Re: [PyMOL] (no subject)

[Thomas H. <sp...@us...>]

Hi Noloofar and Lina,

>> I would like to calculate partial charges of my pdb. Is it possible to do it
> 
> In pymol:
> 
> Action-> compute -> partial charge sum

this doesn't calculate partial charges, sorry.

This does:
Action -> generate -> vacuum electrostatics

But better would be to use pdb2pqr:
http://www.poissonboltzmann.org/pdb2pqr

>> I have another question too, when aligning two structure in Pymol, there is
>> a RMSD for the total structure, is there any command to calculate the RMSD
>> for a specific region of the alignment.

If the two structures have the same sequence (same atom identifiers) and 
you don't need an "alignment", you can use rms_cur.

http://pymolwiki.org/index.php/Rms_Cur

Cheers,
   Thomas

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