[PyMOL] morphing with heteroatoms

Hello all, I am trying to morph two structures using the commercial version of Pymol. Pymol looses heteroatoms (zinc in my case) while morphing. Is there any way around this? (I tried replacing zinc with water and linking it to the protein using CONECT - didn't work) Thanks for your help. Kar

Re: [PyMOL] morphing with heteroatoms

Hi Karthik, Have you tried writing a script based on the "Morphing with Ligand" example? http://wiki.pymol.org/index.php/Morph#Morphing_with_Ligand Cheers, Thomas On 02 Oct 2015, at 09:50, Karthik Rajasekar wrote: > Hello all, > > I am trying to morph two structures using the commercial ve

[PyMOL] measuring wizard

Hi PyMOL users, In measuring wizard I'm consistently facing an annoying property that allows me to measure only one distance between object1 and symmetry mate invoked through symexp command. Whenever I click another atom on symmetry mate a completely different atom from object1 is being chosen.

Re: [PyMOL] measuring wizard

I've run into this before as well. I think the simplest work around is just to alter the chain of the symmetry mate. --paul On 10/02/2015 02:58 PM, Oganesyan, Vaheh wrote: > Hi PyMOL users, > > In measuring wizard I'm consistently facing an annoying property that allows > me to measure only one

Re: [PyMOL] measuring wizard

Hi Vaheh, What PyMOL version do you use? Version 1.4 to 1.6 couldn't handle duplicated IDs with dynamic_measures=1. So either set dynamic_measures to 0, or assign unique IDs with: alter all, ID = index Cheers, Thomas On 02 Oct 2015, at 14:58, Oganesyan, Vaheh wrote: > Hi PyMOL users, > >

Re: [PyMOL] measuring wizard

Thank you reply, Thomas. Invoking alter all, ID = index didn't help. Regards, Vaheh Oganesyan www.medimmune.com -Original Message- From: Thomas Holder [mailto:thomas.hol...@schrodinger.com] Sent: Friday, October 02, 2015 4:05 PM To: Oganesyan, Vaheh Cc: pymol-users@lists.sourceforge.

Re: [PyMOL] measuring wizard

Hi Vaheh, I checked the release notes, there was actually a picking bug related to measurement labels, this was fixed in 1.7.6.2. As an immediate workaround, hide all labels before creating the next measurement. Cheers, Thomas On 02 Oct 2015, at 16:15, Oganesyan, Vaheh wrote: > Thank you r

Re: [PyMOL] measuring wizard

Thank you. Will upgrade. Regards, Vaheh Oganesyan www.medimmune.com -Original Message- From: Thomas Holder [mailto:thomas.hol...@schrodinger.com] Sent: Friday, October 02, 2015 4:34 PM To: Oganesyan, Vaheh Cc: pymol-users@lists.sourceforge.net Subject: Re: [PyMOL] measuring wizard Hi V