[PyMOL] Coordinates of an atom

Hi all, Can anyone please help me in how to get coordinates of a selected atom or residue? Thank you Mohsen -- ___ PyMOL-users mailing list

[PyMOL] difficulty opening EmrE protein (pdb: 3B5D) in Pymol

Hi everyone, Can someone please assist me opening this pdb file? I am trying to open EmrE protein (pdb: 3B5D) in Pymol a and show it as cartoon representation, but it opens up as many little cross signs seem to be corresponding to CA atoms. When I try to preset it pretty or any other preset

[PyMOL] difficulty using Python scripts in PyMOL

Hi all, I have difficulty using Python scripts in PyMOL. I cannot install PyMOL in a way that is compatible to Python. I initially installed Python 3.5.2, and then PyMOL 1.7.4. But PyMOL doesn't recognise a Python script file that I have created in NotePad++. I have put the file in PyMOL active

[PyMOL] ray command

Hi Pymol users, The "ray command" is not working in my Educational version of Pymol. It seems that educational version does not allow to use this command. Does anyone have a solution for this please? Your reply is very much appreciated. Cheers Mohsen

Re: [PyMOL] Alignment of two proteins

uld work. Amin. On 2016-02-25 17:02, Mohsen Chitsaz wrote: Hi Julian, I have two homotrimer proteins, i.e. 3aob and 4mt1. I want to align chain A of 4mt1 to chain B of 3aob. How to tell Pymol to align a specific chain or part of a protein, in my case chain A of 4mt1, to a specific chain or part of

Re: [PyMOL] Alignment of two proteins

Mohsen From: Mohsen Chitsaz Sent: Wednesday, 24 February 2016 11:17 PM To: 'Julian Heinrich' <jul...@joules.de> Cc: pymol-users@lists.sourceforge.net Subject: RE: [PyMOL] Appending a pdb file Hi Julian, Many Thanks for your help. It worked. Cheers Mohsen From: julian.heinr...@gma

Re: [PyMOL] Appending a pdb file

Hi Julian, Many Thanks for your help. It worked. Cheers Mohsen From: julian.heinr...@gmail.com [mailto:julian.heinr...@gmail.com] On Behalf Of Julian Heinrich Sent: Monday, 22 February 2016 8:24 PM To: Mohsen Chitsaz <mohsen.chit...@flinders.edu.au> Cc: pymol-users@lists.sourcefor

[PyMOL] Appending a pdb file

Hi In order to superimpose two protein sequences, I am trying to append a pdb file to an existing protein sequence, which I have already opened in PyMol. The append function is not working in my PyMol. Could someone help me with this please. Cheers Mohsen

[PyMOL] PyMol Question

Hi there, I was wondering how I can make the surface of a selected part of a protein transparent? I tried transparency command, but, I came up with a message that "transparency" was not found. Thank you --