSC) <Bla...@ou...>
Sent: Monday, June 15, 2020 9:44 PM
To: Chen, Qiang <qi...@pi...>; pym...@li... <pym...@li...>
Subject: RE: hydrogen bond list for a series of files
Hi Charles,
Make sure that PyMOL's present working directory is where the pdb files are stored.
Copy and paste each of the four lines below one at a time on the command line in PyMOL.
run list_hb.py<https://urldefense.proofpoint.com/v2/url?u=http-3A__list-5Fhb.py&d=DwQF-g&c=VjzId-SM5S6aVB_cCGQ0d3uo9UfKByQ3sI6Audoy6dY&r=k0gMbcsdOcdbPUNV5tW66KQSZfXL0ewVDPVBp7tqbks&m=X2B3s7D21CBjGtOAQJ2noNR7vnKXPiHiT2eLIRiSC18&s=KYQX_tOI8_HnmseLbJRMv7UTirG78evoaztp35Gg74E&e=>
import glob
chains = [('A','B'), ('A','C'), ('A','D'), ('A','E'), ('B','C'), ('B','D'), ('B','E'), ('C','D'), ('C','E'), ('D','E') ]
[[cmd.do("list_hb chain "+ str(i) +", chain " +str(j) + ", write_distances_file=hb_"+ str(file) + "_" + str(i) + "_" +str( j) + "_001.txt") for i, j in chains] for file in glob.glob("model.??.pdb")]
Note that you do not have to load the pdb files into PyMOL.
If you want to analyze more than 99 files and less than 999 files, add a third question mark to the argument of glob.glob().
Best regards,
Blaine
Blaine Mooers, Ph.D.
Associate Professor
Department of Biochemistry and Molecular Biology
College of Medicine
University of Oklahoma Health Sciences Center
S.L. Young Biomedical Research Center (BRC) Rm. 466
975 NE 10th Street, BRC 466
Oklahoma City, OK 73104-5419
________________________________________
From: Chen, Qiang [qi...@pi...]
Sent: Monday, June 15, 2020 2:53 PM
To: pym...@li...
Subject: [EXTERNAL] [PyMOL] hydrogen bond list for a series of files
Hi, Pymol users
Could you help me do this in an efficient way?
Let me describe the task I try to do.
I have a series of numerically ordered files, say model00.pdb model.01.pdb …… model.30.pdb
All the pdb have the same protein composition, chain A, B, C, D, and E. Their relative position is different in each file.
I would like to check the hydrogen bonds between, say, chain A and B.
Thanks to Prof. Robert L. Campbell, I can list the hydrogen bonds in one pdb and print the list as the follows
list_hb chain A, chain B, write_distances_file=hb_A_B_01.txt
How can I process the 30 files in an efficient way? what if I have 300 pdb files?
Shell script, python, or anything else?
Thanks!
Charles Chen
_______________________________________________
PyMOL-users mailing list
Archives: https://nam05.safelinks.protection.outlook.com/?url=https%3A%2F%2Furldefense.proofpoint.com%2Fv2%2Furl%3Fu%3Dhttp-3A__www.mail-2Darchive.com_pymol-2Dusers-40lists.sourceforge.net%26d%3DDwIGaQ%26c%3DVjzId-SM5S6aVB_cCGQ0d3uo9UfKByQ3sI6Audoy6dY%26r%3Dk0gMbcsdOcdbPUNV5tW66KQSZfXL0ewVDPVBp7tqbks%26m%3DxyAmhZRZYDjhbBLdiMRRk6wCJ14kA5UeQYC4urBFvQw%26s%3DaOpeSOw9Gqop8KF8Xf_lkPoBC_MSbb5i0cKlRaIAulI%26e%3D&data=02%7C01%7Cqic8%40pitt.edu%7C01a30e93a2ca4a40b37308d81196d7ba%7C9ef9f489e0a04eeb87cc3a526112fd0d%7C1%7C0%7C637278686852886299&sdata=H%2BbXZ7ylGnf8aHeqS8UfkWyeYYuKCLZv1GikWVh2gAM%3D&reserved=0<https://urldefense.proofpoint.com/v2/url?u=https-3A__nam05.safelinks.protection.outlook.com_-3Furl-3Dhttps-253A-252F-252Furldefense.proofpoint.com-252Fv2-252Furl-253Fu-253Dhttp-2D3A-5F-5Fwww.mail-2D2Darchive.com-5Fpymol-2D2Dusers-2D40lists.sourceforge.net-2526d-253DDwIGaQ-2526c-253DVjzId-2DSM5S6aVB-5FcCGQ0d3uo9UfKByQ3sI6Audoy6dY-2526r-253Dk0gMbcsdOcdbPUNV5tW66KQSZfXL0ewVDPVBp7tqbks-2526m-253DxyAmhZRZYDjhbBLdiMRRk6wCJ14kA5UeQYC4urBFvQw-2526s-253DaOpeSOw9Gqop8KF8Xf-5FlkPoBC-5FMSbb5i0cKlRaIAulI-2526e-253D-26amp-3Bdata-3D02-257C01-257Cqic8-2540pitt.edu-257C01a30e93a2ca4a40b37308d81196d7ba-257C9ef9f489e0a04eeb87cc3a526112fd0d-257C1-257C0-257C637278686852886299-26amp-3Bsdata-3DH-252BbXZ7ylGnf8aHeqS8UfkWyeYYuKCLZv1GikWVh2gAM-253D-26amp-3Breserved-3D0&d=DwMF-g&c=VjzId-SM5S6aVB_cCGQ0d3uo9UfKByQ3sI6Audoy6dY&r=k0gMbcsdOcdbPUNV5tW66KQSZfXL0ewVDPVBp7tqbks&m=X2B3s7D21CBjGtOAQJ2noNR7vnKXPiHiT2eLIRiSC18&s=Uml8pWJGL1VV1FRsRqY0A8xQ-ZVcOqvXJIUCvJgGjSY&e=>
Unsubscribe: https://nam05.safelinks.protection.outlook.com/?url=https%3A%2F%2Furldefense.proofpoint.com%2Fv2%2Furl%3Fu%3Dhttps-3A__sourceforge.net_projects_pymol_lists_pymol-2Dusers_unsubscribe%26d%3DDwIGaQ%26c%3DVjzId-SM5S6aVB_cCGQ0d3uo9UfKByQ3sI6Audoy6dY%26r%3Dk0gMbcsdOcdbPUNV5tW66KQSZfXL0ewVDPVBp7tqbks%26m%3DxyAmhZRZYDjhbBLdiMRRk6wCJ14kA5UeQYC4urBFvQw%26s%3DPY-g0XYMB9DqXC06Iixbjxfqf8jB9Pb_GFu8zClx3oY%26e%3D&data=02%7C01%7Cqic8%40pitt.edu%7C01a30e93a2ca4a40b37308d81196d7ba%7C9ef9f489e0a04eeb87cc3a526112fd0d%7C1%7C0%7C637278686852886299&sdata=o1asKPIbwdAFwN%2FCJSTCXDg%2BndmmLXC8VJW8z48Y%2BAA%3D&reserved=0<https://urldefense.proofpoint.com/v2/url?u=https-3A__nam05.safelinks.protection.outlook.com_-3Furl-3Dhttps-253A-252F-252Furldefense.proofpoint.com-252Fv2-252Furl-253Fu-253Dhttps-2D3A-5F-5Fsourceforge.net-5Fprojects-5Fpymol-5Flists-5Fpymol-2D2Dusers-5Funsubscribe-2526d-253DDwIGaQ-2526c-253DVjzId-2DSM5S6aVB-5FcCGQ0d3uo9UfKByQ3sI6Audoy6dY-2526r-253Dk0gMbcsdOcdbPUNV5tW66KQSZfXL0ewVDPVBp7tqbks-2526m-253DxyAmhZRZYDjhbBLdiMRRk6wCJ14kA5UeQYC4urBFvQw-2526s-253DPY-2Dg0XYMB9DqXC06Iixbjxfqf8jB9Pb-5FGFu8zClx3oY-2526e-253D-26amp-3Bdata-3D02-257C01-257Cqic8-2540pitt.edu-257C01a30e93a2ca4a40b37308d81196d7ba-257C9ef9f489e0a04eeb87cc3a526112fd0d-257C1-257C0-257C637278686852886299-26amp-3Bsdata-3Do1asKPIbwdAFwN-252FCJSTCXDg-252BndmmLXC8VJW8z48Y-252BAA-253D-26amp-3Breserved-3D0&d=DwMF-g&c=VjzId-SM5S6aVB_cCGQ0d3uo9UfKByQ3sI6Audoy6dY&r=k0gMbcsdOcdbPUNV5tW66KQSZfXL0ewVDPVBp7tqbks&m=X2B3s7D21CBjGtOAQJ2noNR7vnKXPiHiT2eLIRiSC18&s=52GYpWEgXcbl5EqO1gYdzX31C41KuEUPECZU1zDR_TU&e=>
|
|
From: <hon...@bi...> - 2020-06-16 06:03:16
|
---...@li... schrieb: ----- An: pym...@li... Von: pym...@li... Datum: 15.06.2020 22:47 Betreff: PyMOL-users Digest, Vol 169, Issue 20 Send PyMOL-users mailing list submissions to pym...@li... To subscribe or unsubscribe via the World Wide Web, visit https://lists.sourceforge.net/lists/listinfo/pymol-users or, via email, send a message with subject or body 'help' to pym...@li... You can reach the person managing the list at pym...@li... When replying, please edit your Subject line so it is more specific than "Re: Contents of PyMOL-users digest..." Today's Topics: 1. Re: renumber (Mooers, Blaine H.M. (HSC)) 2. Re: renumber (Jared Sampson) ---------------------------------------------------------------------- Message: 1 Date: Mon, 15 Jun 2020 20:11:22 +0000 From: "Mooers, Blaine H.M. (HSC)" <Bla...@ou...> To: "Oganesyan, Vaheh" <vah...@as...>, Jared Sampson <jar...@co...> Cc: "pym...@li..." <pym...@li...> Subject: Re: [PyMOL] renumber Message-ID: <87D...@CO...> Content-Type: text/plain; charset="Windows-1252" Hi Vaheh, I susoect that your issue is an edge case for PyMOL. The resi variable is limited to integers (see https://pymolwiki.org/index.php/Property_Selectors). Atoms with letters in the resi field are invisible to PyMOL. You could write a python script to preprocess the coordinates, run the script from within PyMOL, and then reload the modified coordinates into PyMOL. It might be more expedient to use pdb_set from ccp4, antibody_numbering_converter.macosclangrelease in rosetta, or biopython. Best regards, Blaine PS Half of our students work in OMRF labs. Our interactions with OMRF are as close as ever. Blaine Mooers, Ph.D. Associate Professor Department of Biochemistry and Molecular Biology College of Medicine University of Oklahoma Health Sciences Center S.L. Young Biomedical Research Center (BRC) Rm. 466 975 NE 10th Street, BRC 466 Oklahoma City, OK 73104-5419 ________________________________________ From: Oganesyan, Vaheh [vah...@as...] Sent: Monday, June 15, 2020 2:57 PM To: Jared Sampson Cc: pym...@li... Subject: [EXTERNAL] Re: [PyMOL] renumber Jared, Are you saying it cannot be done within PyMOL? The ccp4 option is well known. Thanks. From: Jared Sampson <jar...@co...> Sent: Monday, June 15, 2020 2:41 PM To: Oganesyan, Vaheh <vah...@as...> Cc: pym...@li... Subject: Re: [PyMOL] renumber Hi Vaheh - Try `pdbset` from the CCP4 suite. http://www.ccp4.ac.uk/html/pdbset.html#renumber<https://urldefense.proofpoint.com/v2/url?u=http-3A__www.ccp4.ac.uk_html_pdbset.html-23renumber&d=DwMGaQ&c=VjzId-SM5S6aVB_cCGQ0d3uo9UfKByQ3sI6Audoy6dY&r=k0gMbcsdOcdbPUNV5tW66KQSZfXL0ewVDPVBp7tqbks&m=YUAB1OMR35mD78DtkN0-jGzM7DXrF2uIqVbgVkypuvQ&s=GnEFkqUJR4dd1O4W5j6uD5OVSJXvwp_ONuPcl6tUB_I&e=> ``` pdbset xyzin in.pdb xyzout out.pdb > pdbset.log << EOF renum 1 chain H renum 1 chain L end EOF ``` Hope that helps. Cheers, Jared From: Oganesyan, Vaheh <vah...@as...><mailto:vah...@as...> Reply: Oganesyan, Vaheh <vah...@as...><mailto:vah...@as...> Date: June 15, 2020 at 1:28:23 PM To: Mooers, Blaine H.M. (HSC) <bla...@ou...><mailto:bla...@ou...>, Jarrett Johnson <jar...@sc...><mailto:jar...@sc...> Cc: pym...@li...<mailto:pym...@li...> <pym...@li...><mailto:pym...@li...> Subject: Re: [PyMOL] renumber Blain, The command will not change the numbering of amino acids starting from #1. But if you got missing ones, like in my case, it will. Except for those having also letter in the number field. I mean the numbering used for CDRs of antibodies, not alternatives. Hence, my question, is there a command that will ignore the letters in the number field and renumber the amino acids in the order they appear in the file. Thank you. From: Mooers, Blaine H.M. (HSC) <Bla...@ou...<mailto:Bla...@ou...>> Sent: Monday, June 15, 2020 12:06 PM To: Oganesyan, Vaheh <vah...@as...<mailto:vah...@as...>>; Jarrett Johnson <jar...@sc...<mailto:jar...@sc...>> Cc: pym...@li...<mailto:pym...@li...> Subject: RE: [PyMOL] renumber Hi Vaheh, alter vh, resi=str(int(resi)+0) will not change the residue numbers because 0 is being added. Replace 0 with your desired residue number offset. Best regards, Blaine Blaine Mooers, Ph.D. Associate Professor Department of Biochemistry and Molecular Biology College of Medicine University of Oklahoma Health Sciences Center S.L. Young Biomedical Research Center (BRC) Rm. 466 975 NE 10th Street, BRC 466 Oklahoma City, OK 73104-5419 ________________________________________ From: Oganesyan, Vaheh [vah...@as...] Sent: Monday, June 15, 2020 10:49 AM To: Jarrett Johnson Cc: pym...@li...<mailto:pym...@li...> Subject: [EXTERNAL] Re: [PyMOL] renumber Thank you Jarrett, Then the command alter vh, resi=str(int(resi)+0) should work, right? But it doesn?t because there are residue numbers with letters. Is there a command that will either remove the letters or won?t pay attention to them and renumber sequentially. Regards, From: Jarrett Johnson <jar...@sc...<mailto:jar...@sc...>> Sent: Monday, June 15, 2020 11:38 AM To: Oganesyan, Vaheh <vah...@as...<mailto:vah...@as...>> Cc: pym...@li...<mailto:pym...@li...> Subject: Re: [PyMOL] renumber Hello, The command shown on this page https://pymolwiki.org/index.php/Renumber<https://urldefense.proofpoint.com/v2/url?u=https-3A__pymolwiki.org_index.php_Renumber&d=DwMGaQ&c=VjzId-SM5S6aVB_cCGQ0d3uo9UfKByQ3sI6Audoy6dY&r=k0gMbcsdOcdbPUNV5tW66KQSZfXL0ewVDPVBp7tqbks&m=YUAB1OMR35mD78DtkN0-jGzM7DXrF2uIqVbgVkypuvQ&s=uEl_YqHefDypoAGkjQR211JPMc8HPqE4NwgLL5ZiZ_4&e=><https://urldefense.proofpoint.com/v2/url?u=https-3A__pymolwiki.org_index.php_Renumber&d=DwMGaQ&c=VjzId-SM5S6aVB_cCGQ0d3uo9UfKByQ3sI6Audoy6dY&r=k0gMbcsdOcdbPUNV5tW66KQSZfXL0ewVDPVBp7tqbks&m=HQhXfRvgQZ3mFRTUuOGKZTZZVlTRi9o87ygYqEDnPog&s=ziFhw29qVsmpI-rra_AyanmqFEsNZVmEsXF4VIjUMmI&e=> is not one that comes with PyMOL by default. Try downloading the script and importing it via the `run` command in the PyMOL command-line: run renumber.py<https://urldefense.proofpoint.com/v2/url?u=http-3A__renumber.py&d=DwQGaQ&c=VjzId-SM5S6aVB_cCGQ0d3uo9UfKByQ3sI6Audoy6dY&r=k0gMbcsdOcdbPUNV5tW66KQSZfXL0ewVDPVBp7tqbks&m=HQhXfRvgQZ3mFRTUuOGKZTZZVlTRi9o87ygYqEDnPog&s=FHmoNz1s1Pj-_paiWCTfneG3RkPiLccu2uI2KNr8ROw&e=> and then you should be able to use the command as shown on the Wiki page. Hope that helps, Jarrett J. On Mon, Jun 15, 2020 at 11:29 AM Oganesyan, Vaheh <vah...@as...<mailto:vah...@as...<mailto:vah...@as...%3cmailto:vah...@as...>>> wrote: Hello PyMOLers, Wiki uses renumber command to alter residue numbers, but PyMOL doesn?t recognize it. Is it that Wiki is old, or my PyMOL version is dusty? Regards, Vaheh _______________________________________________ PyMOL-users mailing list Archives: http://www.mail-archive.com/pym...@li...<https://urldefense.proofpoint.com/v2/url?u=http-3A__www.mail-2Darchive.com_pymol-2Dusers-40lists.sourceforge.net&d=DwMGaQ&c=VjzId-SM5S6aVB_cCGQ0d3uo9UfKByQ3sI6Audoy6dY&r=k0gMbcsdOcdbPUNV5tW66KQSZfXL0ewVDPVBp7tqbks&m=YUAB1OMR35mD78DtkN0-jGzM7DXrF2uIqVbgVkypuvQ&s=Nmqp7za485bsYun2GcEFHuByMMCkM5AIohHa0CVGomo&e=><https://urldefense.proofpoint.com/v2/url?u=http-3A__www.mail-2Darchive.com_pymol-2Dusers-40lists.sourceforge.net&d=DwMGaQ&c=VjzId-SM5S6aVB_cCGQ0d3uo9UfKByQ3sI6Audoy6dY&r=k0gMbcsdOcdbPUNV5tW66KQSZfXL0ewVDPVBp7tqbks&m=HQhXfRvgQZ3mFRTUuOGKZTZZVlTRi9o87ygYqEDnPog&s=0jiLKKRpirp3ZmCRyyo_9R1IshveF24db_HqbNveLVE&e=> Unsubscribe: https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe<https://urldefense.proofpoint.com/v2/url?u=https-3A__sourceforge.net_projects_pymol_lists_pymol-2Dusers_unsubscribe&d=DwMGaQ&c=VjzId-SM5S6aVB_cCGQ0d3uo9UfKByQ3sI6Audoy6dY&r=k0gMbcsdOcdbPUNV5tW66KQSZfXL0ewVDPVBp7tqbks&m=YUAB1OMR35mD78DtkN0-jGzM7DXrF2uIqVbgVkypuvQ&s=kosjPbfawmorCb0u6Sg1TzxU79wJ7O31q6uFq5ApU_A&e=><https://urldefense.proofpoint.com/v2/url?u=https-3A__sourceforge.net_projects_pymol_lists_pymol-2Dusers_unsubscribe&d=DwMGaQ&c=VjzId-SM5S6aVB_cCGQ0d3uo9UfKByQ3sI6Audoy6dY&r=k0gMbcsdOcdbPUNV5tW66KQSZfXL0ewVDPVBp7tqbks&m=HQhXfRvgQZ3mFRTUuOGKZTZZVlTRi9o87ygYqEDnPog&s=u0GfpqJznDAnSRPi-ENNk5i5F203FOoK4e8tFBNx-fc&e=> -- Jarrett Johnson | Senior Developer [Schrodinger Logo]<https://urldefense.proofpoint.com/v2/url?u=https-3A__www.schrodinger.com_&d=DwMGaQ&c=VjzId-SM5S6aVB_cCGQ0d3uo9UfKByQ3sI6Audoy6dY&r=k0gMbcsdOcdbPUNV5tW66KQSZfXL0ewVDPVBp7tqbks&m=HQhXfRvgQZ3mFRTUuOGKZTZZVlTRi9o87ygYqEDnPog&s=my7IR5rxG-1yA5AP52htw3MT5MKRSqHAwEmOVfdcSdc&e=> _______________________________________________ PyMOL-users mailing list Archives: http://www.mail-archive.com/pym...@li...<https://urldefense.proofpoint.com/v2/url?u=http-3A__www.mail-2Darchive.com_pymol-2Dusers-40lists.sourceforge.net&d=DwMGaQ&c=VjzId-SM5S6aVB_cCGQ0d3uo9UfKByQ3sI6Audoy6dY&r=k0gMbcsdOcdbPUNV5tW66KQSZfXL0ewVDPVBp7tqbks&m=YUAB1OMR35mD78DtkN0-jGzM7DXrF2uIqVbgVkypuvQ&s=Nmqp7za485bsYun2GcEFHuByMMCkM5AIohHa0CVGomo&e=> Unsubscribe: https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe<https://urldefense.proofpoint.com/v2/url?u=https-3A__sourceforge.net_projects_pymol_lists_pymol-2Dusers_unsubscribe&d=DwMGaQ&c=VjzId-SM5S6aVB_cCGQ0d3uo9UfKByQ3sI6Audoy6dY&r=k0gMbcsdOcdbPUNV5tW66KQSZfXL0ewVDPVBp7tqbks&m=YUAB1OMR35mD78DtkN0-jGzM7DXrF2uIqVbgVkypuvQ&s=kosjPbfawmorCb0u6Sg1TzxU79wJ7O31q6uFq5ApU_A&e=> ------------------------------ Message: 2 Date: Mon, 15 Jun 2020 16:46:34 -0400 From: Jared Sampson <jar...@co...> To: Oganesyan, Vaheh <vah...@as...> Cc: "=?utf-8?Q?pymol-users=40lists.sourceforge.net?=" <pym...@li...> Subject: Re: [PyMOL] renumber Message-ID: <etP...@co...> Content-Type: text/plain; charset="utf-8" Hi Vaheh -? I wasn't saying it can't be done, just that pdbset is my preferred way to handle renumbering when going in the insertion code --> integer direction. Within PyMOL, here is one way (you'll have to repeat for each chain you wish to renumber): ``` # see:?https://pymolwiki.org/index.php/Pymol.stored from pymol import stored # store the current residue numbers in a list stored.oldresi = [] iterate polymer.protein and chain L and n. CA, stored.oldresi.append(resi) # make a list of the new residue numbers stored.newresi = list(range(1, len(stored.oldresi)+1)) # zip them together into a lookup dict stored.hash = dict(zip(stored.oldresi, stored.newresi)) # change the residue numbers for each atom in your chain alter polymer.protein and chain L, resi=stored.hash[resi] ``` Hope that helps. Cheers, Jared From:?Oganesyan, Vaheh <vah...@as...> Reply:?Oganesyan, Vaheh <vah...@as...> Date:?June 15, 2020 at 3:57:24 PM To:?Jared Sampson <jar...@co...> Cc:?pym...@li... <pym...@li...> Subject:? RE: [PyMOL] renumber Jared, ? Are you saying it cannot be done within PyMOL? The ccp4 option is well known. ? Thanks. ? From: Jared Sampson <jar...@co...> Sent: Monday, June 15, 2020 2:41 PM To: Oganesyan, Vaheh <vah...@as...> Cc: pym...@li... Subject: Re: [PyMOL] renumber ? Hi Vaheh - ? Try `pdbset` from the CCP4 suite. ? http://www.ccp4.ac.uk/html/pdbset.html#renumber ? ``` pdbset xyzin in.pdb xyzout out.pdb > pdbset.log << EOF renum 1 chain H renum 1 chain L end EOF ``` ? Hope that helps. ? Cheers, Jared ? From:?Oganesyan, Vaheh <vah...@as...> Reply:?Oganesyan, Vaheh <vah...@as...> Date:?June 15, 2020 at 1:28:23 PM To:?Mooers, Blaine H.M. (HSC) <bla...@ou...>, Jarrett Johnson <jar...@sc...> Cc:?pym...@li... <pym...@li...> Subject:? Re: [PyMOL] renumber Blain, ? The command will not change the numbering of amino acids starting from #1. But if you got missing ones, like in my case, it will. Except for those having also letter in the number field. I mean the numbering used for CDRs of antibodies, not alternatives. Hence, my question, is there a command that will ignore the letters in the number field and renumber the amino acids in the order they appear in the file. ? Thank you. ? From: Mooers, Blaine H.M. (HSC) <Bla...@ou...> Sent: Monday, June 15, 2020 12:06 PM To: Oganesyan, Vaheh <vah...@as...>; Jarrett Johnson <jar...@sc...> Cc: pym...@li... Subject: RE: [PyMOL] renumber ? Hi Vaheh, alter vh, resi=str(int(resi)+0) will not change the residue numbers because 0 is being added. Replace 0 with your desired residue number offset. Best regards, Blaine Blaine Mooers, Ph.D. Associate Professor Department of Biochemistry and Molecular Biology College of Medicine University of Oklahoma Health Sciences Center S.L. Young Biomedical Research Center (BRC) Rm. 466 975 NE 10th Street, BRC 466 Oklahoma City, OK 73104-5419 ________________________________________ From: Oganesyan, Vaheh [vah...@as...] Sent: Monday, June 15, 2020 10:49 AM To: Jarrett Johnson Cc: pym...@li... Subject: [EXTERNAL] Re: [PyMOL] renumber Thank you Jarrett, Then the command alter vh, resi=str(int(resi)+0) should work, right? But it doesn?t because there are residue numbers with letters. Is there a command that will either remove the letters or won?t pay attention to them and renumber sequentially. Regards, From: Jarrett Johnson <jar...@sc...> Sent: Monday, June 15, 2020 11:38 AM To: Oganesyan, Vaheh <vah...@as...> Cc: pym...@li... Subject: Re: [PyMOL] renumber Hello, The command shown on this page https://pymolwiki.org/index.php/Renumber<https://urldefense.proofpoint.com/v2/url?u=https-3A__pymolwiki.org_index.php_Renumber&d=DwMGaQ&c=VjzId-SM5S6aVB_cCGQ0d3uo9UfKByQ3sI6Audoy6dY&r=k0gMbcsdOcdbPUNV5tW66KQSZfXL0ewVDPVBp7tqbks&m=HQhXfRvgQZ3mFRTUuOGKZTZZVlTRi9o87ygYqEDnPog&s=ziFhw29qVsmpI-rra_AyanmqFEsNZVmEsXF4VIjUMmI&e=> is not one that comes with PyMOL by default. Try downloading the script and importing it via the `run` command in the PyMOL command-line: run renumber.py<https://urldefense.proofpoint.com/v2/url?u=http-3A__renumber.py&d=DwQGaQ&c=VjzId-SM5S6aVB_cCGQ0d3uo9UfKByQ3sI6Audoy6dY&r=k0gMbcsdOcdbPUNV5tW66KQSZfXL0ewVDPVBp7tqbks&m=HQhXfRvgQZ3mFRTUuOGKZTZZVlTRi9o87ygYqEDnPog&s=FHmoNz1s1Pj-_paiWCTfneG3RkPiLccu2uI2KNr8ROw&e=> and then you should be able to use the command as shown on the Wiki page. Hope that helps, Jarrett J. On Mon, Jun 15, 2020 at 11:29 AM Oganesyan, Vaheh <vah...@as...<mailto:vah...@as...>> wrote: Hello PyMOLers, Wiki uses renumber command to alter residue numbers, but PyMOL doesn?t recognize it. Is it that Wiki is old, or my PyMOL version is dusty? Regards, Vaheh _______________________________________________ PyMOL-users mailing list Archives: http://www.mail-archive.com/pym...@li...<https://urldefense.proofpoint.com/v2/url?u=http-3A__www.mail-2Darchive.com_pymol-2Dusers-40lists.sourceforge.net&d=DwMGaQ&c=VjzId-SM5S6aVB_cCGQ0d3uo9UfKByQ3sI6Audoy6dY&r=k0gMbcsdOcdbPUNV5tW66KQSZfXL0ewVDPVBp7tqbks&m=HQhXfRvgQZ3mFRTUuOGKZTZZVlTRi9o87ygYqEDnPog&s=0jiLKKRpirp3ZmCRyyo_9R1IshveF24db_HqbNveLVE&e=> Unsubscribe: https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe<https://urldefense.proofpoint.com/v2/url?u=https-3A__sourceforge.net_projects_pymol_lists_pymol-2Dusers_unsubscribe&d=DwMGaQ&c=VjzId-SM5S6aVB_cCGQ0d3uo9UfKByQ3sI6Audoy6dY&r=k0gMbcsdOcdbPUNV5tW66KQSZfXL0ewVDPVBp7tqbks&m=HQhXfRvgQZ3mFRTUuOGKZTZZVlTRi9o87ygYqEDnPog&s=u0GfpqJznDAnSRPi-ENNk5i5F203FOoK4e8tFBNx-fc&e=> -- Jarrett Johnson | Senior Developer [Schrodinger Logo]<https://urldefense.proofpoint.com/v2/url?u=https-3A__www.schrodinger.com_&d=DwMGaQ&c=VjzId-SM5S6aVB_cCGQ0d3uo9UfKByQ3sI6Audoy6dY&r=k0gMbcsdOcdbPUNV5tW66KQSZfXL0ewVDPVBp7tqbks&m=HQhXfRvgQZ3mFRTUuOGKZTZZVlTRi9o87ygYqEDnPog&s=my7IR5rxG-1yA5AP52htw3MT5MKRSqHAwEmOVfdcSdc&e=> _______________________________________________ PyMOL-users mailing list Archives: http://www.mail-archive.com/pym...@li... Unsubscribe: https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe -------------- next part -------------- An HTML attachment was scrubbed... ------------------------------ ------------------------------ Subject: Digest Footer _______________________________________________ PyMOL-users mailing list PyM...@li... https://lists.sourceforge.net/lists/listinfo/pymol-users Unsubscribe: https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe ------------------------------ End of PyMOL-users Digest, Vol 169, Issue 20 ******************************************** |
|
From: <hon...@bi...> - 2020-06-16 05:58:17
|
Hello Vaheh Antibody structures are a mess to renumber, both due to the many different numbering schemes used in different structures, and to some older files not even adhering to pub standards, using the alternative localisation columns for the insertion letters specified by Kabat or Chothia nomenclature. That's why I titled my own contribution to the mess "Yet another numbering scheme ..." https://www.researchgate.net/publication/2530255_Yet_Another_Numbering_Scheme_for_Immunoglobulin_Variable_Domains_An_Automatic_Modeling_and_Analysis_Tool/stats For mass renumbering of antibody variable domains, I actually use some homemade EXCEL Visual Basic macros that extract the sequences from the coordinates into a sequence alignment, and then renumber the pub files from the alignment. If I had to do it in PyMOL, I would do it in multiple steps process: I would first change the numbering to sequential numbering, allowing me to then clear the insertion letters (resv or alt), then change the numbering to my own (AHo) scheme by shifting the numbering of each segment by adding the appropriate constant, starting with the most C-terminal segment to avoid problems due to duplicate residue numbers. I would offer to send you my macro collection, but right now I am in the middle of fixing a number of things that broke due to the update to EXCEL 2019, so I have to ask you for patience. best regards Annemarie Honegger Hi Vaheh, I susoect that your issue is an edge case for PyMOL. The resi variable is limited to integers (see https://pymolwiki.org/index.php/Property_Selectors). Atoms with letters in the resi field are invisible to PyMOL. You could write a python script to preprocess the coordinates, run the script from within PyMOL, and then reload the modified coordinates into PyMOL. It might be more expedient to use pdb_set from ccp4, antibody_numbering_converter.macosclangrelease in rosetta, or biopython. Best regards, Blaine PS Half of our students work in OMRF labs. Our interactions with OMRF are as close as ever. Blaine Mooers, Ph.D. Associate Professor Department of Biochemistry and Molecular Biology College of Medicine University of Oklahoma Health Sciences Center S.L. Young Biomedical Research Center (BRC) Rm. 466 975 NE 10th Street, BRC 466 Oklahoma City, OK 73104-5419 |
|
From: Chen, Q. <qi...@pi...> - 2020-06-16 05:53:12
|
Thanks, Dr. Mooers.
I modified a little.
It seems the pdb files need be loaded.
I put all the following lines in a file multifile_hb.pml
run C:\Users\user\AppData\Local\Programs\Python\Python38\lib\site-packages\pymol\pymol_path\Pymol-script-repo\list_hb.py
import glob
load model.000.*_minimized.pdb
#chains=[('A','F'),('B', 'F'),('C','F'),('D','F'),('E','F')]
[cmd.do("list_hb chain F, chain A:E, write_distances_file=hb_"+str(file)+".txt") for file in glob.glob("model.000.??_minimized.pdb")]
A little not so perfect is that the output file,
hb_model.000.??_minimized.pdb.txt
Is is possible to do something like this
write_distances_file=hb_"+basename(file)+".txt"
Then the output will be
hb_model.000.??_minimized.txt
I tried, and this simple thing does not work.
Any suggestion?
Thanks!
Charles
________________________________
From: Mooers, Blaine H.M. (HSC) <Bla...@ou...>
Sent: Monday, June 15, 2020 9:44 PM
To: Chen, Qiang <qi...@pi...>; pym...@li... <pym...@li...>
Subject: RE: hydrogen bond list for a series of files
Hi Charles,
Make sure that PyMOL's present working directory is where the pdb files are stored.
Copy and paste each of the four lines below one at a time on the command line in PyMOL.
run list_hb.py
import glob
chains = [('A','B'), ('A','C'), ('A','D'), ('A','E'), ('B','C'), ('B','D'), ('B','E'), ('C','D'), ('C','E'), ('D','E') ]
[[cmd.do("list_hb chain "+ str(i) +", chain " +str(j) + ", write_distances_file=hb_"+ str(file) + "_" + str(i) + "_" +str( j) + "_001.txt") for i, j in chains] for file in glob.glob("model.??.pdb")]
Note that you do not have to load the pdb files into PyMOL.
If you want to analyze more than 99 files and less than 999 files, add a third question mark to the argument of glob.glob().
Best regards,
Blaine
Blaine Mooers, Ph.D.
Associate Professor
Department of Biochemistry and Molecular Biology
College of Medicine
University of Oklahoma Health Sciences Center
S.L. Young Biomedical Research Center (BRC) Rm. 466
975 NE 10th Street, BRC 466
Oklahoma City, OK 73104-5419
________________________________________
From: Chen, Qiang [qi...@pi...]
Sent: Monday, June 15, 2020 2:53 PM
To: pym...@li...
Subject: [EXTERNAL] [PyMOL] hydrogen bond list for a series of files
Hi, Pymol users
Could you help me do this in an efficient way?
Let me describe the task I try to do.
I have a series of numerically ordered files, say model00.pdb model.01.pdb …… model.30.pdb
All the pdb have the same protein composition, chain A, B, C, D, and E. Their relative position is different in each file.
I would like to check the hydrogen bonds between, say, chain A and B.
Thanks to Prof. Robert L. Campbell, I can list the hydrogen bonds in one pdb and print the list as the follows
list_hb chain A, chain B, write_distances_file=hb_A_B_01.txt
How can I process the 30 files in an efficient way? what if I have 300 pdb files?
Shell script, python, or anything else?
Thanks!
Charles Chen
_______________________________________________
PyMOL-users mailing list
Archives: https://nam05.safelinks.protection.outlook.com/?url=https%3A%2F%2Furldefense.proofpoint.com%2Fv2%2Furl%3Fu%3Dhttp-3A__www.mail-2Darchive.com_pymol-2Dusers-40lists.sourceforge.net%26d%3DDwIGaQ%26c%3DVjzId-SM5S6aVB_cCGQ0d3uo9UfKByQ3sI6Audoy6dY%26r%3Dk0gMbcsdOcdbPUNV5tW66KQSZfXL0ewVDPVBp7tqbks%26m%3DxyAmhZRZYDjhbBLdiMRRk6wCJ14kA5UeQYC4urBFvQw%26s%3DaOpeSOw9Gqop8KF8Xf_lkPoBC_MSbb5i0cKlRaIAulI%26e%3D&data=02%7C01%7Cqic8%40pitt.edu%7C01a30e93a2ca4a40b37308d81196d7ba%7C9ef9f489e0a04eeb87cc3a526112fd0d%7C1%7C0%7C637278686852886299&sdata=H%2BbXZ7ylGnf8aHeqS8UfkWyeYYuKCLZv1GikWVh2gAM%3D&reserved=0
Unsubscribe: https://nam05.safelinks.protection.outlook.com/?url=https%3A%2F%2Furldefense.proofpoint.com%2Fv2%2Furl%3Fu%3Dhttps-3A__sourceforge.net_projects_pymol_lists_pymol-2Dusers_unsubscribe%26d%3DDwIGaQ%26c%3DVjzId-SM5S6aVB_cCGQ0d3uo9UfKByQ3sI6Audoy6dY%26r%3Dk0gMbcsdOcdbPUNV5tW66KQSZfXL0ewVDPVBp7tqbks%26m%3DxyAmhZRZYDjhbBLdiMRRk6wCJ14kA5UeQYC4urBFvQw%26s%3DPY-g0XYMB9DqXC06Iixbjxfqf8jB9Pb_GFu8zClx3oY%26e%3D&data=02%7C01%7Cqic8%40pitt.edu%7C01a30e93a2ca4a40b37308d81196d7ba%7C9ef9f489e0a04eeb87cc3a526112fd0d%7C1%7C0%7C637278686852886299&sdata=o1asKPIbwdAFwN%2FCJSTCXDg%2BndmmLXC8VJW8z48Y%2BAA%3D&reserved=0
|
|
From: Mooers, B. H.M. (HSC) <Bla...@ou...> - 2020-06-16 01:44:42
|
Hi Charles,
Make sure that PyMOL's present working directory is where the pdb files are stored.
Copy and paste each of the four lines below one at a time on the command line in PyMOL.
run list_hb.py
import glob
chains = [('A','B'), ('A','C'), ('A','D'), ('A','E'), ('B','C'), ('B','D'), ('B','E'), ('C','D'), ('C','E'), ('D','E') ]
[[cmd.do("list_hb chain "+ str(i) +", chain " +str(j) + ", write_distances_file=hb_"+ str(file) + "_" + str(i) + "_" +str( j) + "_001.txt") for i, j in chains] for file in glob.glob("model.??.pdb")]
Note that you do not have to load the pdb files into PyMOL.
If you want to analyze more than 99 files and less than 999 files, add a third question mark to the argument of glob.glob().
Best regards,
Blaine
Blaine Mooers, Ph.D.
Associate Professor
Department of Biochemistry and Molecular Biology
College of Medicine
University of Oklahoma Health Sciences Center
S.L. Young Biomedical Research Center (BRC) Rm. 466
975 NE 10th Street, BRC 466
Oklahoma City, OK 73104-5419
________________________________________
From: Chen, Qiang [qi...@pi...]
Sent: Monday, June 15, 2020 2:53 PM
To: pym...@li...
Subject: [EXTERNAL] [PyMOL] hydrogen bond list for a series of files
Hi, Pymol users
Could you help me do this in an efficient way?
Let me describe the task I try to do.
I have a series of numerically ordered files, say model00.pdb model.01.pdb …… model.30.pdb
All the pdb have the same protein composition, chain A, B, C, D, and E. Their relative position is different in each file.
I would like to check the hydrogen bonds between, say, chain A and B.
Thanks to Prof. Robert L. Campbell, I can list the hydrogen bonds in one pdb and print the list as the follows
list_hb chain A, chain B, write_distances_file=hb_A_B_01.txt
How can I process the 30 files in an efficient way? what if I have 300 pdb files?
Shell script, python, or anything else?
Thanks!
Charles Chen
_______________________________________________
PyMOL-users mailing list
Archives: https://urldefense.proofpoint.com/v2/url?u=http-3A__www.mail-2Darchive.com_pymol-2Dusers-40lists.sourceforge.net&d=DwIGaQ&c=VjzId-SM5S6aVB_cCGQ0d3uo9UfKByQ3sI6Audoy6dY&r=k0gMbcsdOcdbPUNV5tW66KQSZfXL0ewVDPVBp7tqbks&m=xyAmhZRZYDjhbBLdiMRRk6wCJ14kA5UeQYC4urBFvQw&s=aOpeSOw9Gqop8KF8Xf_lkPoBC_MSbb5i0cKlRaIAulI&e=
Unsubscribe: https://urldefense.proofpoint.com/v2/url?u=https-3A__sourceforge.net_projects_pymol_lists_pymol-2Dusers_unsubscribe&d=DwIGaQ&c=VjzId-SM5S6aVB_cCGQ0d3uo9UfKByQ3sI6Audoy6dY&r=k0gMbcsdOcdbPUNV5tW66KQSZfXL0ewVDPVBp7tqbks&m=xyAmhZRZYDjhbBLdiMRRk6wCJ14kA5UeQYC4urBFvQw&s=PY-g0XYMB9DqXC06Iixbjxfqf8jB9Pb_GFu8zClx3oY&e=
|
|
From: Oganesyan, V. <vah...@as...> - 2020-06-15 21:22:42
|
Thank you Jared. From: Jared Sampson <jar...@co...> Sent: Monday, June 15, 2020 4:47 PM To: Oganesyan, Vaheh <vah...@as...> Cc: pym...@li... Subject: RE: [PyMOL] renumber Hi Vaheh - I wasn't saying it can't be done, just that pdbset is my preferred way to handle renumbering when going in the insertion code --> integer direction. Within PyMOL, here is one way (you'll have to repeat for each chain you wish to renumber): ``` # see: https://pymolwiki.org/index.php/Pymol.stored<https://pymolwiki.org/index.php/Pymol.stored> from pymol import stored # store the current residue numbers in a list stored.oldresi = [] iterate polymer.protein and chain L and n. CA, stored.oldresi.append(resi) # make a list of the new residue numbers stored.newresi = list(range(1, len(stored.oldresi)+1)) # zip them together into a lookup dict stored.hash = dict(zip(stored.oldresi, stored.newresi)) # change the residue numbers for each atom in your chain alter polymer.protein and chain L, resi=stored.hash[resi] ``` Hope that helps. Cheers, Jared From: Oganesyan, Vaheh <vah...@as...><mailto:vah...@as...> Reply: Oganesyan, Vaheh <vah...@as...><mailto:vah...@as...> Date: June 15, 2020 at 3:57:24 PM To: Jared Sampson <jar...@co...><mailto:jar...@co...> Cc: pym...@li...<mailto:pym...@li...> <pym...@li...><mailto:pym...@li...> Subject: RE: [PyMOL] renumber Jared, Are you saying it cannot be done within PyMOL? The ccp4 option is well known. Thanks. From: Jared Sampson <jar...@co...<mailto:jar...@co...>> Sent: Monday, June 15, 2020 2:41 PM To: Oganesyan, Vaheh <vah...@as...<mailto:vah...@as...>> Cc: pym...@li...<mailto:pym...@li...> Subject: Re: [PyMOL] renumber Hi Vaheh - Try `pdbset` from the CCP4 suite. http://www.ccp4.ac.uk/html/pdbset.html#renumber<http://www.ccp4.ac.uk/html/pdbset.html#renumber> ``` pdbset xyzin in.pdb xyzout out.pdb > pdbset.log << EOF renum 1 chain H renum 1 chain L end EOF ``` Hope that helps. Cheers, Jared From: Oganesyan, Vaheh <vah...@as...><mailto:vah...@as...> Reply: Oganesyan, Vaheh <vah...@as...><mailto:vah...@as...> Date: June 15, 2020 at 1:28:23 PM To: Mooers, Blaine H.M. (HSC) <bla...@ou...><mailto:bla...@ou...>, Jarrett Johnson <jar...@sc...><mailto:jar...@sc...> Cc: pym...@li...<mailto:pym...@li...> <pym...@li...><mailto:pym...@li...> Subject: Re: [PyMOL] renumber Blain, The command will not change the numbering of amino acids starting from #1. But if you got missing ones, like in my case, it will. Except for those having also letter in the number field. I mean the numbering used for CDRs of antibodies, not alternatives. Hence, my question, is there a command that will ignore the letters in the number field and renumber the amino acids in the order they appear in the file. Thank you. From: Mooers, Blaine H.M. (HSC) <Bla...@ou...<mailto:Bla...@ou...>> Sent: Monday, June 15, 2020 12:06 PM To: Oganesyan, Vaheh <vah...@as...<mailto:vah...@as...>>; Jarrett Johnson <jar...@sc...<mailto:jar...@sc...>> Cc: pym...@li...<mailto:pym...@li...> Subject: RE: [PyMOL] renumber Hi Vaheh, alter vh, resi=str(int(resi)+0) will not change the residue numbers because 0 is being added. Replace 0 with your desired residue number offset. Best regards, Blaine Blaine Mooers, Ph.D. Associate Professor Department of Biochemistry and Molecular Biology College of Medicine University of Oklahoma Health Sciences Center S.L. Young Biomedical Research Center (BRC) Rm. 466 975 NE 10th Street, BRC 466 Oklahoma City, OK 73104-5419 ________________________________________ From: Oganesyan, Vaheh [vah...@as...] Sent: Monday, June 15, 2020 10:49 AM To: Jarrett Johnson Cc: pym...@li...<mailto:pym...@li...> Subject: [EXTERNAL] Re: [PyMOL] renumber Thank you Jarrett, Then the command alter vh, resi=str(int(resi)+0) should work, right? But it doesn’t because there are residue numbers with letters. Is there a command that will either remove the letters or won’t pay attention to them and renumber sequentially. Regards, From: Jarrett Johnson <jar...@sc...<mailto:jar...@sc...>> Sent: Monday, June 15, 2020 11:38 AM To: Oganesyan, Vaheh <vah...@as...<mailto:vah...@as...>> Cc: pym...@li...<mailto:pym...@li...> Subject: Re: [PyMOL] renumber Hello, The command shown on this page https://pymolwiki.org/index.php/Renumber<https://pymolwiki.org/index.php/Renumber><https://urldefense.proofpoint.com/v2/url?u=https-3A__pymolwiki.org_index.php_Renumber&d=DwMGaQ&c=VjzId-SM5S6aVB_cCGQ0d3uo9UfKByQ3sI6Audoy6dY&r=k0gMbcsdOcdbPUNV5tW66KQSZfXL0ewVDPVBp7tqbks&m=HQhXfRvgQZ3mFRTUuOGKZTZZVlTRi9o87ygYqEDnPog&s=ziFhw29qVsmpI-rra_AyanmqFEsNZVmEsXF4VIjUMmI&e=<https://urldefense.proofpoint.com/v2/url?u=https-3A__pymolwiki.org_index.php_Renumber&d=DwMGaQ&c=VjzId-SM5S6aVB_cCGQ0d3uo9UfKByQ3sI6Audoy6dY&r=k0gMbcsdOcdbPUNV5tW66KQSZfXL0ewVDPVBp7tqbks&m=HQhXfRvgQZ3mFRTUuOGKZTZZVlTRi9o87ygYqEDnPog&s=ziFhw29qVsmpI-rra_AyanmqFEsNZVmEsXF4VIjUMmI&e=>> is not one that comes with PyMOL by default. Try downloading the script and importing it via the `run` command in the PyMOL command-line: run renumber.py<https://urldefense.proofpoint.com/v2/url?u=http-3A__renumber.py&d=DwQGaQ&c=VjzId-SM5S6aVB_cCGQ0d3uo9UfKByQ3sI6Audoy6dY&r=k0gMbcsdOcdbPUNV5tW66KQSZfXL0ewVDPVBp7tqbks&m=HQhXfRvgQZ3mFRTUuOGKZTZZVlTRi9o87ygYqEDnPog&s=FHmoNz1s1Pj-_paiWCTfneG3RkPiLccu2uI2KNr8ROw&e=<https://urldefense.proofpoint.com/v2/url?u=http-3A__renumber.py&d=DwQGaQ&c=VjzId-SM5S6aVB_cCGQ0d3uo9UfKByQ3sI6Audoy6dY&r=k0gMbcsdOcdbPUNV5tW66KQSZfXL0ewVDPVBp7tqbks&m=HQhXfRvgQZ3mFRTUuOGKZTZZVlTRi9o87ygYqEDnPog&s=FHmoNz1s1Pj-_paiWCTfneG3RkPiLccu2uI2KNr8ROw&e=>> and then you should be able to use the command as shown on the Wiki page. Hope that helps, Jarrett J. On Mon, Jun 15, 2020 at 11:29 AM Oganesyan, Vaheh <vah...@as...<mailto:vah...@as...<mailto:vah...@as...%3cmailto:vah...@as...>>> wrote: Hello PyMOLers, Wiki uses renumber command to alter residue numbers, but PyMOL doesn’t recognize it. Is it that Wiki is old, or my PyMOL version is dusty? Regards, Vaheh _______________________________________________ PyMOL-users mailing list Archives: http://www.mail-archive.com/pym...@li...<http://www.mail-archive.com/pym...@li...><https://urldefense.proofpoint.com/v2/url?u=http-3A__www.mail-2Darchive.com_pymol-2Dusers-40lists.sourceforge.net&d=DwMGaQ&c=VjzId-SM5S6aVB_cCGQ0d3uo9UfKByQ3sI6Audoy6dY&r=k0gMbcsdOcdbPUNV5tW66KQSZfXL0ewVDPVBp7tqbks&m=HQhXfRvgQZ3mFRTUuOGKZTZZVlTRi9o87ygYqEDnPog&s=0jiLKKRpirp3ZmCRyyo_9R1IshveF24db_HqbNveLVE&e=<https://urldefense.proofpoint.com/v2/url?u=http-3A__www.mail-2Darchive.com_pymol-2Dusers-40lists.sourceforge.net&d=DwMGaQ&c=VjzId-SM5S6aVB_cCGQ0d3uo9UfKByQ3sI6Audoy6dY&r=k0gMbcsdOcdbPUNV5tW66KQSZfXL0ewVDPVBp7tqbks&m=HQhXfRvgQZ3mFRTUuOGKZTZZVlTRi9o87ygYqEDnPog&s=0jiLKKRpirp3ZmCRyyo_9R1IshveF24db_HqbNveLVE&e=>> Unsubscribe: https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe<https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe><https://urldefense.proofpoint.com/v2/url?u=https-3A__sourceforge.net_projects_pymol_lists_pymol-2Dusers_unsubscribe&d=DwMGaQ&c=VjzId-SM5S6aVB_cCGQ0d3uo9UfKByQ3sI6Audoy6dY&r=k0gMbcsdOcdbPUNV5tW66KQSZfXL0ewVDPVBp7tqbks&m=HQhXfRvgQZ3mFRTUuOGKZTZZVlTRi9o87ygYqEDnPog&s=u0GfpqJznDAnSRPi-ENNk5i5F203FOoK4e8tFBNx-fc&e=<https://urldefense.proofpoint.com/v2/url?u=https-3A__sourceforge.net_projects_pymol_lists_pymol-2Dusers_unsubscribe&d=DwMGaQ&c=VjzId-SM5S6aVB_cCGQ0d3uo9UfKByQ3sI6Audoy6dY&r=k0gMbcsdOcdbPUNV5tW66KQSZfXL0ewVDPVBp7tqbks&m=HQhXfRvgQZ3mFRTUuOGKZTZZVlTRi9o87ygYqEDnPog&s=u0GfpqJznDAnSRPi-ENNk5i5F203FOoK4e8tFBNx-fc&e=>> -- Jarrett Johnson | Senior Developer [Schrodinger Logo]<https://urldefense.proofpoint.com/v2/url?u=https-3A__www.schrodinger.com_&d=DwMGaQ&c=VjzId-SM5S6aVB_cCGQ0d3uo9UfKByQ3sI6Audoy6dY&r=k0gMbcsdOcdbPUNV5tW66KQSZfXL0ewVDPVBp7tqbks&m=HQhXfRvgQZ3mFRTUuOGKZTZZVlTRi9o87ygYqEDnPog&s=my7IR5rxG-1yA5AP52htw3MT5MKRSqHAwEmOVfdcSdc&e=<https://urldefense.proofpoint.com/v2/url?u=https-3A__www.schrodinger.com_&d=DwMGaQ&c=VjzId-SM5S6aVB_cCGQ0d3uo9UfKByQ3sI6Audoy6dY&r=k0gMbcsdOcdbPUNV5tW66KQSZfXL0ewVDPVBp7tqbks&m=HQhXfRvgQZ3mFRTUuOGKZTZZVlTRi9o87ygYqEDnPog&s=my7IR5rxG-1yA5AP52htw3MT5MKRSqHAwEmOVfdcSdc&e=>> _______________________________________________ PyMOL-users mailing list Archives: http://www.mail-archive.com/pym...@li...<http://www.mail-archive.com/pym...@li...> Unsubscribe: https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe<https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe> |
|
From: Jared S. <jar...@co...> - 2020-06-15 20:46:51
|
Hi Vaheh - I wasn't saying it can't be done, just that pdbset is my preferred way to handle renumbering when going in the insertion code --> integer direction. Within PyMOL, here is one way (you'll have to repeat for each chain you wish to renumber): ``` # see: https://pymolwiki.org/index.php/Pymol.stored from pymol import stored # store the current residue numbers in a list stored.oldresi = [] iterate polymer.protein and chain L and n. CA, stored.oldresi.append(resi) # make a list of the new residue numbers stored.newresi = list(range(1, len(stored.oldresi)+1)) # zip them together into a lookup dict stored.hash = dict(zip(stored.oldresi, stored.newresi)) # change the residue numbers for each atom in your chain alter polymer.protein and chain L, resi=stored.hash[resi] ``` Hope that helps. Cheers, Jared From: Oganesyan, Vaheh <vah...@as...> Reply: Oganesyan, Vaheh <vah...@as...> Date: June 15, 2020 at 3:57:24 PM To: Jared Sampson <jar...@co...> Cc: pym...@li... <pym...@li...> Subject: RE: [PyMOL] renumber Jared, Are you saying it cannot be done within PyMOL? The ccp4 option is well known. Thanks. From: Jared Sampson <jar...@co...> Sent: Monday, June 15, 2020 2:41 PM To: Oganesyan, Vaheh <vah...@as...> Cc: pym...@li... Subject: Re: [PyMOL] renumber Hi Vaheh - Try `pdbset` from the CCP4 suite. http://www.ccp4.ac.uk/html/pdbset.html#renumber ``` pdbset xyzin in.pdb xyzout out.pdb > pdbset.log << EOF renum 1 chain H renum 1 chain L end EOF ``` Hope that helps. Cheers, Jared From: Oganesyan, Vaheh <vah...@as...> Reply: Oganesyan, Vaheh <vah...@as...> Date: June 15, 2020 at 1:28:23 PM To: Mooers, Blaine H.M. (HSC) <bla...@ou...>, Jarrett Johnson <jar...@sc...> Cc: pym...@li... <pym...@li...> Subject: Re: [PyMOL] renumber Blain, The command will not change the numbering of amino acids starting from #1. But if you got missing ones, like in my case, it will. Except for those having also letter in the number field. I mean the numbering used for CDRs of antibodies, not alternatives. Hence, my question, is there a command that will ignore the letters in the number field and renumber the amino acids in the order they appear in the file. Thank you. From: Mooers, Blaine H.M. (HSC) <Bla...@ou...> Sent: Monday, June 15, 2020 12:06 PM To: Oganesyan, Vaheh <vah...@as...>; Jarrett Johnson <jar...@sc...> Cc: pym...@li... Subject: RE: [PyMOL] renumber Hi Vaheh, alter vh, resi=str(int(resi)+0) will not change the residue numbers because 0 is being added. Replace 0 with your desired residue number offset. Best regards, Blaine Blaine Mooers, Ph.D. Associate Professor Department of Biochemistry and Molecular Biology College of Medicine University of Oklahoma Health Sciences Center S.L. Young Biomedical Research Center (BRC) Rm. 466 975 NE 10th Street, BRC 466 Oklahoma City, OK 73104-5419 ________________________________________ From: Oganesyan, Vaheh [vah...@as...] Sent: Monday, June 15, 2020 10:49 AM To: Jarrett Johnson Cc: pym...@li... Subject: [EXTERNAL] Re: [PyMOL] renumber Thank you Jarrett, Then the command alter vh, resi=str(int(resi)+0) should work, right? But it doesn’t because there are residue numbers with letters. Is there a command that will either remove the letters or won’t pay attention to them and renumber sequentially. Regards, From: Jarrett Johnson <jar...@sc...> Sent: Monday, June 15, 2020 11:38 AM To: Oganesyan, Vaheh <vah...@as...> Cc: pym...@li... Subject: Re: [PyMOL] renumber Hello, The command shown on this page https://pymolwiki.org/index.php/Renumber<https://urldefense.proofpoint.com/v2/url?u=https-3A__pymolwiki.org_index.php_Renumber&d=DwMGaQ&c=VjzId-SM5S6aVB_cCGQ0d3uo9UfKByQ3sI6Audoy6dY&r=k0gMbcsdOcdbPUNV5tW66KQSZfXL0ewVDPVBp7tqbks&m=HQhXfRvgQZ3mFRTUuOGKZTZZVlTRi9o87ygYqEDnPog&s=ziFhw29qVsmpI-rra_AyanmqFEsNZVmEsXF4VIjUMmI&e=> is not one that comes with PyMOL by default. Try downloading the script and importing it via the `run` command in the PyMOL command-line: run renumber.py<https://urldefense.proofpoint.com/v2/url?u=http-3A__renumber.py&d=DwQGaQ&c=VjzId-SM5S6aVB_cCGQ0d3uo9UfKByQ3sI6Audoy6dY&r=k0gMbcsdOcdbPUNV5tW66KQSZfXL0ewVDPVBp7tqbks&m=HQhXfRvgQZ3mFRTUuOGKZTZZVlTRi9o87ygYqEDnPog&s=FHmoNz1s1Pj-_paiWCTfneG3RkPiLccu2uI2KNr8ROw&e=> and then you should be able to use the command as shown on the Wiki page. Hope that helps, Jarrett J. On Mon, Jun 15, 2020 at 11:29 AM Oganesyan, Vaheh <vah...@as...<mailto:vah...@as...>> wrote: Hello PyMOLers, Wiki uses renumber command to alter residue numbers, but PyMOL doesn’t recognize it. Is it that Wiki is old, or my PyMOL version is dusty? Regards, Vaheh _______________________________________________ PyMOL-users mailing list Archives: http://www.mail-archive.com/pym...@li...<https://urldefense.proofpoint.com/v2/url?u=http-3A__www.mail-2Darchive.com_pymol-2Dusers-40lists.sourceforge.net&d=DwMGaQ&c=VjzId-SM5S6aVB_cCGQ0d3uo9UfKByQ3sI6Audoy6dY&r=k0gMbcsdOcdbPUNV5tW66KQSZfXL0ewVDPVBp7tqbks&m=HQhXfRvgQZ3mFRTUuOGKZTZZVlTRi9o87ygYqEDnPog&s=0jiLKKRpirp3ZmCRyyo_9R1IshveF24db_HqbNveLVE&e=> Unsubscribe: https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe<https://urldefense.proofpoint.com/v2/url?u=https-3A__sourceforge.net_projects_pymol_lists_pymol-2Dusers_unsubscribe&d=DwMGaQ&c=VjzId-SM5S6aVB_cCGQ0d3uo9UfKByQ3sI6Audoy6dY&r=k0gMbcsdOcdbPUNV5tW66KQSZfXL0ewVDPVBp7tqbks&m=HQhXfRvgQZ3mFRTUuOGKZTZZVlTRi9o87ygYqEDnPog&s=u0GfpqJznDAnSRPi-ENNk5i5F203FOoK4e8tFBNx-fc&e=> -- Jarrett Johnson | Senior Developer [Schrodinger Logo]<https://urldefense.proofpoint.com/v2/url?u=https-3A__www.schrodinger.com_&d=DwMGaQ&c=VjzId-SM5S6aVB_cCGQ0d3uo9UfKByQ3sI6Audoy6dY&r=k0gMbcsdOcdbPUNV5tW66KQSZfXL0ewVDPVBp7tqbks&m=HQhXfRvgQZ3mFRTUuOGKZTZZVlTRi9o87ygYqEDnPog&s=my7IR5rxG-1yA5AP52htw3MT5MKRSqHAwEmOVfdcSdc&e=> _______________________________________________ PyMOL-users mailing list Archives: http://www.mail-archive.com/pym...@li... Unsubscribe: https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe |
|
From: Mooers, B. H.M. (HSC) <Bla...@ou...> - 2020-06-15 20:13:44
|
Hi Vaheh, I susoect that your issue is an edge case for PyMOL. The resi variable is limited to integers (see https://pymolwiki.org/index.php/Property_Selectors). Atoms with letters in the resi field are invisible to PyMOL. You could write a python script to preprocess the coordinates, run the script from within PyMOL, and then reload the modified coordinates into PyMOL. It might be more expedient to use pdb_set from ccp4, antibody_numbering_converter.macosclangrelease in rosetta, or biopython. Best regards, Blaine PS Half of our students work in OMRF labs. Our interactions with OMRF are as close as ever. Blaine Mooers, Ph.D. Associate Professor Department of Biochemistry and Molecular Biology College of Medicine University of Oklahoma Health Sciences Center S.L. Young Biomedical Research Center (BRC) Rm. 466 975 NE 10th Street, BRC 466 Oklahoma City, OK 73104-5419 ________________________________________ From: Oganesyan, Vaheh [vah...@as...] Sent: Monday, June 15, 2020 2:57 PM To: Jared Sampson Cc: pym...@li... Subject: [EXTERNAL] Re: [PyMOL] renumber Jared, Are you saying it cannot be done within PyMOL? The ccp4 option is well known. Thanks. From: Jared Sampson <jar...@co...> Sent: Monday, June 15, 2020 2:41 PM To: Oganesyan, Vaheh <vah...@as...> Cc: pym...@li... Subject: Re: [PyMOL] renumber Hi Vaheh - Try `pdbset` from the CCP4 suite. http://www.ccp4.ac.uk/html/pdbset.html#renumber<https://urldefense.proofpoint.com/v2/url?u=http-3A__www.ccp4.ac.uk_html_pdbset.html-23renumber&d=DwMGaQ&c=VjzId-SM5S6aVB_cCGQ0d3uo9UfKByQ3sI6Audoy6dY&r=k0gMbcsdOcdbPUNV5tW66KQSZfXL0ewVDPVBp7tqbks&m=YUAB1OMR35mD78DtkN0-jGzM7DXrF2uIqVbgVkypuvQ&s=GnEFkqUJR4dd1O4W5j6uD5OVSJXvwp_ONuPcl6tUB_I&e=> ``` pdbset xyzin in.pdb xyzout out.pdb > pdbset.log << EOF renum 1 chain H renum 1 chain L end EOF ``` Hope that helps. Cheers, Jared From: Oganesyan, Vaheh <vah...@as...><mailto:vah...@as...> Reply: Oganesyan, Vaheh <vah...@as...><mailto:vah...@as...> Date: June 15, 2020 at 1:28:23 PM To: Mooers, Blaine H.M. (HSC) <bla...@ou...><mailto:bla...@ou...>, Jarrett Johnson <jar...@sc...><mailto:jar...@sc...> Cc: pym...@li...<mailto:pym...@li...> <pym...@li...><mailto:pym...@li...> Subject: Re: [PyMOL] renumber Blain, The command will not change the numbering of amino acids starting from #1. But if you got missing ones, like in my case, it will. Except for those having also letter in the number field. I mean the numbering used for CDRs of antibodies, not alternatives. Hence, my question, is there a command that will ignore the letters in the number field and renumber the amino acids in the order they appear in the file. Thank you. From: Mooers, Blaine H.M. (HSC) <Bla...@ou...<mailto:Bla...@ou...>> Sent: Monday, June 15, 2020 12:06 PM To: Oganesyan, Vaheh <vah...@as...<mailto:vah...@as...>>; Jarrett Johnson <jar...@sc...<mailto:jar...@sc...>> Cc: pym...@li...<mailto:pym...@li...> Subject: RE: [PyMOL] renumber Hi Vaheh, alter vh, resi=str(int(resi)+0) will not change the residue numbers because 0 is being added. Replace 0 with your desired residue number offset. Best regards, Blaine Blaine Mooers, Ph.D. Associate Professor Department of Biochemistry and Molecular Biology College of Medicine University of Oklahoma Health Sciences Center S.L. Young Biomedical Research Center (BRC) Rm. 466 975 NE 10th Street, BRC 466 Oklahoma City, OK 73104-5419 ________________________________________ From: Oganesyan, Vaheh [vah...@as...] Sent: Monday, June 15, 2020 10:49 AM To: Jarrett Johnson Cc: pym...@li...<mailto:pym...@li...> Subject: [EXTERNAL] Re: [PyMOL] renumber Thank you Jarrett, Then the command alter vh, resi=str(int(resi)+0) should work, right? But it doesn’t because there are residue numbers with letters. Is there a command that will either remove the letters or won’t pay attention to them and renumber sequentially. Regards, From: Jarrett Johnson <jar...@sc...<mailto:jar...@sc...>> Sent: Monday, June 15, 2020 11:38 AM To: Oganesyan, Vaheh <vah...@as...<mailto:vah...@as...>> Cc: pym...@li...<mailto:pym...@li...> Subject: Re: [PyMOL] renumber Hello, The command shown on this page https://pymolwiki.org/index.php/Renumber<https://urldefense.proofpoint.com/v2/url?u=https-3A__pymolwiki.org_index.php_Renumber&d=DwMGaQ&c=VjzId-SM5S6aVB_cCGQ0d3uo9UfKByQ3sI6Audoy6dY&r=k0gMbcsdOcdbPUNV5tW66KQSZfXL0ewVDPVBp7tqbks&m=YUAB1OMR35mD78DtkN0-jGzM7DXrF2uIqVbgVkypuvQ&s=uEl_YqHefDypoAGkjQR211JPMc8HPqE4NwgLL5ZiZ_4&e=><https://urldefense.proofpoint.com/v2/url?u=https-3A__pymolwiki.org_index.php_Renumber&d=DwMGaQ&c=VjzId-SM5S6aVB_cCGQ0d3uo9UfKByQ3sI6Audoy6dY&r=k0gMbcsdOcdbPUNV5tW66KQSZfXL0ewVDPVBp7tqbks&m=HQhXfRvgQZ3mFRTUuOGKZTZZVlTRi9o87ygYqEDnPog&s=ziFhw29qVsmpI-rra_AyanmqFEsNZVmEsXF4VIjUMmI&e=> is not one that comes with PyMOL by default. Try downloading the script and importing it via the `run` command in the PyMOL command-line: run renumber.py<https://urldefense.proofpoint.com/v2/url?u=http-3A__renumber.py&d=DwQGaQ&c=VjzId-SM5S6aVB_cCGQ0d3uo9UfKByQ3sI6Audoy6dY&r=k0gMbcsdOcdbPUNV5tW66KQSZfXL0ewVDPVBp7tqbks&m=HQhXfRvgQZ3mFRTUuOGKZTZZVlTRi9o87ygYqEDnPog&s=FHmoNz1s1Pj-_paiWCTfneG3RkPiLccu2uI2KNr8ROw&e=> and then you should be able to use the command as shown on the Wiki page. Hope that helps, Jarrett J. On Mon, Jun 15, 2020 at 11:29 AM Oganesyan, Vaheh <vah...@as...<mailto:vah...@as...<mailto:vah...@as...%3cmailto:vah...@as...>>> wrote: Hello PyMOLers, Wiki uses renumber command to alter residue numbers, but PyMOL doesn’t recognize it. Is it that Wiki is old, or my PyMOL version is dusty? Regards, Vaheh _______________________________________________ PyMOL-users mailing list Archives: http://www.mail-archive.com/pym...@li...<https://urldefense.proofpoint.com/v2/url?u=http-3A__www.mail-2Darchive.com_pymol-2Dusers-40lists.sourceforge.net&d=DwMGaQ&c=VjzId-SM5S6aVB_cCGQ0d3uo9UfKByQ3sI6Audoy6dY&r=k0gMbcsdOcdbPUNV5tW66KQSZfXL0ewVDPVBp7tqbks&m=YUAB1OMR35mD78DtkN0-jGzM7DXrF2uIqVbgVkypuvQ&s=Nmqp7za485bsYun2GcEFHuByMMCkM5AIohHa0CVGomo&e=><https://urldefense.proofpoint.com/v2/url?u=http-3A__www.mail-2Darchive.com_pymol-2Dusers-40lists.sourceforge.net&d=DwMGaQ&c=VjzId-SM5S6aVB_cCGQ0d3uo9UfKByQ3sI6Audoy6dY&r=k0gMbcsdOcdbPUNV5tW66KQSZfXL0ewVDPVBp7tqbks&m=HQhXfRvgQZ3mFRTUuOGKZTZZVlTRi9o87ygYqEDnPog&s=0jiLKKRpirp3ZmCRyyo_9R1IshveF24db_HqbNveLVE&e=> Unsubscribe: https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe<https://urldefense.proofpoint.com/v2/url?u=https-3A__sourceforge.net_projects_pymol_lists_pymol-2Dusers_unsubscribe&d=DwMGaQ&c=VjzId-SM5S6aVB_cCGQ0d3uo9UfKByQ3sI6Audoy6dY&r=k0gMbcsdOcdbPUNV5tW66KQSZfXL0ewVDPVBp7tqbks&m=YUAB1OMR35mD78DtkN0-jGzM7DXrF2uIqVbgVkypuvQ&s=kosjPbfawmorCb0u6Sg1TzxU79wJ7O31q6uFq5ApU_A&e=><https://urldefense.proofpoint.com/v2/url?u=https-3A__sourceforge.net_projects_pymol_lists_pymol-2Dusers_unsubscribe&d=DwMGaQ&c=VjzId-SM5S6aVB_cCGQ0d3uo9UfKByQ3sI6Audoy6dY&r=k0gMbcsdOcdbPUNV5tW66KQSZfXL0ewVDPVBp7tqbks&m=HQhXfRvgQZ3mFRTUuOGKZTZZVlTRi9o87ygYqEDnPog&s=u0GfpqJznDAnSRPi-ENNk5i5F203FOoK4e8tFBNx-fc&e=> -- Jarrett Johnson | Senior Developer [Schrodinger Logo]<https://urldefense.proofpoint.com/v2/url?u=https-3A__www.schrodinger.com_&d=DwMGaQ&c=VjzId-SM5S6aVB_cCGQ0d3uo9UfKByQ3sI6Audoy6dY&r=k0gMbcsdOcdbPUNV5tW66KQSZfXL0ewVDPVBp7tqbks&m=HQhXfRvgQZ3mFRTUuOGKZTZZVlTRi9o87ygYqEDnPog&s=my7IR5rxG-1yA5AP52htw3MT5MKRSqHAwEmOVfdcSdc&e=> _______________________________________________ PyMOL-users mailing list Archives: http://www.mail-archive.com/pym...@li...<https://urldefense.proofpoint.com/v2/url?u=http-3A__www.mail-2Darchive.com_pymol-2Dusers-40lists.sourceforge.net&d=DwMGaQ&c=VjzId-SM5S6aVB_cCGQ0d3uo9UfKByQ3sI6Audoy6dY&r=k0gMbcsdOcdbPUNV5tW66KQSZfXL0ewVDPVBp7tqbks&m=YUAB1OMR35mD78DtkN0-jGzM7DXrF2uIqVbgVkypuvQ&s=Nmqp7za485bsYun2GcEFHuByMMCkM5AIohHa0CVGomo&e=> Unsubscribe: https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe<https://urldefense.proofpoint.com/v2/url?u=https-3A__sourceforge.net_projects_pymol_lists_pymol-2Dusers_unsubscribe&d=DwMGaQ&c=VjzId-SM5S6aVB_cCGQ0d3uo9UfKByQ3sI6Audoy6dY&r=k0gMbcsdOcdbPUNV5tW66KQSZfXL0ewVDPVBp7tqbks&m=YUAB1OMR35mD78DtkN0-jGzM7DXrF2uIqVbgVkypuvQ&s=kosjPbfawmorCb0u6Sg1TzxU79wJ7O31q6uFq5ApU_A&e=> |
|
From: Chen, Q. <qi...@pi...> - 2020-06-15 20:09:32
|
Hi, Pymol users Could you help me do this in an efficient way? Let me describe the task I try to do. I have a series of numerically ordered files, say model00.pdb model.01.pdb …… model.30.pdb All the pdb have the same protein composition, chain A, B, C, D, and E. Their relative position is different in each file. I would like to check the hydrogen bonds between, say, chain A and B. Thanks to Prof. Robert L. Campbell, I can list the hydrogen bonds in one pdb and print the list as the follows list_hb chain A, chain B, write_distances_file=hb_A_B_01.txt How can I process the 30 files in an efficient way? what if I have 300 pdb files? Shell script, python, or anything else? Thanks! Charles Chen |
|
From: Oganesyan, V. <vah...@as...> - 2020-06-15 19:57:39
|
Jared, Are you saying it cannot be done within PyMOL? The ccp4 option is well known. Thanks. From: Jared Sampson <jar...@co...> Sent: Monday, June 15, 2020 2:41 PM To: Oganesyan, Vaheh <vah...@as...> Cc: pym...@li... Subject: Re: [PyMOL] renumber Hi Vaheh - Try `pdbset` from the CCP4 suite. http://www.ccp4.ac.uk/html/pdbset.html#renumber<http://www.ccp4.ac.uk/html/pdbset.html#renumber> ``` pdbset xyzin in.pdb xyzout out.pdb > pdbset.log << EOF renum 1 chain H renum 1 chain L end EOF ``` Hope that helps. Cheers, Jared From: Oganesyan, Vaheh <vah...@as...><mailto:vah...@as...> Reply: Oganesyan, Vaheh <vah...@as...><mailto:vah...@as...> Date: June 15, 2020 at 1:28:23 PM To: Mooers, Blaine H.M. (HSC) <bla...@ou...><mailto:bla...@ou...>, Jarrett Johnson <jar...@sc...><mailto:jar...@sc...> Cc: pym...@li...<mailto:pym...@li...> <pym...@li...><mailto:pym...@li...> Subject: Re: [PyMOL] renumber Blain, The command will not change the numbering of amino acids starting from #1. But if you got missing ones, like in my case, it will. Except for those having also letter in the number field. I mean the numbering used for CDRs of antibodies, not alternatives. Hence, my question, is there a command that will ignore the letters in the number field and renumber the amino acids in the order they appear in the file. Thank you. From: Mooers, Blaine H.M. (HSC) <Bla...@ou...<mailto:Bla...@ou...>> Sent: Monday, June 15, 2020 12:06 PM To: Oganesyan, Vaheh <vah...@as...<mailto:vah...@as...>>; Jarrett Johnson <jar...@sc...<mailto:jar...@sc...>> Cc: pym...@li...<mailto:pym...@li...> Subject: RE: [PyMOL] renumber Hi Vaheh, alter vh, resi=str(int(resi)+0) will not change the residue numbers because 0 is being added. Replace 0 with your desired residue number offset. Best regards, Blaine Blaine Mooers, Ph.D. Associate Professor Department of Biochemistry and Molecular Biology College of Medicine University of Oklahoma Health Sciences Center S.L. Young Biomedical Research Center (BRC) Rm. 466 975 NE 10th Street, BRC 466 Oklahoma City, OK 73104-5419 ________________________________________ From: Oganesyan, Vaheh [vah...@as...] Sent: Monday, June 15, 2020 10:49 AM To: Jarrett Johnson Cc: pym...@li...<mailto:pym...@li...> Subject: [EXTERNAL] Re: [PyMOL] renumber Thank you Jarrett, Then the command alter vh, resi=str(int(resi)+0) should work, right? But it doesn’t because there are residue numbers with letters. Is there a command that will either remove the letters or won’t pay attention to them and renumber sequentially. Regards, From: Jarrett Johnson <jar...@sc...<mailto:jar...@sc...>> Sent: Monday, June 15, 2020 11:38 AM To: Oganesyan, Vaheh <vah...@as...<mailto:vah...@as...>> Cc: pym...@li...<mailto:pym...@li...> Subject: Re: [PyMOL] renumber Hello, The command shown on this page https://pymolwiki.org/index.php/Renumber<https://pymolwiki.org/index.php/Renumber><https://urldefense.proofpoint.com/v2/url?u=https-3A__pymolwiki.org_index.php_Renumber&d=DwMGaQ&c=VjzId-SM5S6aVB_cCGQ0d3uo9UfKByQ3sI6Audoy6dY&r=k0gMbcsdOcdbPUNV5tW66KQSZfXL0ewVDPVBp7tqbks&m=HQhXfRvgQZ3mFRTUuOGKZTZZVlTRi9o87ygYqEDnPog&s=ziFhw29qVsmpI-rra_AyanmqFEsNZVmEsXF4VIjUMmI&e=<https://urldefense.proofpoint.com/v2/url?u=https-3A__pymolwiki.org_index.php_Renumber&d=DwMGaQ&c=VjzId-SM5S6aVB_cCGQ0d3uo9UfKByQ3sI6Audoy6dY&r=k0gMbcsdOcdbPUNV5tW66KQSZfXL0ewVDPVBp7tqbks&m=HQhXfRvgQZ3mFRTUuOGKZTZZVlTRi9o87ygYqEDnPog&s=ziFhw29qVsmpI-rra_AyanmqFEsNZVmEsXF4VIjUMmI&e=>> is not one that comes with PyMOL by default. Try downloading the script and importing it via the `run` command in the PyMOL command-line: run renumber.py<https://urldefense.proofpoint.com/v2/url?u=http-3A__renumber.py&d=DwQGaQ&c=VjzId-SM5S6aVB_cCGQ0d3uo9UfKByQ3sI6Audoy6dY&r=k0gMbcsdOcdbPUNV5tW66KQSZfXL0ewVDPVBp7tqbks&m=HQhXfRvgQZ3mFRTUuOGKZTZZVlTRi9o87ygYqEDnPog&s=FHmoNz1s1Pj-_paiWCTfneG3RkPiLccu2uI2KNr8ROw&e=<https://urldefense.proofpoint.com/v2/url?u=http-3A__renumber.py&d=DwQGaQ&c=VjzId-SM5S6aVB_cCGQ0d3uo9UfKByQ3sI6Audoy6dY&r=k0gMbcsdOcdbPUNV5tW66KQSZfXL0ewVDPVBp7tqbks&m=HQhXfRvgQZ3mFRTUuOGKZTZZVlTRi9o87ygYqEDnPog&s=FHmoNz1s1Pj-_paiWCTfneG3RkPiLccu2uI2KNr8ROw&e=>> and then you should be able to use the command as shown on the Wiki page. Hope that helps, Jarrett J. On Mon, Jun 15, 2020 at 11:29 AM Oganesyan, Vaheh <vah...@as...<mailto:vah...@as...<mailto:vah...@as...%3cmailto:vah...@as...>>> wrote: Hello PyMOLers, Wiki uses renumber command to alter residue numbers, but PyMOL doesn’t recognize it. Is it that Wiki is old, or my PyMOL version is dusty? Regards, Vaheh _______________________________________________ PyMOL-users mailing list Archives: http://www.mail-archive.com/pym...@li...<http://www.mail-archive.com/pym...@li...><https://urldefense.proofpoint.com/v2/url?u=http-3A__www.mail-2Darchive.com_pymol-2Dusers-40lists.sourceforge.net&d=DwMGaQ&c=VjzId-SM5S6aVB_cCGQ0d3uo9UfKByQ3sI6Audoy6dY&r=k0gMbcsdOcdbPUNV5tW66KQSZfXL0ewVDPVBp7tqbks&m=HQhXfRvgQZ3mFRTUuOGKZTZZVlTRi9o87ygYqEDnPog&s=0jiLKKRpirp3ZmCRyyo_9R1IshveF24db_HqbNveLVE&e=<https://urldefense.proofpoint.com/v2/url?u=http-3A__www.mail-2Darchive.com_pymol-2Dusers-40lists.sourceforge.net&d=DwMGaQ&c=VjzId-SM5S6aVB_cCGQ0d3uo9UfKByQ3sI6Audoy6dY&r=k0gMbcsdOcdbPUNV5tW66KQSZfXL0ewVDPVBp7tqbks&m=HQhXfRvgQZ3mFRTUuOGKZTZZVlTRi9o87ygYqEDnPog&s=0jiLKKRpirp3ZmCRyyo_9R1IshveF24db_HqbNveLVE&e=>> Unsubscribe: https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe<https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe><https://urldefense.proofpoint.com/v2/url?u=https-3A__sourceforge.net_projects_pymol_lists_pymol-2Dusers_unsubscribe&d=DwMGaQ&c=VjzId-SM5S6aVB_cCGQ0d3uo9UfKByQ3sI6Audoy6dY&r=k0gMbcsdOcdbPUNV5tW66KQSZfXL0ewVDPVBp7tqbks&m=HQhXfRvgQZ3mFRTUuOGKZTZZVlTRi9o87ygYqEDnPog&s=u0GfpqJznDAnSRPi-ENNk5i5F203FOoK4e8tFBNx-fc&e=<https://urldefense.proofpoint.com/v2/url?u=https-3A__sourceforge.net_projects_pymol_lists_pymol-2Dusers_unsubscribe&d=DwMGaQ&c=VjzId-SM5S6aVB_cCGQ0d3uo9UfKByQ3sI6Audoy6dY&r=k0gMbcsdOcdbPUNV5tW66KQSZfXL0ewVDPVBp7tqbks&m=HQhXfRvgQZ3mFRTUuOGKZTZZVlTRi9o87ygYqEDnPog&s=u0GfpqJznDAnSRPi-ENNk5i5F203FOoK4e8tFBNx-fc&e=>> -- Jarrett Johnson | Senior Developer [Schrodinger Logo]<https://urldefense.proofpoint.com/v2/url?u=https-3A__www.schrodinger.com_&d=DwMGaQ&c=VjzId-SM5S6aVB_cCGQ0d3uo9UfKByQ3sI6Audoy6dY&r=k0gMbcsdOcdbPUNV5tW66KQSZfXL0ewVDPVBp7tqbks&m=HQhXfRvgQZ3mFRTUuOGKZTZZVlTRi9o87ygYqEDnPog&s=my7IR5rxG-1yA5AP52htw3MT5MKRSqHAwEmOVfdcSdc&e=<https://urldefense.proofpoint.com/v2/url?u=https-3A__www.schrodinger.com_&d=DwMGaQ&c=VjzId-SM5S6aVB_cCGQ0d3uo9UfKByQ3sI6Audoy6dY&r=k0gMbcsdOcdbPUNV5tW66KQSZfXL0ewVDPVBp7tqbks&m=HQhXfRvgQZ3mFRTUuOGKZTZZVlTRi9o87ygYqEDnPog&s=my7IR5rxG-1yA5AP52htw3MT5MKRSqHAwEmOVfdcSdc&e=>> _______________________________________________ PyMOL-users mailing list Archives: http://www.mail-archive.com/pym...@li...<http://www.mail-archive.com/pym...@li...> Unsubscribe: https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe<https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe> |
|
From: Jared S. <jar...@co...> - 2020-06-15 18:41:11
|
Hi Vaheh - Try `pdbset` from the CCP4 suite. http://www.ccp4.ac.uk/html/pdbset.html#renumber ``` pdbset xyzin in.pdb xyzout out.pdb > pdbset.log << EOF renum 1 chain H renum 1 chain L end EOF ``` Hope that helps. Cheers, Jared From: Oganesyan, Vaheh <vah...@as...> Reply: Oganesyan, Vaheh <vah...@as...> Date: June 15, 2020 at 1:28:23 PM To: Mooers, Blaine H.M. (HSC) <bla...@ou...>, Jarrett Johnson <jar...@sc...> Cc: pym...@li... <pym...@li...> Subject: Re: [PyMOL] renumber Blain, The command will not change the numbering of amino acids starting from #1. But if you got missing ones, like in my case, it will. Except for those having also letter in the number field. I mean the numbering used for CDRs of antibodies, not alternatives. Hence, my question, is there a command that will ignore the letters in the number field and renumber the amino acids in the order they appear in the file. Thank you. From: Mooers, Blaine H.M. (HSC) <Bla...@ou...> Sent: Monday, June 15, 2020 12:06 PM To: Oganesyan, Vaheh <vah...@as...>; Jarrett Johnson <jar...@sc...> Cc: pym...@li... Subject: RE: [PyMOL] renumber Hi Vaheh, alter vh, resi=str(int(resi)+0) will not change the residue numbers because 0 is being added. Replace 0 with your desired residue number offset. Best regards, Blaine Blaine Mooers, Ph.D. Associate Professor Department of Biochemistry and Molecular Biology College of Medicine University of Oklahoma Health Sciences Center S.L. Young Biomedical Research Center (BRC) Rm. 466 975 NE 10th Street, BRC 466 Oklahoma City, OK 73104-5419 ________________________________________ From: Oganesyan, Vaheh [vah...@as...] Sent: Monday, June 15, 2020 10:49 AM To: Jarrett Johnson Cc: pym...@li... Subject: [EXTERNAL] Re: [PyMOL] renumber Thank you Jarrett, Then the command alter vh, resi=str(int(resi)+0) should work, right? But it doesn’t because there are residue numbers with letters. Is there a command that will either remove the letters or won’t pay attention to them and renumber sequentially. Regards, From: Jarrett Johnson <jar...@sc...> Sent: Monday, June 15, 2020 11:38 AM To: Oganesyan, Vaheh <vah...@as...> Cc: pym...@li... Subject: Re: [PyMOL] renumber Hello, The command shown on this page https://pymolwiki.org/index.php/Renumber<https://urldefense.proofpoint.com/v2/url?u=https-3A__pymolwiki.org_index.php_Renumber&d=DwMGaQ&c=VjzId-SM5S6aVB_cCGQ0d3uo9UfKByQ3sI6Audoy6dY&r=k0gMbcsdOcdbPUNV5tW66KQSZfXL0ewVDPVBp7tqbks&m=HQhXfRvgQZ3mFRTUuOGKZTZZVlTRi9o87ygYqEDnPog&s=ziFhw29qVsmpI-rra_AyanmqFEsNZVmEsXF4VIjUMmI&e=> is not one that comes with PyMOL by default. Try downloading the script and importing it via the `run` command in the PyMOL command-line: run renumber.py<https://urldefense.proofpoint.com/v2/url?u=http-3A__renumber.py&d=DwQGaQ&c=VjzId-SM5S6aVB_cCGQ0d3uo9UfKByQ3sI6Audoy6dY&r=k0gMbcsdOcdbPUNV5tW66KQSZfXL0ewVDPVBp7tqbks&m=HQhXfRvgQZ3mFRTUuOGKZTZZVlTRi9o87ygYqEDnPog&s=FHmoNz1s1Pj-_paiWCTfneG3RkPiLccu2uI2KNr8ROw&e=> and then you should be able to use the command as shown on the Wiki page. Hope that helps, Jarrett J. On Mon, Jun 15, 2020 at 11:29 AM Oganesyan, Vaheh <vah...@as...<mailto:vah...@as...>> wrote: Hello PyMOLers, Wiki uses renumber command to alter residue numbers, but PyMOL doesn’t recognize it. Is it that Wiki is old, or my PyMOL version is dusty? Regards, Vaheh _______________________________________________ PyMOL-users mailing list Archives: http://www.mail-archive.com/pym...@li...<https://urldefense.proofpoint.com/v2/url?u=http-3A__www.mail-2Darchive.com_pymol-2Dusers-40lists.sourceforge.net&d=DwMGaQ&c=VjzId-SM5S6aVB_cCGQ0d3uo9UfKByQ3sI6Audoy6dY&r=k0gMbcsdOcdbPUNV5tW66KQSZfXL0ewVDPVBp7tqbks&m=HQhXfRvgQZ3mFRTUuOGKZTZZVlTRi9o87ygYqEDnPog&s=0jiLKKRpirp3ZmCRyyo_9R1IshveF24db_HqbNveLVE&e=> Unsubscribe: https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe<https://urldefense.proofpoint.com/v2/url?u=https-3A__sourceforge.net_projects_pymol_lists_pymol-2Dusers_unsubscribe&d=DwMGaQ&c=VjzId-SM5S6aVB_cCGQ0d3uo9UfKByQ3sI6Audoy6dY&r=k0gMbcsdOcdbPUNV5tW66KQSZfXL0ewVDPVBp7tqbks&m=HQhXfRvgQZ3mFRTUuOGKZTZZVlTRi9o87ygYqEDnPog&s=u0GfpqJznDAnSRPi-ENNk5i5F203FOoK4e8tFBNx-fc&e=> -- Jarrett Johnson | Senior Developer [Schrodinger Logo]<https://urldefense.proofpoint.com/v2/url?u=https-3A__www.schrodinger.com_&d=DwMGaQ&c=VjzId-SM5S6aVB_cCGQ0d3uo9UfKByQ3sI6Audoy6dY&r=k0gMbcsdOcdbPUNV5tW66KQSZfXL0ewVDPVBp7tqbks&m=HQhXfRvgQZ3mFRTUuOGKZTZZVlTRi9o87ygYqEDnPog&s=my7IR5rxG-1yA5AP52htw3MT5MKRSqHAwEmOVfdcSdc&e=> _______________________________________________ PyMOL-users mailing list Archives: http://www.mail-archive.com/pym...@li... Unsubscribe: https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe |
|
From: Mooers, B. H.M. (HSC) <Bla...@ou...> - 2020-06-15 17:50:32
|
Hi Vaheh, Thank you for the clarification. There are at least five numbering schemes (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6198058). Which one are you following? Best regards, Blaine Blaine Mooers, Ph.D. Associate Professor Department of Biochemistry and Molecular Biology College of Medicine University of Oklahoma Health Sciences Center S.L. Young Biomedical Research Center (BRC) Rm. 466 975 NE 10th Street, BRC 466 Oklahoma City, OK 73104-5419 ________________________________________ From: Oganesyan, Vaheh [vah...@as...] Sent: Monday, June 15, 2020 12:26 PM To: Mooers, Blaine H.M. (HSC); Jarrett Johnson Cc: pym...@li... Subject: [EXTERNAL] RE: [PyMOL] renumber Blain, The command will not change the numbering of amino acids starting from #1. But if you got missing ones, like in my case, it will. Except for those having also letter in the number field. I mean the numbering used for CDRs of antibodies, not alternatives. Hence, my question, is there a command that will ignore the letters in the number field and renumber the amino acids in the order they appear in the file. Thank you. From: Mooers, Blaine H.M. (HSC) <Bla...@ou...> Sent: Monday, June 15, 2020 12:06 PM To: Oganesyan, Vaheh <vah...@as...>; Jarrett Johnson <jar...@sc...> Cc: pym...@li... Subject: RE: [PyMOL] renumber Hi Vaheh, alter vh, resi=str(int(resi)+0) will not change the residue numbers because 0 is being added. Replace 0 with your desired residue number offset. Best regards, Blaine Blaine Mooers, Ph.D. Associate Professor Department of Biochemistry and Molecular Biology College of Medicine University of Oklahoma Health Sciences Center S.L. Young Biomedical Research Center (BRC) Rm. 466 975 NE 10th Street, BRC 466 Oklahoma City, OK 73104-5419 ________________________________________ From: Oganesyan, Vaheh [vah...@as...] Sent: Monday, June 15, 2020 10:49 AM To: Jarrett Johnson Cc: pym...@li...<mailto:pym...@li...> Subject: [EXTERNAL] Re: [PyMOL] renumber Thank you Jarrett, Then the command alter vh, resi=str(int(resi)+0) should work, right? But it doesn’t because there are residue numbers with letters. Is there a command that will either remove the letters or won’t pay attention to them and renumber sequentially. Regards, From: Jarrett Johnson <jar...@sc...<mailto:jar...@sc...>> Sent: Monday, June 15, 2020 11:38 AM To: Oganesyan, Vaheh <vah...@as...<mailto:vah...@as...>> Cc: pym...@li...<mailto:pym...@li...> Subject: Re: [PyMOL] renumber Hello, The command shown on this page https://pymolwiki.org/index.php/Renumber<https://urldefense.proofpoint.com/v2/url?u=https-3A__pymolwiki.org_index.php_Renumber&d=DwMF-g&c=VjzId-SM5S6aVB_cCGQ0d3uo9UfKByQ3sI6Audoy6dY&r=k0gMbcsdOcdbPUNV5tW66KQSZfXL0ewVDPVBp7tqbks&m=4dzsKdOHbAkCGKexdfLvVa0K8k-qU58swt-barF9CJ0&s=TYgabYRElhEIt4RUkDkBQVeUct1uHkGNprlmTIrt35o&e=><https://urldefense.proofpoint.com/v2/url?u=https-3A__pymolwiki.org_index.php_Renumber&d=DwMGaQ&c=VjzId-SM5S6aVB_cCGQ0d3uo9UfKByQ3sI6Audoy6dY&r=k0gMbcsdOcdbPUNV5tW66KQSZfXL0ewVDPVBp7tqbks&m=HQhXfRvgQZ3mFRTUuOGKZTZZVlTRi9o87ygYqEDnPog&s=ziFhw29qVsmpI-rra_AyanmqFEsNZVmEsXF4VIjUMmI&e=> is not one that comes with PyMOL by default. Try downloading the script and importing it via the `run` command in the PyMOL command-line: run renumber.py<https://urldefense.proofpoint.com/v2/url?u=http-3A__renumber.py&d=DwQGaQ&c=VjzId-SM5S6aVB_cCGQ0d3uo9UfKByQ3sI6Audoy6dY&r=k0gMbcsdOcdbPUNV5tW66KQSZfXL0ewVDPVBp7tqbks&m=HQhXfRvgQZ3mFRTUuOGKZTZZVlTRi9o87ygYqEDnPog&s=FHmoNz1s1Pj-_paiWCTfneG3RkPiLccu2uI2KNr8ROw&e=> and then you should be able to use the command as shown on the Wiki page. Hope that helps, Jarrett J. On Mon, Jun 15, 2020 at 11:29 AM Oganesyan, Vaheh <vah...@as...<mailto:vah...@as...<mailto:vah...@as...%3cmailto:vah...@as...>>> wrote: Hello PyMOLers, Wiki uses renumber command to alter residue numbers, but PyMOL doesn’t recognize it. Is it that Wiki is old, or my PyMOL version is dusty? Regards, Vaheh _______________________________________________ PyMOL-users mailing list Archives: http://www.mail-archive.com/pym...@li...<https://urldefense.proofpoint.com/v2/url?u=http-3A__www.mail-2Darchive.com_pymol-2Dusers-40lists.sourceforge.net&d=DwMF-g&c=VjzId-SM5S6aVB_cCGQ0d3uo9UfKByQ3sI6Audoy6dY&r=k0gMbcsdOcdbPUNV5tW66KQSZfXL0ewVDPVBp7tqbks&m=4dzsKdOHbAkCGKexdfLvVa0K8k-qU58swt-barF9CJ0&s=sawruVx__AsYwpdRP2n7U9_YJ8XHRR8IgvXUq-OiwQg&e=><https://urldefense.proofpoint.com/v2/url?u=http-3A__www.mail-2Darchive.com_pymol-2Dusers-40lists.sourceforge.net&d=DwMGaQ&c=VjzId-SM5S6aVB_cCGQ0d3uo9UfKByQ3sI6Audoy6dY&r=k0gMbcsdOcdbPUNV5tW66KQSZfXL0ewVDPVBp7tqbks&m=HQhXfRvgQZ3mFRTUuOGKZTZZVlTRi9o87ygYqEDnPog&s=0jiLKKRpirp3ZmCRyyo_9R1IshveF24db_HqbNveLVE&e=> Unsubscribe: https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe<https://urldefense.proofpoint.com/v2/url?u=https-3A__sourceforge.net_projects_pymol_lists_pymol-2Dusers_unsubscribe&d=DwMF-g&c=VjzId-SM5S6aVB_cCGQ0d3uo9UfKByQ3sI6Audoy6dY&r=k0gMbcsdOcdbPUNV5tW66KQSZfXL0ewVDPVBp7tqbks&m=4dzsKdOHbAkCGKexdfLvVa0K8k-qU58swt-barF9CJ0&s=xsu4EJ4r4LLd_zcm6XImTIDn7zutyAzeapOSu7pKZgc&e=><https://urldefense.proofpoint.com/v2/url?u=https-3A__sourceforge.net_projects_pymol_lists_pymol-2Dusers_unsubscribe&d=DwMGaQ&c=VjzId-SM5S6aVB_cCGQ0d3uo9UfKByQ3sI6Audoy6dY&r=k0gMbcsdOcdbPUNV5tW66KQSZfXL0ewVDPVBp7tqbks&m=HQhXfRvgQZ3mFRTUuOGKZTZZVlTRi9o87ygYqEDnPog&s=u0GfpqJznDAnSRPi-ENNk5i5F203FOoK4e8tFBNx-fc&e=> -- Jarrett Johnson | Senior Developer [Schrodinger Logo]<https://urldefense.proofpoint.com/v2/url?u=https-3A__www.schrodinger.com_&d=DwMGaQ&c=VjzId-SM5S6aVB_cCGQ0d3uo9UfKByQ3sI6Audoy6dY&r=k0gMbcsdOcdbPUNV5tW66KQSZfXL0ewVDPVBp7tqbks&m=HQhXfRvgQZ3mFRTUuOGKZTZZVlTRi9o87ygYqEDnPog&s=my7IR5rxG-1yA5AP52htw3MT5MKRSqHAwEmOVfdcSdc&e=> |
|
From: Mooers, B. H.M. (HSC) <Bla...@ou...> - 2020-06-15 16:06:01
|
Hi Vaheh, alter vh, resi=str(int(resi)+0) will not change the residue numbers because 0 is being added. Replace 0 with your desired residue number offset. Best regards, Blaine Blaine Mooers, Ph.D. Associate Professor Department of Biochemistry and Molecular Biology College of Medicine University of Oklahoma Health Sciences Center S.L. Young Biomedical Research Center (BRC) Rm. 466 975 NE 10th Street, BRC 466 Oklahoma City, OK 73104-5419 ________________________________________ From: Oganesyan, Vaheh [vah...@as...] Sent: Monday, June 15, 2020 10:49 AM To: Jarrett Johnson Cc: pym...@li... Subject: [EXTERNAL] Re: [PyMOL] renumber Thank you Jarrett, Then the command alter vh, resi=str(int(resi)+0) should work, right? But it doesn’t because there are residue numbers with letters. Is there a command that will either remove the letters or won’t pay attention to them and renumber sequentially. Regards, From: Jarrett Johnson <jar...@sc...> Sent: Monday, June 15, 2020 11:38 AM To: Oganesyan, Vaheh <vah...@as...> Cc: pym...@li... Subject: Re: [PyMOL] renumber Hello, The command shown on this page https://pymolwiki.org/index.php/Renumber<https://urldefense.proofpoint.com/v2/url?u=https-3A__pymolwiki.org_index.php_Renumber&d=DwMGaQ&c=VjzId-SM5S6aVB_cCGQ0d3uo9UfKByQ3sI6Audoy6dY&r=k0gMbcsdOcdbPUNV5tW66KQSZfXL0ewVDPVBp7tqbks&m=HQhXfRvgQZ3mFRTUuOGKZTZZVlTRi9o87ygYqEDnPog&s=ziFhw29qVsmpI-rra_AyanmqFEsNZVmEsXF4VIjUMmI&e=> is not one that comes with PyMOL by default. Try downloading the script and importing it via the `run` command in the PyMOL command-line: run renumber.py<https://urldefense.proofpoint.com/v2/url?u=http-3A__renumber.py&d=DwQGaQ&c=VjzId-SM5S6aVB_cCGQ0d3uo9UfKByQ3sI6Audoy6dY&r=k0gMbcsdOcdbPUNV5tW66KQSZfXL0ewVDPVBp7tqbks&m=HQhXfRvgQZ3mFRTUuOGKZTZZVlTRi9o87ygYqEDnPog&s=FHmoNz1s1Pj-_paiWCTfneG3RkPiLccu2uI2KNr8ROw&e=> and then you should be able to use the command as shown on the Wiki page. Hope that helps, Jarrett J. On Mon, Jun 15, 2020 at 11:29 AM Oganesyan, Vaheh <vah...@as...<mailto:vah...@as...>> wrote: Hello PyMOLers, Wiki uses renumber command to alter residue numbers, but PyMOL doesn’t recognize it. Is it that Wiki is old, or my PyMOL version is dusty? Regards, Vaheh _______________________________________________ PyMOL-users mailing list Archives: http://www.mail-archive.com/pym...@li...<https://urldefense.proofpoint.com/v2/url?u=http-3A__www.mail-2Darchive.com_pymol-2Dusers-40lists.sourceforge.net&d=DwMGaQ&c=VjzId-SM5S6aVB_cCGQ0d3uo9UfKByQ3sI6Audoy6dY&r=k0gMbcsdOcdbPUNV5tW66KQSZfXL0ewVDPVBp7tqbks&m=HQhXfRvgQZ3mFRTUuOGKZTZZVlTRi9o87ygYqEDnPog&s=0jiLKKRpirp3ZmCRyyo_9R1IshveF24db_HqbNveLVE&e=> Unsubscribe: https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe<https://urldefense.proofpoint.com/v2/url?u=https-3A__sourceforge.net_projects_pymol_lists_pymol-2Dusers_unsubscribe&d=DwMGaQ&c=VjzId-SM5S6aVB_cCGQ0d3uo9UfKByQ3sI6Audoy6dY&r=k0gMbcsdOcdbPUNV5tW66KQSZfXL0ewVDPVBp7tqbks&m=HQhXfRvgQZ3mFRTUuOGKZTZZVlTRi9o87ygYqEDnPog&s=u0GfpqJznDAnSRPi-ENNk5i5F203FOoK4e8tFBNx-fc&e=> -- Jarrett Johnson | Senior Developer [Schrodinger Logo]<https://urldefense.proofpoint.com/v2/url?u=https-3A__www.schrodinger.com_&d=DwMGaQ&c=VjzId-SM5S6aVB_cCGQ0d3uo9UfKByQ3sI6Audoy6dY&r=k0gMbcsdOcdbPUNV5tW66KQSZfXL0ewVDPVBp7tqbks&m=HQhXfRvgQZ3mFRTUuOGKZTZZVlTRi9o87ygYqEDnPog&s=my7IR5rxG-1yA5AP52htw3MT5MKRSqHAwEmOVfdcSdc&e=> |
|
From: Oganesyan, V. <vah...@as...> - 2020-06-15 15:51:10
|
Thank you Jarrett, Then the command alter vh, resi=str(int(resi)+0) should work, right? But it doesn’t because there are residue numbers with letters. Is there a command that will either remove the letters or won’t pay attention to them and renumber sequentially. Regards, From: Jarrett Johnson <jar...@sc...> Sent: Monday, June 15, 2020 11:38 AM To: Oganesyan, Vaheh <vah...@as...> Cc: pym...@li... Subject: Re: [PyMOL] renumber Hello, The command shown on this page https://pymolwiki.org/index.php/Renumber<https://pymolwiki.org/index.php/Renumber> is not one that comes with PyMOL by default. Try downloading the script and importing it via the `run` command in the PyMOL command-line: run renumber.py and then you should be able to use the command as shown on the Wiki page. Hope that helps, Jarrett J. On Mon, Jun 15, 2020 at 11:29 AM Oganesyan, Vaheh <vah...@as...<mailto:vah...@as...>> wrote: Hello PyMOLers, Wiki uses renumber command to alter residue numbers, but PyMOL doesn’t recognize it. Is it that Wiki is old, or my PyMOL version is dusty? Regards, Vaheh _______________________________________________ PyMOL-users mailing list Archives: http://www.mail-archive.com/pym...@li...<http://www.mail-archive.com/pym...@li...> Unsubscribe: https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe<https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe> -- Jarrett Johnson | Senior Developer [Schrodinger Logo]<https://www.schrodinger.com/> |
|
From: Jarrett J. <jar...@sc...> - 2020-06-15 15:37:53
|
Hello, The command shown on this page https://pymolwiki.org/index.php/Renumber is not one that comes with PyMOL by default. Try downloading the script and importing it via the `run` command in the PyMOL command-line: *run renumber.py* and then you should be able to use the command as shown on the Wiki page. Hope that helps, Jarrett J. On Mon, Jun 15, 2020 at 11:29 AM Oganesyan, Vaheh < vah...@as...> wrote: > > > Hello PyMOLers, > > > > Wiki uses renumber command to alter residue numbers, but PyMOL doesn’t > recognize it. Is it that Wiki is old, or my PyMOL version is dusty? > > > > > > Regards, > > > > Vaheh > > > _______________________________________________ > PyMOL-users mailing list > Archives: http://www.mail-archive.com/pym...@li... > Unsubscribe: > https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe -- *Jarrett Johnson* | Senior Developer [image: Schrodinger Logo] <https://www.schrodinger.com/> |
|
From: Oganesyan, V. <vah...@as...> - 2020-06-15 15:28:17
|
Hello PyMOLers, Wiki uses renumber command to alter residue numbers, but PyMOL doesn't recognize it. Is it that Wiki is old, or my PyMOL version is dusty? Regards, Vaheh |
115 messages has been excluded from this view by a project administrator.
