pymol-users — Collaborative support and tips for PyMOL users

Re: [PyMOL] Surface and cartoon transparency together?

[Petro <sub...@kh...>]

Thanks.
I will try it.
Best regards.
Petro.


On Wed, 17 May 2023 at 19:49, Jarrett Johnson <
jar...@sc...> wrote:

> Hi Petro,
>
> You might have luck using Order Independent Transparency:
>
> `set transparency_mode, 3`
>
> Hope that helps,
> Jarrett J
>
> On Wed, May 17, 2023 at 10:50 AM Petro <sub...@kh...> wrote:
>
>> HI., I have tried to use surface and cartoon transparency together but
>> then I can see only the surface. Cartoon disappears completely. Any trick
>> to get it working? Thanks,
>> Petro
>> _______________________________________________
>> 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, PyMOL
>
>

Re: [PyMOL] Surface and cartoon transparency together?

[Jarrett J. <jar...@sc...>]

Hi Petro,

You might have luck using Order Independent Transparency:

`set transparency_mode, 3`

Hope that helps,
Jarrett J

On Wed, May 17, 2023 at 10:50 AM Petro <sub...@kh...> wrote:

> HI., I have tried to use surface and cartoon transparency together but
> then I can see only the surface. Cartoon disappears completely. Any trick
> to get it working? Thanks,
> Petro
> _______________________________________________
> 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, PyMOL

Re: [PyMOL] [EXTERNAL] Generate electrostatics by Python command

[Petro <sub...@kh...>]

Hi Blaine.
Thank you for your reply.
I was not clear. I meant the surface which can be generated via action ->
generate -> vacuum electrostatic -> protein contact potential (local)
Is there a way to access it via Python?

Thank you and best regards.
Petro.


On Wed, 17 May 2023 at 17:32, Mooers, Blaine H.M. (HSC) <
Bla...@ou...> wrote:

> Hi Petro,
>
> APBS is a plugin and not directly part of PyMOL.
>
> You can run apbs from the command line via subprocess in Python.
>
> https://apbs.readthedocs.io/en/latest/using/index.html
>
> Best regards,
>
> Blaine
>
> Blaine Mooers, Ph.D.
> Associate Professor
> Department of Biochemistry and Molecular Biology, College of Medicine
> Director of the Laboratory of Biomolecular Structure and Function
> Academic Director, Biomolecular Structure Core, COBRE in Structural Biology
> Full Member, Cancer Biology Program, Stephenson Cancer Center
> University of Oklahoma Health Sciences Center
>
> Mailing Address:
> 975 NE 10th Street, BRC 466
> Oklahoma City, OK 73104-5419
> Office: 405-271-8300 Lab: 405-271-8312
>
> Websites:
> Faculty page:
> https://basicsciences.ouhsc.edu/bmb/Faculty/bio_details/mooers-blaine-hm-phd
> BSC-OKC (LBSF):
> https://research.ouhsc.edu/Core-Facilities/Laboratory-of-Biomolecular-Structure-and-Function
> COBRE in Structural Biology: https://www.ou.edu/structuralbiology
> ------------------------------
> *From:* Petro <sub...@kh...>
> *Sent:* Tuesday, May 16, 2023 2:19 PM
> *To:* pym...@li... <pym...@li...
> >
> *Subject:* [EXTERNAL] [PyMOL] Generate electrostatics by Python command
>
> Hi.
> How can I generate electrostatics using Python API?
> Thanks.
> Petro.
>

Re: [PyMOL] [EXTERNAL] Disable cartoon representation on load

[Khoroshyy P. <kho...@gm...>]

Thank you.
I will try that.
Best regards.
Petro.


On Wed, 17 May 2023 at 17:17, Mooers, Blaine H.M. (HSC) <
Bla...@ou...> wrote:

> Hi Petro,
>
> Add the following to your .pymolrc file (pymolrc.pml on Windows)
>
> cmd.do("hide cartoon")
> cmd.do("show sticks")
>
> # I also add these lines to my pymolrc
> set bg_rgb, white
> set stick_radius, 0.125
> set valence, off
>
> Best regards,
>
> Blaine
>
> Blaine Mooers, Ph.D.
> Associate Professor
> Department of Biochemistry and Molecular Biology, College of Medicine
> Director of the Laboratory of Biomolecular Structure and Function
> Academic Director, Biomolecular Structure Core, COBRE in Structural Biology
> Full Member, Cancer Biology Program, Stephenson Cancer Center
> University of Oklahoma Health Sciences Center
>
> Mailing Address:
> 975 NE 10th Street, BRC 466
> Oklahoma City, OK 73104-5419
> Office: 405-271-8300 Lab: 405-271-8312
>
> Websites:
> Faculty page:
> https://basicsciences.ouhsc.edu/bmb/Faculty/bio_details/mooers-blaine-hm-phd
> BSC-OKC (LBSF):
> https://research.ouhsc.edu/Core-Facilities/Laboratory-of-Biomolecular-Structure-and-Function
> COBRE in Structural Biology: https://www.ou.edu/structuralbiology
> ------------------------------
> *From:* Khoroshyy Petro <kho...@gm...>
> *Sent:* Tuesday, May 16, 2023 8:00 AM
> *To:* pym...@li... <pym...@li...
> >
> *Subject:* [EXTERNAL] [PyMOL] Disable cartoon representation on load
>
> Hi.
> How can I force pymol to show things in lines, not in cartoons, by default?
> Thanks.
> Petro.
>
>
> --
> ______________________________
> Petro Khoroshyy
>

Re: [PyMOL] [EXTERNAL] Disable cartoon representation on load

[Mooers, B. H.M. (HSC) <Bla...@ou...>]

Hi Petro,

Add the following to your .pymolrc file (pymolrc.pml on Windows)

cmd.do("hide cartoon")
cmd.do("show sticks")

# I also add these lines to my pymolrc
set bg_rgb, white
set stick_radius, 0.125
set valence, off

Best regards,

Blaine

Blaine Mooers, Ph.D.
Associate Professor
Department of Biochemistry and Molecular Biology, College of Medicine
Director of the Laboratory of Biomolecular Structure and Function
Academic Director, Biomolecular Structure Core, COBRE in Structural Biology
Full Member, Cancer Biology Program, Stephenson Cancer Center
University of Oklahoma Health Sciences Center

Mailing Address:
975 NE 10th Street, BRC 466
Oklahoma City, OK 73104-5419
Office: 405-271-8300 Lab: 405-271-8312

Websites:
Faculty page: https://basicsciences.ouhsc.edu/bmb/Faculty/bio_details/mooers-blaine-hm-phd
BSC-OKC (LBSF): https://research.ouhsc.edu/Core-Facilities/Laboratory-of-Biomolecular-Structure-and-Function
COBRE in Structural Biology: https://www.ou.edu/structuralbiology
________________________________
From: Khoroshyy Petro <kho...@gm...>
Sent: Tuesday, May 16, 2023 8:00 AM
To: pym...@li... <pym...@li...>
Subject: [EXTERNAL] [PyMOL] Disable cartoon representation on load

Hi.
How can I force pymol to show things in lines, not in cartoons, by default?
Thanks.
Petro.


--
______________________________
Petro Khoroshyy

Re: [PyMOL] [EXTERNAL] Generate electrostatics by Python command

[Mooers, B. H.M. (HSC) <Bla...@ou...>]

Hi Petro,

APBS is a plugin and not directly part of PyMOL.

You can run apbs from the command line via subprocess in Python.

https://apbs.readthedocs.io/en/latest/using/index.html

Best regards,

Blaine

Blaine Mooers, Ph.D.
Associate Professor
Department of Biochemistry and Molecular Biology, College of Medicine
Director of the Laboratory of Biomolecular Structure and Function
Academic Director, Biomolecular Structure Core, COBRE in Structural Biology
Full Member, Cancer Biology Program, Stephenson Cancer Center
University of Oklahoma Health Sciences Center

Mailing Address:
975 NE 10th Street, BRC 466
Oklahoma City, OK 73104-5419
Office: 405-271-8300 Lab: 405-271-8312

Websites:
Faculty page: https://basicsciences.ouhsc.edu/bmb/Faculty/bio_details/mooers-blaine-hm-phd
BSC-OKC (LBSF): https://research.ouhsc.edu/Core-Facilities/Laboratory-of-Biomolecular-Structure-and-Function
COBRE in Structural Biology: https://www.ou.edu/structuralbiology
________________________________
From: Petro <sub...@kh...>
Sent: Tuesday, May 16, 2023 2:19 PM
To: pym...@li... <pym...@li...>
Subject: [EXTERNAL] [PyMOL] Generate electrostatics by Python command

Hi.
How can I generate electrostatics using Python API?
Thanks.
Petro.

[PyMOL] save format for molecule files

[Xavier F. <xav...@gm...>]

Hi,

I'm trying to save some molecule files (protein+ligand complex) from pymol
to a format that is readable by maestro. I've tried saving in .mae or .pdb
format, but bond orders in ligands are lost (all bonds are single). I've
played with the "PDB options" in the save command and managed to get double
bonds right, but the aromatic ones are ignored.

Does anyone know how to write files that can be read properly by maestro?

Alternatively, is there a way to convert aromatic bonds into alternating
single/double bonds, as I think this would be easier to output based on my
tests?

thanks,
Xavier

-- 
Xavier Fradera

[PyMOL] Surface and cartoon transparency together?

[Petro <sub...@kh...>]

HI., I have tried to use surface and cartoon transparency together but then
I can see only the surface. Cartoon disappears completely. Any trick to get
it working? Thanks,
Petro

[PyMOL] Generate electrostatics by Python command

[Petro <sub...@kh...>]

Hi.
How can I generate electrostatics using Python API?
Thanks.
Petro.

[PyMOL] Disable cartoon representation on load

[Khoroshyy P. <kho...@gm...>]

Hi.
How can I force pymol to show things in lines, not in cartoons, by default?
Thanks.
Petro.


-- 
______________________________
Petro Khoroshyy

[PyMOL] Opening grd files from the Open3DQSAR program

[Vytautas R. <vyt...@ya...>]

Hi, I try to open grd files from the Open3DQSAR program.I do not see some significant errors, but I see nothing in the visualization window.
Here is the text log from Pymol program:https://pastebin.com/qqCHDzUjHow can I resolve this issue?

[PyMOL] Successful integration of Pymol with ChatGPT

[Dr. V. M. <vij...@gm...>]

Dear PyMOL Users
We are delighted to share that it is possible to use PyMOL with ChatGPT.
PyMOL is versatile in many ways, thereby always fascinating its users to
integrate new and developing technologies.  The following webpage describes
the method to use PyMOL with ChatGPT:

https://techserr.com/chatgpt-the-future-of-pymol-automation/

I hope it will be useful for you.
Cheers
from
Vijay Masand

With Warm Regards
*Dr. Vijay H. Masand*
Department of Chemistry,
Vidya Bharati College, Amravati, 444 602
Maharashtra, India.
Phone number- +91-9403312628
https://sites.google.com/site/vijaymasand/

[PyMOL] Problem with morphing RNA structures

[Mehmet G. <mg...@ku...>]

Dear Pymol Users,

I am having an issue while performing morph between two RNA structures. The
morphed structure loses the phosphate backbone and some parts of the side
chains (see attachment). Does anybody know why this problem occurs and how
to solve it if possible?
Thank you in advance.

Best regards,
Mehmet

Re: [PyMOL] Question on rmsd alignment

[Kyle M. <kmo...@fa...>]

Hi Jarret,

Since I don’t have a microphone on my computer, may we talk on the phone while we screen share come 9:30 this morning?

Ph: 562-360-7713

Get Outlook for iOS<https://aka.ms/o0ukef>
________________________________
From: Jarrett Johnson <jar...@sc...>
Sent: Monday, March 27, 2023 5:34:41 PM
To: Neena Susan Eappen <nee...@gm...>
Cc: pymol-users <pym...@li...>
Subject: Re: [PyMOL] Question on rmsd alignment

                EXTERNAL EMAIL : Exercise caution when responding, opening links, or opening attachments.


Hi Neena,

I wouldn't put too much stock into what you're observing in the first image with the red arrow. PyMOL doesn't make the determination of whether that structure is stable; but it can provide visual aid and secondary structure assignment/hinting from coordinates and residue/atomic information.

As for the second question, Not all 177 atoms were used in the alignment to calculate the RMSD. This depends on your alignment method and other parameters that you set. In your case, 144 atom pairs were used for the alignment.

Hope this helps,
Jarrett J.

On Tue, Mar 21, 2023 at 11:11 AM Neena Susan Eappen <nee...@gm...<mailto:nee...@gm...>> wrote:
Hello PyMOL users,

1. I see this unusual secondary structural element in the peptide structure shown below. It was generated from computations, so the unusual element arose from positive dihedral across lysine residue. My question is whether it is structurally possible or if it is a stable structure?
[image.png]
[image.png]

2. Also when using alignment tool on PyMOL for the below two structures, RMSD is displayed with a certain number of atoms in parentheses (144 atoms). However, there are 177 atoms in total. So does this RMSD mean that the total difference in RMSD between these two structures is 0.602 Angstroms and only 144 out of 177 atoms with very close alignment/ position?


RMSD =    0.602 (144 atoms)

[image.png]
Any insight would be appreciated!

Thank you so much for your help,
Neena



_______________________________________________
PyMOL-users mailing list
Archives: http://www.mail-archive.com/pym...@li...<https://nam02.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.mail-archive.com%2Fpymol-users%40lists.sourceforge.net&data=05%7C01%7Ckmoorman2023%40fau.edu%7C3b490696bea241487b8908db2f0b6119%7C63c3c9c1e824413fb4352f0cabb2828f%7C0%7C0%7C638155498158070038%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=HcWP%2BtO7QbmhtmHmEmBe%2F3RAInpT2O3OALve1MU5Bfk%3D&reserved=0>
Unsubscribe: https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe<https://nam02.safelinks.protection.outlook.com/?url=https%3A%2F%2Fsourceforge.net%2Fprojects%2Fpymol%2Flists%2Fpymol-users%2Funsubscribe&data=05%7C01%7Ckmoorman2023%40fau.edu%7C3b490696bea241487b8908db2f0b6119%7C63c3c9c1e824413fb4352f0cabb2828f%7C0%7C0%7C638155498158070038%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=6tdPzmYIAisLZxdTTfog4no4U9AIwJpCt6t6%2BCpvt1c%3D&reserved=0>


--

Jarrett Johnson | Senior Developer, PyMOL

[https://drive.google.com/uc?id=1zOlB9fluGZyuInRUQgKsdjtjpR5L9z6R&export=download]

Re: [PyMOL] Question on rmsd alignment

[Jarrett J. <jar...@sc...>]

Hi Neena,

I wouldn't put too much stock into what you're observing in the first image
with the red arrow. PyMOL doesn't make the determination of whether that
structure is stable; but it can provide visual aid and secondary structure
assignment/hinting from coordinates and residue/atomic information.

As for the second question, Not all 177 atoms were used in the alignment to
calculate the RMSD. This depends on your alignment method and other
parameters that you set. In your case, 144 atom pairs were used for the
alignment.

Hope this helps,
Jarrett J.

On Tue, Mar 21, 2023 at 11:11 AM Neena Susan Eappen <nee...@gm...>
wrote:

> Hello PyMOL users,
>
> 1. I see this unusual secondary structural element in the peptide
> structure shown below. It was generated from computations, so the
> unusual element arose from positive dihedral across lysine residue. My
> question is whether it is structurally possible or if it is a stable
> structure?
> [image: image.png]
> [image: image.png]
>
> 2. Also when using alignment tool on PyMOL for the below two structures,
> RMSD is displayed with a certain number of atoms in parentheses (144
> atoms). However, there are 177 atoms in total. So does this RMSD mean that
> the total difference in RMSD between these two structures is 0.602
> Angstroms and only 144 out of 177 atoms with very close alignment/
> position?
>
> RMSD =    0.602 (144 atoms)
> [image: image.png]
> Any insight would be appreciated!
>
> Thank you so much for your help,
> Neena
>
>
>
> _______________________________________________
> 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, PyMOL

Re: [PyMOL] PLEASE HELP

[Jarrett J. <jar...@sc...>]

Hi Kyle,

The approach you listed looks about right to me. Using conda commands from
the PyMOL commandline in the bundles don't seem to be working in those
builds, but should be fine if you use another terminal. Either way, I will
reach out to you directly.

Best,
Jarrett J.

On Mon, Mar 27, 2023 at 3:46 PM Kyle Moorman via PyMOL-users <
pym...@li...> wrote:

> To whom it may concern,
>
>
>
> While I am a licensed user of PyMol, he...@sc... has still not
> responded to me. I have some very technical installation questions which
> upon trying to solve on my own is only making the problem worse.
>
>
>
> Below is all the information I have and what I’ve sent to
> he...@sc... This has truly been a huge impediment to my work and
> your help in this matter would be greatly appreciated. Currently conda is
> crashing every time I try to open it and the instructions I’ve found on
> pymolwiki as well as various other sites I’ve come across are not very
> clear at all. Below is the message I sent to he...@sc...  Could
> you help please? Thanks in advance:
>
>
>
> PyMOL 2.5.4
> Windows-10-10.0.19041-SP0
> ATI Technologies Inc.
> AMD Radeon(TM) HD8490
> 4.5.13399 Compatibility Profile Context 15.201.1151.1008
> PyMOL Invoice #49406
> 01-mar-2024
>
> Filename of downloaded installer: PyMOL-2.5.4_404-Win64-portable-py37
>
>
>
>
>
>
>
> I’m requesting help once more. An extension is not downloading for me.
> Please let me know if there is any other information I need to provide in
> order to receive installation help. This has thus far been a very
> unsatisfactory experience. Below is the email I sent before:
>
>
>
> To whom it may concern,
>
> I have used the following commands in attempt to download psico:
>
> I used this file path:
> "C:\Users\admin\PyMOL\condabin\conda.bat"
>
> In order to install this code:
>
> conda install -c schrodinger pymol
> conda install -c schrodinger pymol-psico
> conda install -c rdkit rdkit
> conda install -c speleo3 csb
>
> I am now having trouble using the commands in this code within the command
> line in PyMol. I believe that I need to use some sort of API in order to
> use the commands from psico. I am installing these packages specifically to
> use the 'mcsalign' function to calculate better rmsd's based off structural
> overlap of molecules I'm studying in school right now.
>
>
> I have version of 2.5.4 of PyMol and 2.7 version of Python. Could you
> please provide help as to how specifically download an API so I may employ
> the commands from psico? This function would be incredibly useful but I'm
> getting very caught up with the installation. If there is someone I can
> share my screen with so I can get this going, I'd really appreciate it. I'm
> really stuck and in need of help.
>
> Thanks so much in advance,
>
> Kyle
>
>
> _______________________________________________
> 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, PyMOL

Re: [PyMOL] PLEASE HELP

[Kyle M. <kmo...@fa...>]

Thank you SO MUCH. My computer is going into overdrive. I want to use another terminal, but I’ve spent all last night and all day today trying to figure it out.

My phone number is 562-360-7713.

I’m really doing whatever it takes to make this work. Thank you again.

Kyle

Get Outlook for iOS<https://aka.ms/o0ukef>
________________________________
From: Jarrett Johnson <jar...@sc...>
Sent: Monday, March 27, 2023 4:23:30 PM
To: Kyle Moorman <kmo...@fa...>
Cc: pym...@li... <pym...@li...>
Subject: Re: [PyMOL] PLEASE HELP

                EXTERNAL EMAIL : Exercise caution when responding, opening links, or opening attachments.


Hi Kyle,

The approach you listed looks about right to me. Using conda commands from the PyMOL commandline in the bundles don't seem to be working in those builds, but should be fine if you use another terminal. Either way, I will reach out to you directly.

Best,
Jarrett J.

On Mon, Mar 27, 2023 at 3:46 PM Kyle Moorman via PyMOL-users <pym...@li...<mailto:pym...@li...>> wrote:

To whom it may concern,



While I am a licensed user of PyMol, he...@sc...<mailto:he...@sc...> has still not responded to me. I have some very technical installation questions which upon trying to solve on my own is only making the problem worse.



Below is all the information I have and what I’ve sent to he...@sc...<mailto:he...@sc...> This has truly been a huge impediment to my work and your help in this matter would be greatly appreciated. Currently conda is crashing every time I try to open it and the instructions I’ve found on pymolwiki as well as various other sites I’ve come across are not very clear at all. Below is the message I sent to he...@sc...<mailto:he...@sc...>  Could you help please? Thanks in advance:



PyMOL 2.5.4
Windows-10-10.0.19041-SP0
ATI Technologies Inc.
AMD Radeon(TM) HD8490
4.5.13399 Compatibility Profile Context 15.201.1151.1008
PyMOL Invoice #49406
01-mar-2024

Filename of downloaded installer: PyMOL-2.5.4_404-Win64-portable-py37







I’m requesting help once more. An extension is not downloading for me. Please let me know if there is any other information I need to provide in order to receive installation help. This has thus far been a very unsatisfactory experience. Below is the email I sent before:



To whom it may concern,

I have used the following commands in attempt to download psico:

I used this file path:
"C:\Users\admin\PyMOL\condabin\conda.bat"

In order to install this code:

conda install -c schrodinger pymol
conda install -c schrodinger pymol-psico
conda install -c rdkit rdkit
conda install -c speleo3 csb

I am now having trouble using the commands in this code within the command line in PyMol. I believe that I need to use some sort of API in order to use the commands from psico. I am installing these packages specifically to use the 'mcsalign' function to calculate better rmsd's based off structural overlap of molecules I'm studying in school right now.


I have version of 2.5.4 of PyMol and 2.7 version of Python. Could you please provide help as to how specifically download an API so I may employ the commands from psico? This function would be incredibly useful but I'm getting very caught up with the installation. If there is someone I can share my screen with so I can get this going, I'd really appreciate it. I'm really stuck and in need of help.

Thanks so much in advance,

Kyle



_______________________________________________
PyMOL-users mailing list
Archives: http://www.mail-archive.com/pym...@li...<https://nam02.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.mail-archive.com%2Fpymol-users%40lists.sourceforge.net&data=05%7C01%7Ckmoorman2023%40fau.edu%7Cc293b855a2484d080f6608db2f012a6c%7C63c3c9c1e824413fb4352f0cabb2828f%7C0%7C0%7C638155454309873971%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=ZovpU7sPBR0gIkBN6GFIxDfRMCVJJQxU5fi%2Fu5JTe5E%3D&reserved=0>
Unsubscribe: https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe<https://nam02.safelinks.protection.outlook.com/?url=https%3A%2F%2Fsourceforge.net%2Fprojects%2Fpymol%2Flists%2Fpymol-users%2Funsubscribe&data=05%7C01%7Ckmoorman2023%40fau.edu%7Cc293b855a2484d080f6608db2f012a6c%7C63c3c9c1e824413fb4352f0cabb2828f%7C0%7C0%7C638155454309873971%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=e1O30bUEQSki1uoIfSoKA7HZfmHmhHsWmLX%2BuSn0BVE%3D&reserved=0>


--

Jarrett Johnson | Senior Developer, PyMOL

[https://drive.google.com/uc?id=1zOlB9fluGZyuInRUQgKsdjtjpR5L9z6R&export=download]

[PyMOL] PLEASE HELP

[Kyle M. <kmo...@fa...>]

To whom it may concern,

While I am a licensed user of PyMol, he...@sc...<mailto:he...@sc...> has still not responded to me. I have some very technical installation questions which upon trying to solve on my own is only making the problem worse.

Below is all the information I have and what I've sent to he...@sc...<mailto:he...@sc...> This has truly been a huge impediment to my work and your help in this matter would be greatly appreciated. Currently conda is crashing every time I try to open it and the instructions I've found on pymolwiki as well as various other sites I've come across are not very clear at all. Below is the message I sent to he...@sc...<mailto:he...@sc...>  Could you help please? Thanks in advance:


PyMOL 2.5.4
Windows-10-10.0.19041-SP0
ATI Technologies Inc.
AMD Radeon(TM) HD8490
4.5.13399 Compatibility Profile Context 15.201.1151.1008
PyMOL Invoice #49406
01-mar-2024

Filename of downloaded installer: PyMOL-2.5.4_404-Win64-portable-py37




I'm requesting help once more. An extension is not downloading for me. Please let me know if there is any other information I need to provide in order to receive installation help. This has thus far been a very unsatisfactory experience. Below is the email I sent before:

To whom it may concern,

I have used the following commands in attempt to download psico:

I used this file path:
"C:\Users\admin\PyMOL\condabin\conda.bat"

In order to install this code:

conda install -c schrodinger pymol
conda install -c schrodinger pymol-psico
conda install -c rdkit rdkit
conda install -c speleo3 csb

I am now having trouble using the commands in this code within the command line in PyMol. I believe that I need to use some sort of API in order to use the commands from psico. I am installing these packages specifically to use the 'mcsalign' function to calculate better rmsd's based off structural overlap of molecules I'm studying in school right now.


I have version of 2.5.4 of PyMol and 2.7 version of Python. Could you please provide help as to how specifically download an API so I may employ the commands from psico? This function would be incredibly useful but I'm getting very caught up with the installation. If there is someone I can share my screen with so I can get this going, I'd really appreciate it. I'm really stuck and in need of help.

Thanks so much in advance,

Kyle

[PyMOL] Question on rmsd alignment

[Neena S. E. <nee...@gm...>]

Hello PyMOL users,

1. I see this unusual secondary structural element in the peptide structure
shown below. It was generated from computations, so the unusual element
arose from positive dihedral across lysine residue. My question is whether
it is structurally possible or if it is a stable structure?
[image: image.png]
[image: image.png]

2. Also when using alignment tool on PyMOL for the below two structures,
RMSD is displayed with a certain number of atoms in parentheses (144
atoms). However, there are 177 atoms in total. So does this RMSD mean that
the total difference in RMSD between these two structures is 0.602
Angstroms and only 144 out of 177 atoms with very close alignment/
position?

RMSD =    0.602 (144 atoms)
[image: image.png]
Any insight would be appreciated!

Thank you so much for your help,
Neena

[PyMOL] Gaps in cartoon representation due to non-continuous residue numbers

[Norbert S. <st...@bb...>]

Dear PyMOL experts,

in GPCR crystal structures it is quite common to have fusions with 
lysozyme or BRIL in the third intracellular loop. The residue numbers of 
the inserted domains are often incremented by 1000. As a result, the two 
residues at the fusion point jump from for example 223 to 1002. As a 
result, gaps exist in the cartoon representation at the fusion points. 
Increasing cartoon_gap_cutoff does not help as PyMOL rather connects the 
C- and N-termini of the GPCR fold. In stick representation, the peptide 
bonds at the fusion points are represented fine. I could not find any 
options like "cartoon_use_peptide_bonds" or  "bond_cartoon selection, 
selection". A workaround would probably be to renumber the residues of 
the fusion protein and use insertion codes, I did not try this yet. An 
example is pdb id 4eiy.

Is there a better solution, have I overlooked an option?

Best regards,

Norbert

[PyMOL] Education license

[Kimble-Hill, A. C. <ank...@iu...>]

Are they still sending out Education licenses? I teach a research class where we/students need it for 1-2 semesters.



Dr. Ann Kimble-Hill, Ph.D.
Asst. Director DEI, IU Simon Comprehensive Cancer Center
IUPUI PREP Program Coordinator
Asst. Research Professor
Dept. Biochemistry & Mol. Biology
Indiana University School of Medicine
ank...@iu...
Pronouns: She/Her/Hers

“Ignorance is a cure for nothing. ” ― W. E. B. Dubois
________________________________
From: MILY BHATTACHARYA via PyMOL-users <pym...@li...>
Sent: Saturday, March 11, 2023 11:10:57 AM
To: pym...@li... <pym...@li...>
Subject: [External] [PyMOL] Unable to install PyTM plugin in PyMOL

You don't often get email from pym...@li.... Learn why this is important<https://aka.ms/LearnAboutSenderIdentification>
This message was sent from a non-IU address. Please exercise caution when clicking links or opening attachments from external sources.

Hello PyMOL support team,

I am unable to install the post-translational modification (PyTM) plugin in my PyMOL. If I try to copy-paste the PyMOLwiki or the respective repository URL in the given box under the "Install new plugins" tab (Plugin manager), it shows some error (...sscl:504, 1407742e...etc.). I would appreciate it if you could kindly assist me in sorting this out. I am using the educational version of PyMOL on Windows.

Thank you in advance.

Sincerely,
Mily.

======================================================
Dr. Mily Bhattacharya, Ph.D.

Assistant Professor
School of Chemistry and Biochemistry,

Thapar Institute of Engineering & Technology (Deemed to be University),

Thapar Technology Campus, Post Box No. 32, Bhadson Road.
Patiala - 147004, Punjab, India.

Email: mil...@th...<mailto:mil...@th...> and mi...@gm...<mailto:mi...@gm...>
Homepage: https://sites.google.com/site/milybhattacharyamohali/home<https://nam12.safelinks.protection.outlook.com/?url=https%3A%2F%2Fsites.google.com%2Fsite%2Fmilybhattacharyamohali%2Fhome&data=05%7C01%7Cankimble%40iu.edu%7C92c3d96303ef40eefc7008db224f4db1%7C1113be34aed14d00ab4bcdd02510be91%7C0%7C0%7C638141496224819199%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=a%2BxjF2YjdU%2FccMmSHdFQozOWrQuYz5r%2FuayLYvDeORs%3D&reserved=0>
ORCID: http://orcid.org/0000-0003-2670-6709<https://nam12.safelinks.protection.outlook.com/?url=http%3A%2F%2Forcid.org%2F0000-0003-2670-6709&data=05%7C01%7Cankimble%40iu.edu%7C92c3d96303ef40eefc7008db224f4db1%7C1113be34aed14d00ab4bcdd02510be91%7C0%7C0%7C638141496224819199%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=q9TGrmN83DAepm3%2BVq63et8rUIKR6E2VNi7xJqVEKOA%3D&reserved=0>

[PyMOL] Unable to install PyTM plugin in PyMOL

[MILY B. <mil...@th...>]

Hello PyMOL support team,

I am unable to install the post-translational modification (PyTM) plugin in
my PyMOL. If I try to copy-paste the PyMOLwiki or the respective repository
URL in the given box under the "Install new plugins" tab (Plugin manager),
it shows some error (...sscl:504, 1407742e...etc.). I would appreciate it
if you could kindly assist me in sorting this out. I am using the
educational version of PyMOL on Windows.

Thank you in advance.

Sincerely,
Mily.

======================================================
Dr. Mily Bhattacharya, Ph.D.

Assistant Professor
School of Chemistry and Biochemistry,

Thapar Institute of Engineering & Technology (Deemed to be University),
Thapar Technology Campus, Post Box No. 32, Bhadson Road.
Patiala - 147004, Punjab, India.

Email: mil...@th... and mi...@gm...
Homepage: https://sites.google.com/site/milybhattacharyamohali/home
ORCID: http://orcid.org/0000-0003-2670-6709

[PyMOL] Cartoon tube in no-backbone atoms

[Miguel G. <mga...@iq...>]

Dear All,

I have a pdb structure of a triple helix having a non-nucleotide residue conjugated between two residues of one of the strands. I would like to represent the backbone of all the three strands as a continuous tube. However, the tube of the modified strand gets interrupted right before and after the conjugate. I assume that pymol is not recognizing the atoms linking the non-nucleotidic modification to both ends of the strands as backbone atoms. The backbone in nucleic acids is P(i)-O5’(i)-C5’(i)-C4’(i)-C3’(i+1)-O3’(i+1)-P(i+1), in the case of my molecule the linkage is P(i)-O5’(i)-C5’(i)-C3’(i+1)-O3’(i+1). So the C4’ (and no other sugar atoms are present in the “modified” residue that is conjugate between the flanking nucleotides.

Is there any way to make Pymol consider some atoms as atoms of the backbone or to represent certain atoms like a “tube” or cartoon-like backbone?

Thank you very much for you help.

All the best,

Miguel

Re: [PyMOL] Align in PyMOL via Python script

[Irwin S. <irw...@po...>]

Hi,

Thanks, that's sorted it.

A follow up question is that when printing the results of the align command, I've noticed that the number of cycles seems to max out at 1 regardless of what I set it to - is that because it's reaching convergence after the first cycle?

All the best,

Irwin
________________________________
From: Tamas Hegedus <bio...@gm...>
Sent: Thursday, March 2, 2023 8:24 AM
To: pym...@li... <pym...@li...>
Subject: Re: [PyMOL] Align in PyMOL via Python script


Hi,


You probably use the script version. In this case you have to use "print"


cmd: align x, y

output: ... Executive: RMSD =    4.030 (10847 to 10847 atoms)


cmd: print(cmd.align("x", "y"))
output: (4.0296430587768555, 10847, 5, 24.87837028503418, 13476, 1234.0, 1192)


Bests, Tamas


On 2023. 03. 02. 8:54, Irwin Selvam wrote:
Hi,

I would like to run the Align Python script found on the Align page of the PyMOLwiki (https://pymolwiki.org/index.php/Align). I've tweaked it slightly for my uses and it seems to run fine on PyMOL 2.5.0 but according to the wiki it should output a list of results (RMSD etc) in the internal feedback (or command prompt?), but it doesn't in my case. Does anyone know why? It does seem like there some missing lines to the script in order to achieve this. Apologies for the basic question!

All the best,

Irwin







_______________________________________________
PyMOL-users mailing list
Archives: http://www.mail-archive.com/pym...@li...
Unsubscribe: https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe

Re: [PyMOL] Align in PyMOL via Python script

[Tamas H. <bio...@gm...>]

Hi,


You probably use the script version. In this case you have to use "print"


cmd: align x, y

output: ... Executive: RMSD =    4.030 (10847 to 10847 atoms)


cmd: print(cmd.align("x", "y"))
output: 
(4.0296430587768555, 10847, 5, 24.87837028503418, 13476, 1234.0, 1192)


Bests, Tamas


On 2023. 03. 02. 8:54, Irwin Selvam wrote:
> Hi,
>
> I would like to run the Align Python script found on the Align page of 
> the PyMOLwiki (https://pymolwiki.org/index.php/Align). I've tweaked it 
> slightly for my uses and it seems to run fine on PyMOL 2.5.0 but 
> according to the wiki it should output a list of results (RMSD etc) in 
> the internal feedback (or command prompt?), but it doesn't in my case. 
> Does anyone know why? It does seem like there some missing lines to 
> the script in order to achieve this. Apologies for the basic question!
>
> All the best,
>
> Irwin
>
>
>
>
>
> _______________________________________________
> PyMOL-users mailing list
> Archives:http://www.mail-archive.com/pym...@li...
> Unsubscribe:https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe