pymol-users — Collaborative support and tips for PyMOL users

[PyMOL] handling of multiple files in batch mode

[Enrico M. <jms...@gm...>]

Dear Pymol Users!
My Pymol batch script loads all pdb filles from the output directory
split states and saves the pse session

pymol "${output}"/*.pdb -c -d "
  from pymol import cmd
  #cmd.load('${output}/*.pdb')
  cmd.set('grid_mode','1')
  cmd.orient()
  cmd.bg_color('white')
  cmd.show('sticks', 'not polymer')
  cmd.show('spheres', 'not polymer')
  cmd.set('stick_radius', '0.12', 'not polymer')
  cmd.set('sphere_scale', '0.20', 'not polymer')
  cmd.save('${output_pse}/${project}.pse')
"

1) As you may see I load the filles using bash syntax as *.pdb. Is it
possible to do it directly in the pymol script e.g. using glob ? Could
you please show me the example of such syntax?
e.g. I''e already tried   #cmd.load('${output}/*.pdb')
but it did not recognize the pattern.

2) is it possible to print the name of each separate pdb in the
splitted grid display?
Many thanks in advance!
Cheers
Enrico

[PyMOL] cmd.align does not work

[Tereza Č. <ter...@na...>]

Hello,
I am trying to use the Pymol API to align some structures with the
`cmd.align` command.
It seems that it does not work correctly though.
I have made a picture before running the `cmd.align` and after running it,
the pictures look the same.
Before alignment: https://pasteboard.co/1RtHTgy7iOKC.png/
[image: test_nonaligned.png]
After alignment: https://pasteboard.co/ta0YVyaLbaE4.png
[image: test_aligned.png]

When I use the Pymol user interface on the same computer and I align the
same structures, they align very well.
Aligned: https://pasteboard.co/gr2hsa8whb47.png
[image: aligned_structures.png]

The version of Pymol I am using: pymol-2.3.4
Here is the script which I used:

#!/bin/env python

from pymol import cmd
import os

cmd.load('tps_structures/' + 'A0A140AZ69' + '.pdb')
cmd.load('tps_structures/' + 'A0A140AZ72' + '.pdb')

cmd.show_as('cartoon')

cmd.spectrum( "resi", "rainbow", 'A0A140AZ69')
cmd.spectrum( "resi", "rainbow", 'A0A140AZ72')
cmd.png(os.path.join('test_nonaligned' + '.png'), 1200, 1200, 300, 1)

reference = 'A0A140AZ69'
cmd.align(reference, 'A0A140AZ72', cutoff=2.0, cycles=20, quiet=0)
cmd.png(os.path.join('test_aligned' + '.png'), 1200, 1200, 300, 1)

cmd.hide('cartoon', 'A0A140AZ69')
cmd.hide('cartoon', 'A0A140AZ72')

cmd.show_as('cartoon', 'A0A140AZ69')
cmd.png(os.path.join('test_aligned_A0A140AZ69' + '.png'), 1200, 1200, 300, 1
)
cmd.hide('cartoon', 'A0A140AZ69')

cmd.show_as('cartoon', 'A0A140AZ72')
cmd.png(os.path.join('test_aligned_A0A140AZ72' + '.png'), 1200, 1200, 300, 1
)
cmd.hide('cartoon', 'A0A140AZ72')

I appreciate any help on how to make the cmd.align work.
Thank you

Tereza
-- 
Tereza Čalounová

Charles University
Faculty of Science
Albertov 6, 128 43 Praha 2
www.natur.cuni.cz/en

Re: [PyMOL] How to show a viral capsid?

[Thomas H. <th...@th...>]

Hi JJ,

This should come pretty close:

set assembly
set async_builds
set pick_surface
fetch 1ej6
spectrum chain
remove not guide
alter guide, vdw=4
set solvent_radius, 4
as surface

Showing the surface will take a moment, about 10 seconds on my computer.

See also:
https://pymolwiki.org/index.php/Assembly
https://pymolwiki.org/index.php/Huge_surfaces (Strategy 2)

Cheers,
  Thomas

On Sat, Apr 23, 2022 at 5:19 PM JJ Oliveira <joa...@gm...> wrote:
>
> Hi guys
>
> Please, how to show a full viral capsid in PyMol as seen below?
>
> Reovirus capsid: https://www.rcsb.org/3d-view/1EJ6
>
> Thank you!
> _______________________________________________
> PyMOL-users mailing list
> Archives: http://www.mail-archive.com/pym...@li...
> Unsubscribe: https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe

[PyMOL] How to show a viral capsid?

[JJ O. <joa...@gm...>]

Hi guys

Please, how to show a full viral capsid in PyMol as seen below?

Reovirus capsid: https://www.rcsb.org/3d-view/1EJ6

Thank you!

[PyMOL] Electron density map carving issue

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

I am trying to create figures showing only the ligand with electron density
using an mtz file. The commands I am using to create the density map are as
follows:
map_double h.map
select local,resn GEN
isomesh map,h.map,1.0,local,carve=2.5

It works fine for one structure but I am having an issue for the others.
The issue is that the density around the ligand has gaps at both ends of
the molecule, instead of covering it entirely. I am attaching two figures
showing the difference. Thank you in advance for your help.

[image: c1_local.png][image: siso_local.png]

Re: [PyMOL] Help - how mutation affects protein structure

[Marco S. <se...@un...>]

Dear Susanna,

in addition to MD calculations I suggest you to perform a check on your 
mutated protein. Circular dichroism is a simple technique that allows to 
monitor the global fold of your protein.

Mutating a residue may affect the folding and this seems an 
underestimated problem in the literature.

Best,

Marco Sette

Il 12/04/2022 16:34, susanna pagni ha scritto:
> Hello,
>
> I am quite new to PyMOL. I would like to assess how an amino acid change might affect the protein structure. I used the Wizard Mutagenesis to change the amino acid of interest but don’t know how I can see how the protein structure is affected by the mutation.
>
> Can you please help me with this?
>
> Many thanks in advance.
>
> Best wishes,
> Susanna
>
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> PyMOL-users mailing list
> Archives: http://www.mail-archive.com/pym...@li...
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via della Ricerca Scientifica, 00133, Rome, Italy
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Tel.: +39-0672594424
Fax: +39-0672594328
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Re: [PyMOL] Help - how mutation affects protein structure

[Sorin D. <sor...@gm...>]

Hi Susanna,

As you can see, pymol allows you to mutate residues. However, in order to
assess their influence, you should most likely run MD simulations on both
the wild type protein and mutant(s) and compare.

Kind  regards,

Sorin

On Tue, Apr 12, 2022, 5:35 PM susanna pagni <pag...@gm...> wrote:

> Hello,
>
> I am quite new to PyMOL. I would like to assess how an amino acid change
> might affect the protein structure. I used the Wizard Mutagenesis to change
> the amino acid of interest but don’t know how I can see how the protein
> structure is affected by the mutation.
>
> Can you please help me with this?
>
> Many thanks in advance.
>
> Best wishes,
> Susanna
>
> _______________________________________________
> PyMOL-users mailing list
> Archives: http://www.mail-archive.com/pym...@li...
> Unsubscribe:
> https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe

[PyMOL] Help - how mutation affects protein structure

[susanna p. <pag...@gm...>]

Hello,

I am quite new to PyMOL. I would like to assess how an amino acid change might affect the protein structure. I used the Wizard Mutagenesis to change the amino acid of interest but don’t know how I can see how the protein structure is affected by the mutation.

Can you please help me with this?

Many thanks in advance.

Best wishes,
Susanna

Re: [PyMOL] Virtual Annual CCP4/APS Crystallographic School (2022) in the US

[Xu, Q. <qx...@an...>]

Dear Colleagues

This is a final reminder that the registration for the upcoming CCP4/APS school will be closed on Apr 15, 2022. Please submit your application soon if you plan to attend.


Charles, Andrey, Garib and Qingping



________________________________
From: Xu, Qingping
Sent: Monday, January 24, 2022 10:07 AM
To: CC...@JI... <CC...@JI...>; pym...@li... <pym...@li...>; phe...@ph... <phe...@ph...>; Ahrens, Kristin <ka...@an...>
Subject: Virtual Annual CCP4/APS Crystallographic School (2022) in the US


Dear Colleagues,

We are pleased to announce the virtual annual CCP4/APS crystallographic school “From data collection to structure refinement and beyond” will be held on June 13-24, 2022 at the Advanced Photon Source (APS), Argonne National Laboratory (ANL), near Chicago, Illinois, USA. All details can be found at the school website: http://www.ccp4.ac.uk/schools/APS-2022/index.php.

Dates: June 6 (Bioinformatics & setup) and June 13 through 24, 2022 (with a weekend break on June 18 and 19th)

Location: Virtual/Remote

The school comprises two parts: remote data collection workshop and virtual crystallographic computing workshop. Data collection workshop includes beamline training, data collection on GM/CA at APS beamlines 23ID-D and 23ID-B equipped with Pilatus3 6M and Eiger 16M detectors respectively, and data processing. For data collection, only the participants’ crystals will be used. Crystallographic computation workshop will feature many modern crystallographic software packages taught by authors and other experts. The daily schedule will be organized in three sections – lectures, tutorials, and hands-on (interactive troubleshooting of the technical difficulties the participants face in their projects). We have had considerable success resolving these problems in past years, attested by resulting publications (see http://www.ccp4.ac.uk/schools/APS-school/publications.php). A draft of the program, contact info and other details can be found at the School website. Note that for the virtual school, an additional day (June 6th, 2022) was scheduled to prepare for the main event, with lectures on generating AlphaFold models to use in later part of the school.

Applicants: Graduate students, postdoctoral researchers and early-career faculty, along with commercial/industrial researchers are encouraged to apply. Only about 20 applicants will be selected for participation. Participants of the workshop are strongly encouraged to bring their own problem data sets or crystals so the problems can be addressed during data collection and/or computation workshops.

Application: Application deadline is April 15th, 2022. To apply, visit https://www.ccp4.ac.uk/schools/APS-2022/application.php.

Fees: There is no fee for attending the virtual school for the chosen applicants.

We hope to see you at the school.

Charles, Andrey, Garib and Qingping

[PyMOL] Problem with the legacy plugin CASTp pocket loader

[Lionel M. P. <lio...@ip...>]

Dear all,

I encounter problems using the legacy plugin CASTp pocket loader on 
PyMOL Version 2.4.1. It fails to open poc files and terminates with 
"Error: unsupported file type poc". Any idea on how to solve this problem?

Thanks a lot!

With kind regards,

Lionel
-- 
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<mailto:Lio...@ip...>

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<http://cribligand.ipbs.fr/>

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ipbs.cnrs <https://www.facebook.com/IPBS.CNRS/>

[PyMOL] Ambient setting for a selection

[Daniel B. <db...@ia...>]

Hello,

Is there a way to get  “set ambient” to work on a selection?  

I am trying to find a way to have a single atom sphere representation appear to glow.

Thank you,

Dan

Re: [PyMOL] hydrogen-bonds detected in the protein-ligand complexes

[EDUARDO J. A. C. <ed...@ep...>]

Good Question
I like to know Too.
And about Hydrophobic interaction , Is it possible to show the
hydrophobic interactions on pymol too?

Em qui., 31 de mar. de 2022 às 06:49, Enrico Martinez <
jms...@gm...> escreveu:

> Dear Pymol users!
> Another question related to the analysis of the multi-model pdb
> obtained from protein-ligand docking calculations.
>
> I am using pymol to visualise protein-ligand interactions between each
> pose predicted by docking and protein in my script:
>
> preset.ligand_cartoon('my_pdb*',_self=cmd)
>
> then I may use the following command to switch to the state in
> multi_model pdb, which could be important:
> cmd.set('state','5','my_pdb*')
>
> Is it possible to print the number of the state which has
> 1) the maximal number of the hydrogen bonds?
> 2) has a particular hydrogen bond of my interest?
> Cheers,
> Enrico
>
>
> _______________________________________________
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> Archives: http://www.mail-archive.com/pym...@li...
> Unsubscribe:
> https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe
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[PyMOL] hydrogen-bonds detected in the protein-ligand complexes

[Enrico M. <jms...@gm...>]

Dear Pymol users!
Another question related to the analysis of the multi-model pdb
obtained from protein-ligand docking calculations.

I am using pymol to visualise protein-ligand interactions between each
pose predicted by docking and protein in my script:

preset.ligand_cartoon('my_pdb*',_self=cmd)

then I may use the following command to switch to the state in
multi_model pdb, which could be important:
cmd.set('state','5','my_pdb*')

Is it possible to print the number of the state which has
1) the maximal number of the hydrogen bonds?
2) has a particular hydrogen bond of my interest?
Cheers,
Enrico

[PyMOL] Yale morph server results. All scenes displayed.

[Bruce O. <bco...@gm...>]

Hi!

I just got output from the Yale morph server
*http://morph2.molmovdb.org/submit.html
<http://morph2.molmovdb.org/submit.html>* that allows construction of
movies given structures of protein conformers.

I opened the result in PyMol and see all the scenes displayed at the same
time.

Does anyone have experience creating a movie from their output?

Thx!

Bruce

Re: [PyMOL] Analysis of docking results in multi-model format

[Enrico M. <jms...@gm...>]

just as an update of my first topic.
Is there any possibility to associate any plugin or external tool
(rdkit) to calculate pharmacophore model for each docking pose loaded
in multi-model format (i) as well as for the ligand in X-ray structure
(ii) and then compare i with ii in order to find instantly the docking
pose which is more similar to X-ray structure according to some part
of the pharmacophore shared between the both molecules ?

чт, 24 мар. 2022 г. в 14:11, Enrico Martinez <jms...@gm...>:
>
> Dear Pymol Users!
> I am dealing with the analysis of the results of protein-ligand
> docking poses representing the multi-model pdb.  I need to find a
> possibility (e.g. via some script that could be executed in the pymol)
> to compare each docking pose with the X-ray structure (loaded as the
> separate model in pymol) in order to find automatically the model (=
> docking solution) which may fit better to it (e.g. via estimating RMSD
> of some part of the ligand in each docking solution compared to the
> X-ray structure).
>
> Assuming that the both pdbs ((docking poses, and X-ray structure))
> have been superimposed (based on the protein atoms) how could I
> automatically switch to the model (in the ensemble) with the identical
> position of the ligand as in the X-ray structure?  I would be grateful
> for any suggestions
> With kind regards,
> Enrico

Re: [PyMOL] set_view based on origin and a vector

[Jared S. <jar...@co...>]

Hi Wei -

Fun problem!  Not a "smart" way to do it, but I think functional, using
pseudoatoms and orient to set the view angle:

```
# Create an origin pseudoatom
ori_coords = [0.4017522, 23.15367207, 6.68992345]
cmd.pseudoatom("ori", pos=ori_coords)
color red, ori
show nb_spheres, ori

# Second pseudoatom as a stand-in for the camera
axis = [0.74, 0.18, -0.65]
cam_coords = [sum(x) for x in zip(ori_coords, axis)]
cmd.pseudoatom("cam", pos=cam_coords)

# Adjust the view so the sphere is centered and crosshairs are aligned on
camera Z axis
orient
center ori
turn y, -90

# Print the current view matrix
get_view
```
yields
```
set_view (\
    -0.673201025,    0.023786053,    0.739076912,\
     0.231151611,    0.956164062,    0.179775774,\
    -0.702402592,    0.291863978,   -0.649188757,\
     0.000000000,    0.000000000,  -14.178204536,\
     0.401752204,   23.153671265,    6.689923286,\
    11.178205490,   17.178203583,  -20.000000000 )
```
[image: image.png]

Hope that helps.

Cheers,
Jared


On Fri, Mar 25, 2022 at 12:44 PM Wei Wang <ww...@co...> wrote:

> Dear PyMOL community,
>
> I have a need to adjust my view point in python script. I want to achieve
> the following:
>
>    1. I have a origin with coordinates [ 0.4017522 23.15367207 6.68992345]
>    2. I have a vector/rotation axis [0.74, 0.18, -0.65]
>    3. I want to look directly down that vector using above origin.
>
> Theoretically I should be able to use those information to determine the
> values needed to put in set_view. However, I’m not smart enough to do that.
> Would anyone please show me the way?
>
> Many thanks,
>
> Wei
> _______________________________________________
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[PyMOL] set_view based on origin and a vector

[Wei W. <ww...@co...>]

Dear PyMOL community,

I have a need to adjust my view point in python script. I want to achieve the following:

1. I have a origin with coordinates [ 0.4017522 23.15367207 6.68992345]
2. I have a vector/rotation axis [0.74, 0.18, -0.65]
3. I want to look directly down that vector using above origin.

Theoretically I should be able to use those information to determine the values needed to put in set_view. However, I’m not smart enough to do that. Would anyone please show me the way?

Many thanks,

Wei

Re: [PyMOL] Analysis of docking results in multi-model format

[Enrico M. <jms...@gm...>]

Hello Joel,
Actually I am using VINA that indeed provides us with these RMSD
values. However the goal is to compare the docking poses with the
X-ray structure containing another (but very similar in terms of the
functional groups) ligand.
I've already tried some pymol built-in commands like pair_fit but I
could not adapt it to the multi-model pdb in order to select
"on-the-fly" the pose which has better similarity to the pose observed
in the X-ray structure.
Cheers,
Enrico

пт, 25 мар. 2022 г. в 01:28, Joel Tyndall <joe...@ot...>:
>
> Hi Enrico,
>
> Which docking protocol are you using as this may already have RMSD to a reference ligand and presentation of best poses (based on scoring)
>
> Joel
>
> -----Original Message-----
> From: Enrico Martinez <jms...@gm...>
> Sent: Friday, 25 March 2022 2:11 AM
> To: pymol-users <pym...@li...>
> Subject: [PyMOL] Analysis of docking results in multi-model format
>
> Dear Pymol Users!
> I am dealing with the analysis of the results of protein-ligand docking poses representing the multi-model pdb.  I need to find a possibility (e.g. via some script that could be executed in the pymol) to compare each docking pose with the X-ray structure (loaded as the separate model in pymol) in order to find automatically the model (= docking solution) which may fit better to it (e.g. via estimating RMSD of some part of the ligand in each docking solution compared to the X-ray structure).
>
> Assuming that the both pdbs ((docking poses, and X-ray structure)) have been superimposed (based on the protein atoms) how could I automatically switch to the model (in the ensemble) with the identical position of the ligand as in the X-ray structure?  I would be grateful for any suggestions With kind regards, Enrico
>
>
> _______________________________________________
> PyMOL-users mailing list
> Archives: https://apc01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.mail-archive.com%2Fpymol-users%40lists.sourceforge.net&amp;data=04%7C01%7Cjoel.tyndall%40otago.ac.nz%7C5801f6d4300c4429df4008da0d996aa8%7C0225efc578fe4928b1579ef24809e9ba%7C0%7C0%7C637837249971556989%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000&amp;sdata=%2FH4rWyrcccM8UDMCjpXhzfhvbWIRK7iVxT3WTHhd11Q%3D&amp;reserved=0
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Re: [PyMOL] Analysis of docking results in multi-model format

[Joel T. <joe...@ot...>]

Hi Enrico,

Which docking protocol are you using as this may already have RMSD to a reference ligand and presentation of best poses (based on scoring)

Joel

-----Original Message-----
From: Enrico Martinez <jms...@gm...> 
Sent: Friday, 25 March 2022 2:11 AM
To: pymol-users <pym...@li...>
Subject: [PyMOL] Analysis of docking results in multi-model format

Dear Pymol Users!
I am dealing with the analysis of the results of protein-ligand docking poses representing the multi-model pdb.  I need to find a possibility (e.g. via some script that could be executed in the pymol) to compare each docking pose with the X-ray structure (loaded as the separate model in pymol) in order to find automatically the model (= docking solution) which may fit better to it (e.g. via estimating RMSD of some part of the ligand in each docking solution compared to the X-ray structure).

Assuming that the both pdbs ((docking poses, and X-ray structure)) have been superimposed (based on the protein atoms) how could I automatically switch to the model (in the ensemble) with the identical position of the ligand as in the X-ray structure?  I would be grateful for any suggestions With kind regards, Enrico


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[PyMOL] Analysis of docking results in multi-model format

[Enrico M. <jms...@gm...>]

Dear Pymol Users!
I am dealing with the analysis of the results of protein-ligand
docking poses representing the multi-model pdb.  I need to find a
possibility (e.g. via some script that could be executed in the pymol)
to compare each docking pose with the X-ray structure (loaded as the
separate model in pymol) in order to find automatically the model (=
docking solution) which may fit better to it (e.g. via estimating RMSD
of some part of the ligand in each docking solution compared to the
X-ray structure).

Assuming that the both pdbs ((docking poses, and X-ray structure))
have been superimposed (based on the protein atoms) how could I
automatically switch to the model (in the ensemble) with the identical
position of the ligand as in the X-ray structure?  I would be grateful
for any suggestions
With kind regards,
Enrico

[PyMOL] fixing atom order in multi-model pdb

[Enrico M. <jms...@gm...>]

Dear Pymol Users!
I am dealing with the multi-model pdb containing the docking poses
that were merged with the protein atoms. Initially the part containing
the ligand poses also included some flexible side-chains of the
receptor (obtained from VINA) that were subsequently merged ( in each
model) with the static part of the protein using some script.

The complex may be correctly visualised in pymol, however (due to the
reorganizations of the atoms in the protein part) there are some
problems in the visualisations of the interatomic interactions between
the static part of the protein and the ligands.

May we use some pymol in no-gui mode to "fix" the atomic order problem
in the loaded pdb (in each models!) and then save it as a new pdb?
Here is the model of the workflow:

pymol -c -d "
from pymol import cmddb')
cmd.load('complex.pdb')
# execute some command to fix atom order in the multi-model pdb
cmd.save('complex_fixed_pdb.pdb')
"

Re: [PyMOL] pymol cartoon for hexamer

[<tna...@os...>]

Hi,

You have to predict how six monomers assemble into a hexamer.
This can be done by AlphaFold multimer or ColabFold notebook.

Best regards,

Takanori Nakane

________________________________________
差出人: vivek ambastha <vi...@mi...>
送信日時: 2022年3月22日 12:56
宛先: pym...@li...
件名: [PyMOL] pymol cartoon for hexamer

Hello all,
I am naïve to pymol or even protein structure. I need help in creating the hexameric model of a protein whose structure is in predicted through alpha folds.
I can download the monomer. My objective is to develop a cartoon for the hexamer using these six individual monomers. Is this possible using Pymol? If yes then how to do that

Best,

Vivek.A

[PyMOL] pymol cartoon for hexamer

[vivek a. <vi...@mi...>]

Hello all,
I am naïve to pymol or even protein structure. I need help in creating the hexameric model of a protein whose structure is in predicted through alpha folds.
I can download the monomer. My objective is to develop a cartoon for the hexamer using these six individual monomers. Is this possible using Pymol? If yes then how to do that

Best,

Vivek.A

[PyMOL] RMSD from DCD

[Mcguire, K. <klm...@UC...>]

I have been using VMD for most of my MD analysis, but I am trying to learn PyMol now.  I know how to load a pdb and a dcd onto that pdb.  But how do I measure the RMSD of each frame in the DCD aligned to the starting structure, and then output a graph like of RMSD vs frame? Doing this through scripting would be great. Thanks!

Re: [PyMOL] Combine two states into one state?

[Thomas H. <th...@th...>]

Hi Nicholas,

You can use the "split_states" command.
https://pymolwiki.org/index.php/Split_states

Cheers,
  Thomas

On Wed, Mar 16, 2022 at 6:57 AM Nicholas Gao <dom...@gm...> wrote:
>
> Dear PyMOL users,
>
> I have an antibody-antigen structure where the authors have put the antigen atoms in state 1 and put the antibody atoms in state 2.  Is there a good way via command line to collapse state 1 and 2 into a single state, where both antibody and antigen atoms are viewable together?
>
> Sincerely,
> Nicholas Gao
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