pymol-users — Collaborative support and tips for PyMOL users

Re: [PyMOL] [EXTERNAL] Re: Centre of mass pymol script

[Jeff S. <jms...@gm...>]

Sorry Blaine, I misspelled your name!
Cheers,
J.

сб, 7 нояб. 2020 г. в 16:18, Jeff Saxon <jms...@gm...>:
>
> Hi Blame,
> I was talking about this pymol script (it can be downloaded directly
> from the page below)
> https://pymolwiki.org/index.php/Center_of_mass
>
> I used all of the post-processing steps in bash scripts using AWK. Now
> I would like to understand how it may work inside this python script.
> Here is my shell solution :-)
>
> #!/bin/bash
> pymol='/Applications/PyMOL.app/Contents/MacOS/MacPyMOL'
> home=$PWD
> # this is multi-model pdb with the ligand
> pdb=${home}/lig_1AllBoxes_7000_cne_998.pdb
> # remove previous outputs
> rm "${home}"/*.txt
> #
> #it has begun!
> #calculate com using pymol, grep the important lines with the results
> $pymol $pdb center_of_mass.py -d 'select all;com all' -c >
> ${home}/log.txt; grep '^State' ${home}/log.txt  > ${home}/out.txt
>
> # convert output to python like list format
> awk -F'[ :]' 'BEGIN{
>                 printf "["
>               }
>               NR>0{
>                 printf "[%.3f,%.3f,%.3f],",$3,$4,$5
>               }
>               END{
>                 printf "]\n"
>               }' ${home}/out.txt | sed 's/,\]$/]/' > ${home}/COM_array.txt
>
> echo "Well done!"
>
> сб, 7 нояб. 2020 г. в 16:08, Mooers, Blaine H.M. (HSC)
> <Bla...@ou...>:
> >
> > Hi Jeff,
> >
> > You can use Python commands to reformat the output.
> > The Python commands can be included in your Python script or
> > with the pml code that you pass with the -d keyword  in the terminal
> > if the Python code is separated by semicolons from the pml code.
> >
> > My email security system mangled the link to your Python script.
> > You can paste the Python code into the body of the email to avoid such issues.
> >
> > 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: Jeff Saxon [jms...@gm...]
> > Sent: Saturday, November 07, 2020 7:34 AM
> > To: pymol-users
> > Subject: [EXTERNAL] Re: [PyMOL] Centre of mass pymol script
> >
> > P.S. sorry I ought to further precise my question:
> > From what I have not I can execute pymol in batch mode together with
> > the py script and pdb
> > pymol my.pdb https://urldefense.proofpoint.com/v2/url?u=http-3A__center-5Fof-5Fmass.py&d=DwIGaQ&c=VjzId-SM5S6aVB_cCGQ0d3uo9UfKByQ3sI6Audoy6dY&r=k0gMbcsdOcdbPUNV5tW66KQSZfXL0ewVDPVBp7tqbks&m=NjIje-z1Dq70jac-RIey36yonAOn8GSzwN-J8OEd9pQ&s=FZzhGIvdiSGI8pO9ZgK0Q0zMauIkq-qCa3HZwNxp_z8&e=  -d 'select all;com all' -c >> log.txt
> > which gives me log.txt contained COM for each model in the following format:
> >
> > State 1:118.851979 120.668604 84.472229
> > State 2:126.789728 149.506520 103.196917
> > State 3:126.379687 149.382354 104.504792
> > State 4:126.989312 149.372811 103.499396
> > .....
> > State 20:125.555854 133.653730 88.441501
> > Obviously I can pipe this output to another program to convert it into
> > the list format, but
> > is it possible rather to modify the python script, automatically
> > loading all pdbs located from the current directory and save the
> > output automatically in the list format indicated in my first message?
> >
> > сб, 7 нояб. 2020 г. в 14:16, Jeff Saxon <jms...@gm...>:
> > >
> > > Dear Pymol Users,
> > > I am using the Centre of mass python script found in PymolWIKI with
> > > the aim to calculate the centre of mass of the loaded ligand
> > > structure. Could you tell me if it would be possible to apply this
> > > script on the multi_model pdb loaded in pymol in the similar way and
> > > to obtain XYZ coordinates of COM for each conformation? Is it possible
> > > to do it in some scripting manner using no-gui pymol and save output
> > > in the list format like {[name the conformation_1],[x,y,z].... name of
> > > the conformation_N,[x,y,z]}?
> > > Thank you in advance
> > > Cheers,
> > > J.
> >
> >
> > _______________________________________________
> > 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=NjIje-z1Dq70jac-RIey36yonAOn8GSzwN-J8OEd9pQ&s=rHFOXfWCHk9XymS9CsAsCKjrHxeVNqjVZBQGphA-r0Y&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=NjIje-z1Dq70jac-RIey36yonAOn8GSzwN-J8OEd9pQ&s=pdU1DssN4zD2FhI_7dcRfdaksVEZvqe6WNN0-5_ygy0&e=

Re: [PyMOL] [EXTERNAL] Re: Centre of mass pymol script

[Jeff S. <jms...@gm...>]

Hi Blame,
I was talking about this pymol script (it can be downloaded directly
from the page below)
https://pymolwiki.org/index.php/Center_of_mass

I used all of the post-processing steps in bash scripts using AWK. Now
I would like to understand how it may work inside this python script.
Here is my shell solution :-)

#!/bin/bash
pymol='/Applications/PyMOL.app/Contents/MacOS/MacPyMOL'
home=$PWD
# this is multi-model pdb with the ligand
pdb=${home}/lig_1AllBoxes_7000_cne_998.pdb
# remove previous outputs
rm "${home}"/*.txt
#
#it has begun!
#calculate com using pymol, grep the important lines with the results
$pymol $pdb center_of_mass.py -d 'select all;com all' -c >
${home}/log.txt; grep '^State' ${home}/log.txt  > ${home}/out.txt

# convert output to python like list format
awk -F'[ :]' 'BEGIN{
                printf "["
              }
              NR>0{
                printf "[%.3f,%.3f,%.3f],",$3,$4,$5
              }
              END{
                printf "]\n"
              }' ${home}/out.txt | sed 's/,\]$/]/' > ${home}/COM_array.txt

echo "Well done!"

сб, 7 нояб. 2020 г. в 16:08, Mooers, Blaine H.M. (HSC)
<Bla...@ou...>:
>
> Hi Jeff,
>
> You can use Python commands to reformat the output.
> The Python commands can be included in your Python script or
> with the pml code that you pass with the -d keyword  in the terminal
> if the Python code is separated by semicolons from the pml code.
>
> My email security system mangled the link to your Python script.
> You can paste the Python code into the body of the email to avoid such issues.
>
> 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: Jeff Saxon [jms...@gm...]
> Sent: Saturday, November 07, 2020 7:34 AM
> To: pymol-users
> Subject: [EXTERNAL] Re: [PyMOL] Centre of mass pymol script
>
> P.S. sorry I ought to further precise my question:
> From what I have not I can execute pymol in batch mode together with
> the py script and pdb
> pymol my.pdb https://urldefense.proofpoint.com/v2/url?u=http-3A__center-5Fof-5Fmass.py&d=DwIGaQ&c=VjzId-SM5S6aVB_cCGQ0d3uo9UfKByQ3sI6Audoy6dY&r=k0gMbcsdOcdbPUNV5tW66KQSZfXL0ewVDPVBp7tqbks&m=NjIje-z1Dq70jac-RIey36yonAOn8GSzwN-J8OEd9pQ&s=FZzhGIvdiSGI8pO9ZgK0Q0zMauIkq-qCa3HZwNxp_z8&e=  -d 'select all;com all' -c >> log.txt
> which gives me log.txt contained COM for each model in the following format:
>
> State 1:118.851979 120.668604 84.472229
> State 2:126.789728 149.506520 103.196917
> State 3:126.379687 149.382354 104.504792
> State 4:126.989312 149.372811 103.499396
> .....
> State 20:125.555854 133.653730 88.441501
> Obviously I can pipe this output to another program to convert it into
> the list format, but
> is it possible rather to modify the python script, automatically
> loading all pdbs located from the current directory and save the
> output automatically in the list format indicated in my first message?
>
> сб, 7 нояб. 2020 г. в 14:16, Jeff Saxon <jms...@gm...>:
> >
> > Dear Pymol Users,
> > I am using the Centre of mass python script found in PymolWIKI with
> > the aim to calculate the centre of mass of the loaded ligand
> > structure. Could you tell me if it would be possible to apply this
> > script on the multi_model pdb loaded in pymol in the similar way and
> > to obtain XYZ coordinates of COM for each conformation? Is it possible
> > to do it in some scripting manner using no-gui pymol and save output
> > in the list format like {[name the conformation_1],[x,y,z].... name of
> > the conformation_N,[x,y,z]}?
> > Thank you in advance
> > Cheers,
> > J.
>
>
> _______________________________________________
> 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=NjIje-z1Dq70jac-RIey36yonAOn8GSzwN-J8OEd9pQ&s=rHFOXfWCHk9XymS9CsAsCKjrHxeVNqjVZBQGphA-r0Y&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=NjIje-z1Dq70jac-RIey36yonAOn8GSzwN-J8OEd9pQ&s=pdU1DssN4zD2FhI_7dcRfdaksVEZvqe6WNN0-5_ygy0&e=

Re: [PyMOL] [EXTERNAL] Re: Centre of mass pymol script

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

Hi Jeff,

You can use Python commands to reformat the output.
The Python commands can be included in your Python script or 
with the pml code that you pass with the -d keyword  in the terminal
if the Python code is separated by semicolons from the pml code.

My email security system mangled the link to your Python script.
You can paste the Python code into the body of the email to avoid such issues.

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: Jeff Saxon [jms...@gm...]
Sent: Saturday, November 07, 2020 7:34 AM
To: pymol-users
Subject: [EXTERNAL] Re: [PyMOL] Centre of mass pymol script

P.S. sorry I ought to further precise my question:
>From what I have not I can execute pymol in batch mode together with
the py script and pdb
pymol my.pdb https://urldefense.proofpoint.com/v2/url?u=http-3A__center-5Fof-5Fmass.py&d=DwIGaQ&c=VjzId-SM5S6aVB_cCGQ0d3uo9UfKByQ3sI6Audoy6dY&r=k0gMbcsdOcdbPUNV5tW66KQSZfXL0ewVDPVBp7tqbks&m=NjIje-z1Dq70jac-RIey36yonAOn8GSzwN-J8OEd9pQ&s=FZzhGIvdiSGI8pO9ZgK0Q0zMauIkq-qCa3HZwNxp_z8&e=  -d 'select all;com all' -c >> log.txt
which gives me log.txt contained COM for each model in the following format:

State 1:118.851979 120.668604 84.472229
State 2:126.789728 149.506520 103.196917
State 3:126.379687 149.382354 104.504792
State 4:126.989312 149.372811 103.499396
.....
State 20:125.555854 133.653730 88.441501
Obviously I can pipe this output to another program to convert it into
the list format, but
is it possible rather to modify the python script, automatically
loading all pdbs located from the current directory and save the
output automatically in the list format indicated in my first message?

сб, 7 нояб. 2020 г. в 14:16, Jeff Saxon <jms...@gm...>:
>
> Dear Pymol Users,
> I am using the Centre of mass python script found in PymolWIKI with
> the aim to calculate the centre of mass of the loaded ligand
> structure. Could you tell me if it would be possible to apply this
> script on the multi_model pdb loaded in pymol in the similar way and
> to obtain XYZ coordinates of COM for each conformation? Is it possible
> to do it in some scripting manner using no-gui pymol and save output
> in the list format like {[name the conformation_1],[x,y,z].... name of
> the conformation_N,[x,y,z]}?
> Thank you in advance
> Cheers,
> J.


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Re: [PyMOL] Centre of mass pymol script

[Jeff S. <jms...@gm...>]

P.S. sorry I ought to further precise my question:
>From what I have not I can execute pymol in batch mode together with
the py script and pdb
pymol my.pdb center_of_mass.py -d 'select all;com all' -c >> log.txt
which gives me log.txt contained COM for each model in the following format:

State 1:118.851979 120.668604 84.472229
State 2:126.789728 149.506520 103.196917
State 3:126.379687 149.382354 104.504792
State 4:126.989312 149.372811 103.499396
.....
State 20:125.555854 133.653730 88.441501
Obviously I can pipe this output to another program to convert it into
the list format, but
is it possible rather to modify the python script, automatically
loading all pdbs located from the current directory and save the
output automatically in the list format indicated in my first message?

сб, 7 нояб. 2020 г. в 14:16, Jeff Saxon <jms...@gm...>:
>
> Dear Pymol Users,
> I am using the Centre of mass python script found in PymolWIKI with
> the aim to calculate the centre of mass of the loaded ligand
> structure. Could you tell me if it would be possible to apply this
> script on the multi_model pdb loaded in pymol in the similar way and
> to obtain XYZ coordinates of COM for each conformation? Is it possible
> to do it in some scripting manner using no-gui pymol and save output
> in the list format like {[name the conformation_1],[x,y,z].... name of
> the conformation_N,[x,y,z]}?
> Thank you in advance
> Cheers,
> J.

[PyMOL] Centre of mass pymol script

[Jeff S. <jms...@gm...>]

Dear Pymol Users,
I am using the Centre of mass python script found in PymolWIKI with
the aim to calculate the centre of mass of the loaded ligand
structure. Could you tell me if it would be possible to apply this
script on the multi_model pdb loaded in pymol in the similar way and
to obtain XYZ coordinates of COM for each conformation? Is it possible
to do it in some scripting manner using no-gui pymol and save output
in the list format like {[name the conformation_1],[x,y,z].... name of
the conformation_N,[x,y,z]}?
Thank you in advance
Cheers,
J.

[PyMOL] How to get the object name from chempy.Atom

[Pedro L. <psl...@gm...>]

Hi,

I got an `chempy.Atom` instance via `cmd.get_model().atom`.

How to get the state and object name.


Thank you!

-- 
Pedro Sousa Lacerda

Laboratório de Bioinformática e Modelagem Molecular / UFBA
Mestrando em Ciências Farmácias / UEFS

@pslacerda
+55 71 9 9981-1856
http://lattes.cnpq.br/8338596525330907

[PyMOL] Fwd: Join us: Augmenting PyMOL’s World-Class Visualisation with Cutting Edge Science Webinar on November 12th and 19th

[Thomas H. <tho...@sc...>]

Greetings,

Schrödinger is hosting some free webinars which could be relevant for PyMOL users.
If you are interested, please follow the registration links below.

Cheers,
  Thomas


> Begin forwarded message:
> 
> From: Schrödinger <edu...@sc...>
> Subject: Join us: Augmenting PyMOL’s World-Class Visualisation with Cutting Edge Science Webinar on November 12th and 19th
> 
> 
>  
> Join us online!
> We hope you'll join us on November 12th and 19th for webinar presentations focusing on the topic of Augmenting PyMOL’s World-Class Visualisation with Cutting Edge Science <https://go.schrodinger.com/Q0OU07O0EJ3aU0j3P00L2r0>. In these presentations, we will explore some of the limitations of relying solely on PyMOL, showing how Schrödinger’s more chemistry/biology-aware modelling platform, Maestro, yields quantitatively superior insights and conclusions.  
> 
> These presentations will conclude the "Schrödinger Autumn of Design Webinar Series" but there is still time to register. Please click on the buttons below to register or visit the event website <https://go.schrodinger.com/Q0OU07O0EJ3aU0j3P00L2r0> for more information. 
>  
>  
> Augmenting PyMOL’s World-Class Visualisation with Cutting Edge Science: Working towards Small Molecule Design for Chemists 
> featuring Tatjana Braun at Schrödinger 
> Time: 11.00 CET 
> Date: Thursday, Nov. 12 
> REGISTER  <https://go.schrodinger.com/wO7Uj2PEa0000r3M00U3K0O>
>  
>  
> Augmenting PyMOL’s World-Class Visualisation with Cutting Edge Science: Working towards Detailed Structural Analysis for Biologists 
> featuring Jas Bhachoo at Schrödinger 
> Time: 11.00 CET 
> Date: Thursday, Nov. 19  
> REGISTER  <https://go.schrodinger.com/har3L2O00E000UPOj030UN7>
>  
>  <https://go.schrodinger.com/a0300a03UE0700OUMOjO2rP>  <https://go.schrodinger.com/R00a273OUP0030r0ENUOPj0>
> Copyright © 2020 Schrödinger, Inc.
> Our address is 120 West 45th Street, 17th Floor, New York, NY 10036, USA
> 

--
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.

[PyMOL] Autodock analisis in Pymol

[Jeff S. <jms...@gm...>]

Dear all,
probably it is not a very pymol-oriented question, but otherwise I am
looking for people who worked with autodock tools, or maybe who dealt
with some pymol plugins suitable to handle DLG filles of AT runs?
Particularly, I am looking for some methods for
combining/reclusterization of autodock conformations (in DLG or PDB...
), with the possibility to sort the clusters according to the energies
computed by AT as well as using custom selections (for example centre
of mass of the ligand).  I will be thankful for any suggestions!
Cheers,
J.

Re: [PyMOL] Detect library mode

[Pedro L. <psl...@gm...>]

My plugin fail in library mode because it tries to add a Qt menu. Just an
error message appears.

If there is two init functions, one for GUI and other for CL, would work.

__init_plugin__
__init_gui_plugin__

Em ter, 27 de out de 2020 21:00, Pedro Lacerda <psl...@gm...>
escreveu:

> Hi,
>
> How to detect if we are in the library mode or on the GUI mode?
>
> --
> Pedro Sousa Lacerda
>
> Laboratório de Bioinformática e Modelagem Molecular / UFBA
> Mestrando em Ciências Farmácias / UEFS
>
> @pslacerda
> +55 71 9 9981-1856
> http://lattes.cnpq.br/8338596525330907
>

Re: [PyMOL] [EXTERNAL] pymolrc.pml file location

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

Hi Michael,

PyMOL will search your home directory for your pymolrc.pml file.
I would store it there.

You can check that pymol is finding it by starting PyMOL and 
going to the pull-down menus File-->Edit pyrmolrc.
PyMOL's built-in editor should find and open your pymolrc.pml file.

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: Michael Morgan [mic...@gm...]
Sent: Sunday, November 01, 2020 11:46 PM
To: pym...@li...
Subject: [EXTERNAL] [PyMOL] pymolrc.pml file location

Dear friends,

I have successfully installed windows version open-source pymol according to instructions:
https://pymolwiki.org/index.php/Windows_Install<https://urldefense.proofpoint.com/v2/url?u=https-3A__pymolwiki.org_index.php_Windows-5FInstall&d=DwMFAg&c=VjzId-SM5S6aVB_cCGQ0d3uo9UfKByQ3sI6Audoy6dY&r=k0gMbcsdOcdbPUNV5tW66KQSZfXL0ewVDPVBp7tqbks&m=b0XxD5JXBQRz5vOkWVm--MTbRwIrp2NV4VfDrEZNODQ&s=5T4ZtRt_7u6kXXx8dsEH8DeDa1JVtCnI22_1UvHTX1I&e=>

I have a copy of "pymolrc.pml" file from my previous pymol, which is not open-source version and was kept in "$pymol/share/pymol" folder. Where should I put this file for my new open-source version?

Thank you very much.

Michael

[PyMOL] pymolrc.pml file location

[Michael M. <mic...@gm...>]

Dear friends,

 

I have successfully installed windows version open-source pymol according to
instructions:

https://pymolwiki.org/index.php/Windows_Install

 

I have a copy of "pymolrc.pml" file from my previous pymol, which is not
open-source version and was kept in "$pymol/share/pymol" folder. Where
should I put this file for my new open-source version?

 

Thank you very much.

 

Michael

[PyMOL] Fw: How to iterate commands in pymol

[Brown, Z. <zb...@cu...>]

Dear all,

I received two answers to my question.

Either call the function as part of cmd.do('function') or import it into my script and call it that way (see below):

"You need to import the colorbyrmsd.py script within your script, then you can call it that way.  For example your script could say:

import colorbyrmsd as cbr

for obj in seleobjs:
  cmd.enable(obj)
  cbr.colorbyrmsd(obj,target)"

Thank you both for your help!
Best regards,

Zuben

________________________________
From: Mooers, Blaine H.M. (HSC) <Bla...@ou...>
Sent: Saturday, October 31, 2020 5:59 PM
To: Brown, Zuben <zb...@cu...>
Subject: [EXTERNAL] RE: How to iterate commands in pymol

Hi Zuben,

Good question!

ColorByRMSD is described here https://urldefense.proofpoint.com/v2/url?u=https-3A__pymolwiki.org_index.php_ColorByRMSD&d=DwIFAg&c=G2MiLlal7SXE3PeSnG8W6_JBU6FcdVjSsBSbw6gcR0U&r=8AY7h2N3TQ7k7n9RDhxT46t0ViqfY3ViGGLPrQZPtGw&m=2AkS9-9GiZXwGwqONju_wOfjSdAj3CjsKQUt50x7cBA&s=r2yosmTOrZ53GB7PLAAUYfXQpvhQKkCSsQkNyawkJR8&e= .
The script is under a BSD-2-Clause License.

You have to "run colorbyrmsd.py" to load the colorbyrmd function into memory that is in this file.

The Python function colorbyrmsd() has been extended so that it can act like a command in the PyMOL macro language.
Such commands can be executed in your Python "for loop" by using the command inside of quotes as the argument to cmd.do().
For example,

cmd.do("colorbyrmsd 1ake, 4ake")

I know. It is silly to a convert a Python function to a PML command than call this command from Python, but this
approach requires the least amount of effort on your part.

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: Brown, Zuben [zb...@cu...]
Sent: Saturday, October 31, 2020 3:36 PM
To: PyM...@li...
Subject: [EXTERNAL] [PyMOL] How to iterate commands in pymol

Hi,

I'd like to iterate using a script in pymol but one of the commands I'd like to use does not have an associated cmd.API.
For example, how do I run:

for obj in seleobjs:
cmd.enable(obj)
colorbyrmsd(obj, target)   <--- This third line doesn't work since colorbyrmsd does not have a cmd.colorbyrmsd.

Is there a way I can run something like:
cmd.executecommand("colorbyrmsd {0}, target".format(obj))  ?

Best regards,

Zuben

[PyMOL] Pyvol steps

[ALBAYATI S. H. K. / U. <gs...@st...>]

Hi I want yo use pyvol plugin in pymall I already install it but dont know
how to use it to measure the binding site and how to compare the binding
sit, any help in manual users.Thanks
Samah Hashim

Re: [PyMOL] How to iterate commands in pymol

[Robert C. <rob...@qu...>]

Hi Zuben,

You need to import the colorbyrmsd.py script within your script, then you can call it that way.  For example your script could say:

import colorbyrmsd as cbr

for obj in seleobjs:
  cmd.enable(obj)
  cbr.colorbyrmsd(obj,target)

Cheers,
Rob

On Sat, 2020-10-31 20:36  +0000,  "Brown, Zuben" <zb...@cu...> wrote:

> Hi,
> 
> I'd like to iterate using a script in pymol but one of the commands
> I'd like to use does not have an associated cmd.API. For example, how
> do I run:
> 
> for obj in seleobjs:
> cmd.enable(obj)
> colorbyrmsd(obj, target)   <--- This third line doesn't work since
> colorbyrmsd does not have a cmd.colorbyrmsd.
> 
> Is there a way I can run something like:
> cmd.executecommand("colorbyrmsd {0}, target".format(obj))  ?
> 
> Best regards,
> 
> Zuben



-- 
Robert L. Campbell, Ph.D.
Academic Advisor, BHSc Program
Assistant Professor, Dept. of Biomedical & Molecular Sciences, 
Queen's University, Kingston, ON K7L 3N6  Canada
Botterell Hall Rm 644     Tel: 613-533-6821
<rob...@qu...>  http://pldserver1.biochem.queensu.ca/~rlc

[PyMOL] How to iterate commands in pymol

[Brown, Z. <zb...@cu...>]

Hi,

I'd like to iterate using a script in pymol but one of the commands I'd like to use does not have an associated cmd.API.
For example, how do I run:

for obj in seleobjs:
cmd.enable(obj)
colorbyrmsd(obj, target)   <--- This third line doesn't work since colorbyrmsd does not have a cmd.colorbyrmsd.

Is there a way I can run something like:
cmd.executecommand("colorbyrmsd {0}, target".format(obj))  ?

Best regards,

Zuben

[PyMOL] Dose the thickness of residues reflect b-factor in cartoon putty representation?

[sunyeping <sun...@al...>]

Dear all,

When you use "cartoon putty[, selection]" command in pymol, you will get the cartoon putty representation of your selection. And the backbond of the selection show different thickness. So dose the thickness of residues reflect b-factor in cartoon putty representation?

Best regards

Yeping Sun

[PyMOL] Detect library mode

[Pedro L. <psl...@gm...>]

Hi,

How to detect if we are in the library mode or on the GUI mode?

-- 
Pedro Sousa Lacerda

Laboratório de Bioinformática e Modelagem Molecular / UFBA
Mestrando em Ciências Farmácias / UEFS

@pslacerda
+55 71 9 9981-1856
http://lattes.cnpq.br/8338596525330907

Re: [PyMOL] [EXTERNAL] from pymol import cmd

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

Hi Jason,

Did you create a kernel for the python interpreter that is used by PyMOL?

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: Jason Li [jas...@gm...]
Sent: Tuesday, October 27, 2020 11:10 AM
To: pymol-users
Subject: [EXTERNAL] [PyMOL] from pymol import cmd

Dear all,

I am running pymol in Python (jupyter notebook) using Mac IOS10.15.
After importing pymol, I wonder why can't cmd be imported?

import __main__
__main__.pymol_argv = [ 'pymol', '-qc'] # Quiet and no GUI
import cgi
import pickle
import pymol
import sys

from pymol import cmd

ImportError: cannot import name 'cmd' from 'pymol' (unknown location)


Thanks a lot.

Jason

[PyMOL] from pymol import cmd

[Jason Li <jas...@gm...>]

Dear all,

I am running pymol in Python (jupyter notebook) using Mac IOS10.15.
After importing pymol, I wonder why can't cmd be imported?

import __main__
__main__.pymol_argv = [ 'pymol', '-qc'] # Quiet and no GUI
import cgi
import pickle
import pymol
import sys

from pymol import cmd

ImportError: cannot import name 'cmd' from 'pymol' (unknown location)


Thanks a lot.

Jason

Re: [PyMOL] [EXTERNAL] present b factor putty on select

[sunyeping <sun...@al...>]

Hi, Blaine, 

Thank you, that's helpful. But a problem with creating a new object is that the conformation of the newly created object for the selection is sightly different from its counterpart in the original object. If the original object is shown as cartoon, then both the putty presentation of new object and the cartoon presentation of its counterpart in the original object at site of the conformational difference will appear in the image produced in this way, and that's ugly. Is there a way the avoid this shortcoming?

Best,
------------------------------------------------------------------
From:Mooers, Blaine H.M. (HSC) <Bla...@ou...>
Sent At:2020 Oct. 27 (Tue.) 18:09
To:孙业平 <sun...@al...>; pymol-users <pym...@li...>
Subject:RE: [PyMOL] [EXTERNAL] present b factor putty on select

I am sorry. I am wrong. I should have tested by suggestion. 
 Irregardless of the selection that I specify, the entire chain is changed.
I would go with your plan B and create a new object for the selection.

create test, resi 100:150
preset.b_factor_putty("test")

The above worked with pdb file 4dgr.

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: Mooers, Blaine H.M.  (HSC) [Bla...@ou...]
Sent: Tuesday, October 27, 2020 4:54 AM
To: sunyeping; pymol-users
Subject: Re: [PyMOL] [EXTERNAL]  present b factor putty on select

Hi sunyeping,

You are right; there is a way via the command line:

preset.b_factor_putty(selection='all')

Replace "all" with your selection.

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: sunyeping via PyMOL-users [pym...@li...]
Sent: Tuesday, October 27, 2020 3:09 AM
To: pymol-users
Subject: [EXTERNAL] [PyMOL] present b factor putty on select

Dear all,

I know that if you want to visualize b facotor of a objector in pymol, you can use A>Present>b factor putty. However, how can show the b factor putty on a certain selection of the object? Is there any command line to do this or do I have to create a new object for the selection and still use the A>Present>b factor putty operation?

Thank you,
Best regards


_______________________________________________
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Re: [PyMOL] [EXTERNAL] present b factor putty on select

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

I am sorry. I am wrong. I should have tested by suggestion. 
 Irregardless of the selection that I specify, the entire chain is changed.
I would go with your plan B and create a new object for the selection.

create test, resi 100:150
preset.b_factor_putty("test")

The above worked with pdb file 4dgr.

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: Mooers, Blaine H.M.  (HSC) [Bla...@ou...]
Sent: Tuesday, October 27, 2020 4:54 AM
To: sunyeping; pymol-users
Subject: Re: [PyMOL] [EXTERNAL]  present b factor putty on select

Hi sunyeping,

You are right; there is a way via the command line:

preset.b_factor_putty(selection='all')

Replace "all" with your selection.

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: sunyeping via PyMOL-users [pym...@li...]
Sent: Tuesday, October 27, 2020 3:09 AM
To: pymol-users
Subject: [EXTERNAL] [PyMOL] present b factor putty on select

Dear all,

I know that if you want to visualize b facotor of a objector in pymol, you can use A>Present>b factor putty. However, how can show the b factor putty on a certain selection of the object? Is there any command line to do this or do I have to create a new object for the selection and still use the A>Present>b factor putty operation?

Thank you,
Best regards


_______________________________________________
PyMOL-users mailing list
Archives: https://urldefense.proofpoint.com/v2/url?u=http-3A__www.mail-2Darchive.com_pymol-2Dusers-40lists.sourceforge.net&d=DwICAg&c=VjzId-SM5S6aVB_cCGQ0d3uo9UfKByQ3sI6Audoy6dY&r=k0gMbcsdOcdbPUNV5tW66KQSZfXL0ewVDPVBp7tqbks&m=BSbjOkK0hwBIwGPqAfzg6VuZ4G17ti5wnwV6_wT6joo&s=VChEP3IpjfnXt-V_J6Qsm9wC5UhAp9DCoyG_LAe27mk&e=
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Re: [PyMOL] [EXTERNAL] present b factor putty on select

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

Hi sunyeping,

You are right; there is a way via the command line:

preset.b_factor_putty(selection='all')

Replace "all" with your selection.

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: sunyeping via PyMOL-users [pym...@li...]
Sent: Tuesday, October 27, 2020 3:09 AM
To: pymol-users
Subject: [EXTERNAL] [PyMOL] present b factor putty on select

Dear all,

I know that if you want to visualize b facotor of a objector in pymol, you can use A>Present>b factor putty. However, how can show the b factor putty on a certain selection of the object? Is there any command line to do this or do I have to create a new object for the selection and still use the A>Present>b factor putty operation?

Thank you,
Best regards

[PyMOL] present b factor putty on select

[sunyeping <sun...@al...>]

Dear all,

I know that if you want to visualize b facotor of a objector in pymol, you can use A>Present>b factor putty. However, how can show the b factor putty on a certain selection of the object? Is there any command line to do this or do I have to create a new object for the selection and still use the A>Present>b factor putty operation?

Thank you,
Best regards

Re: [PyMOL] pref_get() on library mode

[Pedro L. <psl...@gm...>]

Let me be honest. It worked like an old car.

Qt wasn't loaded so an error message appears because my plugin uses Qt. The
plugin initialization failed.

Despite the message everything was ok and the preferences showed up.

Em seg, 26 de out de 2020 13:21, Pedro Lacerda <psl...@gm...>
escreveu:

> It worked like a charm, thank you.
>
> Em seg., 26 de out. de 2020 às 04:37, Thomas Holder <
> tho...@sc...> escreveu:
>
>> Hi Pedro,
>>
>> If you call `plugin_load` that will trigger initialization.
>>
>> pymol.plugins.plugin_load('yourplugin')
>> value = pymol.plugins.pref_get('YOUPLUGIN_SOME_KEY')
>>
>>
>> I feel like this plugin API is due for an overhaul, there are no great
>> answers to your various questions :-/
>>
>> Cheers,
>>   Thomas
>>
>>
>> > On Oct 26, 2020, at 5:40 AM, Pedro Lacerda <psl...@gm...> wrote:
>> >
>> > Hi,
>> >
>> > How to use pref_get() on library mode.
>> >
>> > Or even better, how to use pref_get() even before library mode?
>> >
>> > --
>> > Pedro Sousa Lacerda
>> >
>> > Laboratório de Bioinformática e Modelagem Molecular / UFBA
>> > Mestrando em Ciências Farmácias / UEFS
>> >
>> > @pslacerda
>> > +55 71 9 9981-1856
>> > http://lattes.cnpq.br/8338596525330907
>> > _______________________________________________
>> > PyMOL-users mailing list
>> > Archives: http://www.mail-archive.com/pym...@li...
>> > Unsubscribe:
>> https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe
>>
>> --
>> Thomas Holder
>> PyMOL Principal Developer
>> Schrödinger, Inc.
>>
>>
>
> --
> Pedro Sousa Lacerda
>
> Laboratório de Bioinformática e Modelagem Molecular / UFBA
> Mestrando em Ciências Farmácias / UEFS
>
> @pslacerda
> +55 71 9 9981-1856
> http://lattes.cnpq.br/8338596525330907
>

Re: [PyMOL] pref_get() on library mode

[Pedro L. <psl...@gm...>]

It worked like a charm, thank you.

Em seg., 26 de out. de 2020 às 04:37, Thomas Holder <
tho...@sc...> escreveu:

> Hi Pedro,
>
> If you call `plugin_load` that will trigger initialization.
>
> pymol.plugins.plugin_load('yourplugin')
> value = pymol.plugins.pref_get('YOUPLUGIN_SOME_KEY')
>
>
> I feel like this plugin API is due for an overhaul, there are no great
> answers to your various questions :-/
>
> Cheers,
>   Thomas
>
>
> > On Oct 26, 2020, at 5:40 AM, Pedro Lacerda <psl...@gm...> wrote:
> >
> > Hi,
> >
> > How to use pref_get() on library mode.
> >
> > Or even better, how to use pref_get() even before library mode?
> >
> > --
> > Pedro Sousa Lacerda
> >
> > Laboratório de Bioinformática e Modelagem Molecular / UFBA
> > Mestrando em Ciências Farmácias / UEFS
> >
> > @pslacerda
> > +55 71 9 9981-1856
> > http://lattes.cnpq.br/8338596525330907
> > _______________________________________________
> > PyMOL-users mailing list
> > Archives: http://www.mail-archive.com/pym...@li...
> > Unsubscribe:
> https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe
>
> --
> Thomas Holder
> PyMOL Principal Developer
> Schrödinger, Inc.
>
>

-- 
Pedro Sousa Lacerda

Laboratório de Bioinformática e Modelagem Molecular / UFBA
Mestrando em Ciências Farmácias / UEFS

@pslacerda
+55 71 9 9981-1856
http://lattes.cnpq.br/8338596525330907