Dear PyMol users!


I have some structure.pdb from the md simulation wich consist of 1 chain not defined in the pdb file explicitly ( missing chain id in the pdb file). So the pymol recognise that chain as the  ' '  . I need to rename this chain to the desired name ( e.g to chain A ).

How I could do it?

James

1 апреля 2012 г. 15:04 пользователь James Starlight <jmsstarlight@gmail.com> написал:
Thomas,


thank you I'll test your script with modeller after obtaining of this software on my workstation and post here results :)


James

1 апреля 2012 г. 12:30 пользователь Thomas Holder <speleo3@users.sourceforge.net> написал:

Hi James,

I use Modeller for exactly such tasks (build missing residues). It's free for academic use.

http://salilab.org/modeller/

Using modeller is also not "comfortable" since it only has a python scripting interface and thus requires you to write a script for each task. But I wrote a general purpose automodel client which is quite convenient for simple modelling tasks. See attachment.

Usage:
python automodeller.py sequence.fasta template.pdb

I provide this script "as is" without any warranty :) Let me know if it works for you.

Cheers,
 Thomas

James Starlight wrote, On 04/01/12 08:55:

Hi Thomas!

Thanks for help- this works good :)


By the way I have some question not about pymol :)
 I've already looked for some software for processing of my PDB structure for a long time ( often I need to build missing residues and flexible LOOP fragments with some refining of the result ). For such purposes I've used amber tools software but I've found that this tools are not very comfortable for me :)

Also I've found exactly what I need for in the MAESTRO's prime module but this tools avialable for the licensing only.

Is there any other free software for structure processing with easy-to-use interface and free academical ussage ?

Thanks again

James

--
Thomas Holder
MPI for Developmental Biology
Spemannstr. 35
D-72076 Tübingen