pymol-users — Collaborative support and tips for PyMOL users

Re: [PyMOL] pymol education license

[Xiang Z. <zx...@ma...>]

-----Original Messages-----
From:"Xiang Zhang" <zx...@ma...>
Sent Time:2022-06-17 12:13:07 (Friday)
To: pym...@li...
Cc:
Subject: pymol education license

Hi 
I can't receive pymol education license in my mail box even though I tried 2 mail address.


Best,
Xiang Zhang

[PyMOL] Default altloc selection

[Ioannis R. <riz...@eb...>]

Hello,

Is there a way to set a default altloc to be selected, if the residue/atom is disordered? I can do this manually with a notation like ‘select foo, obj//chain/resid/atom and alt A’ but if the residue/atom is not disordered, the selection will be empty (I call this through a script for a set of structures so I cannot know if there is disorder beforehand). 

If the ‘and alt A’ conditional is omitted, all the alternative residues/atoms are selected, but I don’t want that. It would be very handy to be able to select a default altloc for these kinds of selections.

Cheers,

--
Ioannis G. Riziotis
PhD Fellow - Thornton Group
European Bioinformatics Institute (EMBL-EBI)
European Molecular Biology Laboratory
Wellcome Trust Genome Campus
Hinxton
Cambridge CB10 1SD
United Kingdom

Re: [PyMOL] apbs: program locations

[Matic K. <Mat...@ki...>]

Hi Michael,

if you haven't figured it out yet, this thread might help you:
https://sourceforge.net/p/pymol/mailman/pymol-users/thread/EAA6862A-4914-483F-A12F-92B5A1E81233%40schrodinger.com/

It can be done in the configuration file of the plugin.

Best regards!
Matic


On 1. 06. 22 05:26, mic...@gm...<mailto:mic...@gm...> wrote:
Dear all,

Can I save the “program locations” information in APBS plugin? Once I exit the plugin and open it again, the previous input disappears.
I am using windows version pymol.

Thank you very much.

Michael


[cid:par...@ki...]




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[PyMOL] morphing problem

[Criss H. <cri...@gm...>]

I have two objects of the same protein in different conformational states
and I want to show the conformational change using morph.
Each object is a homopentamer, chains A-E.
However, one object has the chains arranged in a clockwise direction and
the second object has them arranged in a counterclockwise direction. When I
morph them, I get a wierd twisty thing as a result of chains swapping with
one another.
I tried to fix this by changing the names of the chains (alter PDB1 and
chain B, chain="E" ...and so on) so that now chain names A-E of both PDBs
are clockwise. Although I succeed in renaming the chains, this has has no
effect on the morphing. SO, I wondered if the segment identifer was the
problem. Each chain also has a corresponding segment identifier (for
example, originally PDB1/B/B which has now been changed to PDB1/B/E). I
tried changing the segment identifier using the same syntax (alter PDB1 and
segment B, segment="E"). Although the output message shows "modified 2667
atoms" the segment identifier in the sequencce window does not change and
selection of segment E yields nothing and the morphing is unchanged.
Sorry for the long narrative, but the main question is: what can I do to
make this morphing work? Thanks.

Re: [PyMOL] [EXTERNAL] PyMOL scripting issues

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

 Hi Martin,

Which version of PyMOL are you using?
How did you install PyMOL?
These details matter because there are several paths for installing PyMOL on Linux.
Some paths use the system python and some do not.
The incentive PyMOL has Anaconda Python bundled inside.

You could install Ancaonda3 and then create a conda env called pymolconda.
Then you can activate this env, install pymol with conda, and then call pymol as module with the Anaconda Python.

Best regards,

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: Martin Urban <mar...@st...>
Sent: Saturday, June 11, 2022 2:34 AM
To: pym...@li... <pym...@li...>
Subject: [EXTERNAL] [PyMOL] PyMOL scripting issues

Hello,

I have a problem with PyMOL. I am writing a more complex automation
script, and I want to import pymol's cmd module. The problem is that the
python interpreter on my linux system doesn't recognize pymol and it
throws an ModuleNotFound Error. I have a Ubuntu system and I installed
pymol with the apt package manager. Does anyone know how the systems
python3 interpreter can find the cmd module from PyMOL?

Greetings from Germany,

Martin

--

Martin Urban

Westfälische Hochschule / Westphalian University of Applied Sciences
Fachbereich Ingenieur- und Naturwissenschaften (FB 8) / Department of
Engineering and Natural Sciences
August-Schmidt-Ring 10
D-45665 Recklinghausen, Germany


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[PyMOL] PyMOL scripting issues

[Martin U. <mar...@st...>]

Hello,

I have a problem with PyMOL. I am writing a more complex automation 
script, and I want to import pymol's cmd module. The problem is that the 
python interpreter on my linux system doesn't recognize pymol and it 
throws an ModuleNotFound Error. I have a Ubuntu system and I installed 
pymol with the apt package manager. Does anyone know how the systems 
python3 interpreter can find the cmd module from PyMOL?

Greetings from Germany,

Martin

--

Martin Urban

Westfälische Hochschule / Westphalian University of Applied Sciences
Fachbereich Ingenieur- und Naturwissenschaften (FB 8) / Department of 
Engineering and Natural Sciences
August-Schmidt-Ring 10
D-45665 Recklinghausen, Germany

[PyMOL] black shadows on povray mesh2

[Suzuki, R. <rs...@af...>]

Hello,

Do you have any idea to calculate nice normal vectors that can be
rendered cleanly?

When I draw with povray using include files created by pymol, sometimes
black shadows appear on the secondary structures, especially in the
planes near perpendicular to the picture.

I removed the normal vectors and these shadows disappeared. But the
smoothing process between the triangles that make up the mesh2 objects
was also not performed.

I calculated the average of the unit normal vectors of the triangles
that contain each vertex and compose the same plane and set in place of
the original normal vectors, and the black shadows disappeared.
Smoothing also took place, but was less smooth than in the original
file. Also, some edges was emphasized compared to the original.

Thanks,

Rintarou

[PyMOL] apbs: program locations

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

Dear all,

 

Can I save the "program locations" information in APBS plugin? Once I exit
the plugin and open it again, the previous input disappears. 

I am using windows version pymol.

 

Thank you very much.

 

Michael

 

 

[PyMOL] setting specific state in no-gui mode

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

Dear Pymol Users!
I am using pymol in batch mode to select specific state from the
multi-state object and then save screen-shoot and the pse session for
it.

cmd.set('state','5','my_object*')
cmd.png('image.png',dpi=50,ray=1)
cmd.save('session.pse')

The problem is that in the pse session I may see only the selected
state. I've tried to change the states using arrows in the GUI but it
always frozen to the state selected before saving the pse session. Is
it possible via some command to reset to the default (1) state before
saving the pymol session ?
Cheers,
Enrico

[PyMOL] ImportError when launching open-source pymol

[Ioannis R. <riz...@eb...>]

Hello,

Anyone any idea how to tackle this error when launching pymol after compiling from source?

ImportError: /hps/software/users/xx/xx/miniconda3/envs/py3/lib/python3.8/site-packages/pymol/_cmd.cpython-38-x86_64-linux-gnu.so: undefined symbol: _Z15MapSetupExpressP7MapType

Trial version works fine though.

Cheers,
Yannis

--
Ioannis G. Riziotis
PhD Fellow - Thornton Group
European Bioinformatics Institute (EMBL-EBI)
European Molecular Biology Laboratory
Wellcome Trust Genome Campus
Hinxton
Cambridge CB10 1SD
United Kingdom

[PyMOL] Help superimposing protein and sugar

[Savannah S. <sav...@gm...>]

Hello all,

TLDR; What’s the best way to place one molecule over a geometrically similar but unrelated second molecule?

I’m a scientist studying the docking of glycans to antibodies. I’m trying to use pymol to position my glycan, a 10-mer called gxm, close to its putative binding site. My glycan has a protein mimetic, p1, an 11-mer, that I already have docked to my antibody. 

Since p1 and gxm have similar structures, I’d like to align gxm as close as possible to where p1 goes on my p1-antibody co-crystal structure. However, since my glycan and my protein have no sequence alignment, I haven’t been able to use align, super, fit, etc. I tried using pair fit and pymol kept crashing when I called it. Cealign sounded like a good option, but, because I’m using a 10-mer and an 11-mer, I got an error that the sequences were too short.

The best I’ve been able to do is translate gxm to p1’s center of mass, then manually adjust gxm with my mouse. However, that’s obviously imprecise. Does anyone have any ideas for how I could overlap my glycan more closely to my protein?

Thanks!

Savannah Speir

Post Baccalaureate Fellow
Rosetta Commons
Johns Hopkins University

[PyMOL] Problem to get RMSD between crystal ligand and docked ligand

[Maximiliano J. G. t. <max...@co...>]

Hello everyone, I am trying to obtain the RMSD value between a docked
ligand I got with Autodock Vina (PDBQT file) and a crystal ligand structure
i downloaded from rcsb.org (PDB file).

The thing is when I open the crystal ligand file on PyMOL this error
appears:

Warning: Invalid characters in 'MLN_Cristalizado_PDB' have been
replaced or stripped
 ObjectMolecule: Read crystal symmetry information.
 CmdLoad: "" loaded as "MLN_Cristalizado_PDB".


And when I try to run the rms command this error appears:


PyMOL>rms MLN_Cristalizado_PDB (crystal ligand), MLN_H-4760_prueba21R4L
(docked ligand)
ExecutiveRMS-Error: No atoms selected.


Previously running the rms command, I run these commands:


alter all, segi=""

alter all, chain=""


How can I get an easier way of solving this problem? Can I get an
approximate RMSD value with another command?


I attach the two files for you to try for yourselves if you want to.


I want to add that when i open the two files on the notepad the identifiers
of the atoms are different, I have also gotten the error of mismatched
identifiers before too.


Thanks in advance to anyone who replies, good luck!

[PyMOL] why does coordinates not overlap with map

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

Dear pymol users,

I have a coordinate file (pdb) and a map file (mtz), and I want to make a image that shows both the coordinate and the map. I generate a .map.ccp4 file using fft in CCP4 program. However, when I open the pdb file and the .map.ccp4 in pymol, I find the coordinates are out of the map. Please see the image at the following link:
       https://drive.google.com/file/d/1TmH-mFCnsCNghcq4RQJ9mNOBlTfCRsHW/view?usp=sharing
Could anyone tell me how to map them overlap?

Thank you in advance.

Best regards

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

-- 
Dr.Marco Sette, Ph.D.
Department of Chemical Sciences and Technology
University of Rome, "Tor Vergata"
via della Ricerca Scientifica, 00133, Rome, Italy
e-mail: se...@un...
e-mail: m7...@ya...
Tel.: +39-0672594424
Fax: +39-0672594328
http://stc.uniroma2.it/?page_id=622&cn-entry-slug=marco-sette


Ai sensi del Regolamento (UE) 2016/679 e dei principi contenuti nelle linee guida del Garante per posta elettronica e interne (artt. 2 e 15 Cost.; Corte cost. 17 luglio 1998, n. 281 e 11 marzo 1993, n. 81; art. 49 Codice dell’amministrazione digitale) si precisa che le informazioni contenute in questo messaggio -come pure i dati esteriori delle comunicazioni e i file allegati- sono riservate e ad uso esclusivo del destinatario. Divulgazione, copia, stampa o qualunque altro uso da parte di altri non è autorizzato. Qualora il messaggio in parola Le fosse pervenuto per errore, La preghiamo di eliminarlo senza copiarlo e di non inoltrarlo a terzi, dandocene gentilmente comunicazione al seguente indirizzo e-mail pr...@un....

On the basis of “(UE) Rules 2016/679 and the codes in general guidelines of Garante for electronic and internal mail (artt. 2 e 15 Cost.; Corte cost. 17 luglio 1998, n. 281 e 11 marzo 1993, n. 81; art. 49 Codice dell’amministrazione digitale) information here contained and any attachments is confidential and intended for the recipient(s) only. Dissemination, copying, printing or use by anybody else is unauthorized. If you are not the intended recipient, please delete this message and any attachments and advise the sender by return e-mail to pr...@un....

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
-- 
logo-ipbs


  Lionel Mourey


    CNRS research Director | Team leader

+33 5 61 17 54 36 | +33 6 73 50 95 51 | Lio...@ip... 
<mailto:Lio...@ip...>

UMR5089 | CNRS - UT3 | 205 Route de Narbonne BP 64182 - 31077 Toulouse 
Cedex 4

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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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-- 

*Eduardo José Azevedo Corrêa*

Biólogo| Professor e Pesquisador


(37)9997-5771

(37)3271-4673

*www.epamig.br <http://www.epamig.br/>*

*EPAMIG Pitangui*
Rodovia BR - MG352 Km35 Zona Rural

Caixa Postal 43

CEP 35650-000 - Pitangui - MG