Re: [PyMOL] Valence_Mode issue

[Ali K. <aku...@un...>]

Hi Vijay,

I have never through to use PyMOL to look at 2D molecules, its an interesting idea but software like chemdraw will offer you more functionality for situation like this.

Have you tried applying the valuence_mode command to a selection, i.e.:

Set valuence_mode, 1, testing # applies it to the “testing” object in the PyMOL session

Kind regards,

Ali

From: "Dr. Vijay Masand" <vij...@gm...>
Date: Sunday, 21 June 2020 at 5:58 pm
To: pymol-users <pym...@li...>
Subject: [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?
[cid:image001.jpg@01D647FD.0528DB70]

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://protect-au.mimecast.com/s/822SCWLVXkUl8Vm3t6wWP3?domain=sites.google.com/>