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
Regards
Joel
From: James Starlight [mailto:jmsstarli...@gmail.com]
Sent: Friday, 27 April 2012 8:25 p.m.
To: pymol-users
Subject: Re: [PyMOL] Editing of the pdb structure
Dear all!
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
James
26 апреля 2012 г. 12:55 пользователь James Starlight
<jmsstarli...@gmail.com<mailto:jmsstarli...@gmail.com>> написал:
Thanks Thomas!
Another question-
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
<spel...@users.sourceforge.net<mailto:spel...@users.sourceforge.net>> написал:
Hi James,
use the alter command:
alter chain "", chain="A"
See also http://pymolwiki.org/index.php/Alter
Cheers,
Thomas
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?
James
--
Thomas Holder
MPI for Developmental Biology
Spemannstr. 35
D-72076 Tübingen
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