Surely you could use pymol mutagenesis wizard to do tis.
Also James, It is a good practice to start a new thread (new email with new subject for each set of questions you have
From: James Starlight [mailto:email@example.com]
Sent: Friday, 27 April 2012 8:25 p.m.
Subject: Re: [PyMOL] Editing of the pdb structure
I want to prepare my pdb structure for MD simulation. I've done all required things but my protein consist of some missing heavy atoms the list of which I've obtained from my pdb hedader
REMARK 470 M RES CSSEQI ATOMS
REMARK 470 ARG A 220 CG CD NE CZ NH1 NH2
REMARK 470 ARG A 222 CG CD NE CZ NH1 NH2
REMARK 470 ASN B 212 O CG OD1 ND2
REMARK 470 LYS C 43 CG CD CE NZ
REMARK 470 GLY C 225 O
I've heard that there are some web servers wich could be usefull to build such missing atoms.
In particular in my structure there are lack not only side chain atoms but also two backbone Oxygens in the Gly and Asn wich could be the main problem of such task.
In any case I'll be very thankfull if you provide me with such server
26 апреля 2012 г. 12:55 пользователь James Starlight <firstname.lastname@example.org> написал:
I have my protein.pdb with some inserted crystall waters within protein interiour as well as water surrounded of my protein. I want to remove only sorrounding water but prevent internal water ( wich could be functional relevant ).
How I could to select such surrounded water ( e.g via some cutoff radius relative my protein etc) wich I'd like to remove further ?
26 апреля 2012 г. 11:22 пользователь Thomas Holder <email@example.com> написал:
use the alter command:
alter chain "", chain="A"
See also http://pymolwiki.org/index.php/Alter
James Starlight wrote, On 04/26/12 09:18:
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?
MPI for Developmental Biology