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 []
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



26 апреля 2012 г. 12:55 пользователь James Starlight <> 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 <> написал:


Hi James,

use the alter command:

alter chain "", chain="A"

See also


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?



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