Comments on: PyMOL scripts

By: Ajay joshi

Ajay joshi — Fri, 24 Jun 2011 12:46:00 +0000

Hi Angela , the problem u can solve easily on VMD software

By: amber

amber — Sat, 26 Mar 2011 10:26:39 +0000

can some body tell me the way to find hydrophobic and ionic interaction using pymol????

Thanks in advance

By: Anto01

Anto01 — Thu, 02 Sep 2010 20:51:44 +0000

Hi, I would like to ask if anyone knows how to build D aminoacid peptide with PYMOL, Thanks for any help!
Anto01

By: Dustin

Dustin — Tue, 31 Aug 2010 21:35:26 +0000

Hi,

I am having some trouble and thought someone here might be able to answer my question. I am trying to make a model of a fusion protein using pymol. I want to create a model composed of four triangular proteins arranged into a tetrahedron, but not placed against each other. The proteins are to be connected by a peptide linker. Does anyone know how to spacially modify proteins independently of one another? Also I was trying to fuse a peptide to a protein but I received an error that “bond was not created”. The peptide and protein is located far from each other, as I noted I don’t know how to manipulate things independantly, is that the problem. I appreciate any help and advice.

Thanks,

Dustin

By: barry kesner

barry kesner — Mon, 26 Jul 2010 12:34:55 +0000

I am trying to copy the color of one object from another. How do you do this?

By: ken_mo

ken_mo — Mon, 14 Jun 2010 17:50:07 +0000

hi every1,

I am trying to get pymol to color based on occupancy (which i’ve edited to suit my purpose), but there seems to be no option to do it.There, only seems to be an option to color it by b-factor……..pls help

By: admin

admin — Tue, 20 Apr 2010 20:26:25 +0000

You can load any structure of a protein-protein complex and examine the different features of the interactions such as the details of the interface.

By: Kaushik

Kaushik — Tue, 20 Apr 2010 10:59:51 +0000

how can we represent protein-protein interactions using pymol??

By: Angela

Angela — Fri, 16 Apr 2010 10:54:33 +0000

Hi everyone,

I am trying to find a way, in Pymol, to remove an amino acid from a peptide and insert any other amino acid. I have been able to do this for one residue at a time using the command

editor.attach_fragment(‘pk1′,’my_fragment_name’,11,0)

but I have to do this in two parts so that the new amino acid binds at both ends. I was wondering if there is a way in which Pymol can “swap” an existing side chain at position N on the peptide for any other side chain in an automated fashion?

Any help much appreciated.

Angela

By: Teek

Teek — Fri, 11 Dec 2009 08:42:31 +0000

If it’s just a question of renumbering all the residues in an object/selection based on some offset, then just use alter in PyMol. Adapted from the alter documentation:

alter (objectname/selection), resi=str(int(resi)+100)