Re: [PyMOL] [EXTERNAL] Valence_Mode issue

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

Hi Vijay,

It is unlikely that PyMOL can correctly interpret the atom names in your ligand. 
I suspect that you have to manually unbound and then bond each pair of atoms
of interest in your ligand. You can do so by pasting a pair of commands like 
the following on the command line at the PyMOL> prompt below the command history window.

unbond name CBE, name CBF;bond name CBE, name CBF, 2

See the  attached images for a ligand after applying the above two commands.
The Ball-and-Stick representation is found in the Presets under the A menu
in the internal gui on the right.

You can get the atom names printed to the command history window 
by switching the selection mode in the lower right hand corner to 'Atoms' and 
then left-click on the atom of interest.


Explanation:

One would hope that the following command would work:

set valence, 1, ligand; set valence_mode, 1, ligamd

See https://pymolwiki.org/index.php/Valence

A work around would be to add the ligand atoms of interest the wonderful script by Andreas Warnecke:

https://raw.githubusercontent.com/Pymol-Scripts/Pymol-script-repo/master/format_bonds.py

This will require edits in several locations, but it would provide a longer term solution.
See https://pymolwiki.org/index.php/Format_bonds

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: Dr. Vijay Masand [vij...@gm...]
Sent: Sunday, June 21, 2020 2:53 AM
To: pymol-users
Subject: [EXTERNAL] [PyMOL] Valence_Mode issue

Dear All
I am trying to get a nice 2D- like representation for a small molecule using PyMOL.

I am using PyMOL 2.4 (Windows 10, Python3). I tried to set valence and valence_mode to get 'bonds inside' using the following commands:

set valence, 1
set valence_mode, 1

Unfortunately, I am getting 'delocalized bonds' for a small molecule. Please see the attached figure. How to activate valence_mode?
[Pymol-Issue-Valence-Mode.jpg]

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/<https://urldefense.proofpoint.com/v2/url?u=https-3A__sites.google.com_site_vijaymasand_&d=DwMFaQ&c=VjzId-SM5S6aVB_cCGQ0d3uo9UfKByQ3sI6Audoy6dY&r=k0gMbcsdOcdbPUNV5tW66KQSZfXL0ewVDPVBp7tqbks&m=9MKqEVQDvZHvSVvXmAO0iMXc1SCkh4ZQH2hhrRwy6XE&s=qmWnnUG9myB1HzBx_ttJjOPs1FaJRMYe3F8xI6qvmrU&e=>