Re: [PyMOL] Electrostatic surface visualization

[Gerebtzoff, G. <gre...@ro...>]

Marco,

Maybe you could replace (alter) the B-factor of your protein with the
electrostatic values, and color it accordingly; some googling should
give you more hints about how you could solve this issue, like
http://pldserver1.biochem.queensu.ca/~rlc/work/pymol/data2bfactor.py
and
http://pldserver1.biochem.queensu.ca/~rlc/work/pymol/color_b.py
from Robert Campbell.
A lot of useful scripts are posted on his website:
http://pldserver1.biochem.queensu.ca/~rlc/work/pymol/

Cheers,

Greg


-----Original Message-----
From: se...@un... [mailto:se...@un...]=20
Sent: Saturday, March 03, 2007 11:40 AM
To: pym...@li...
Subject: [PyMOL] Electrostatic surface visualization


Dear all,

I'm new to this list and to the software.
I used PyMOL and APBS to calculate an electrostatic surface for a
small protein (I'm using the WindowsXP version) and everything seems
fine.
Now I would like to visualize this surface AND the secondary structure
of the protein, in order to understand the positive and negative
regions.
How I can do? Some software show the surface in trasparency but it
seems this is not possible in PyMOL.

A related question: it is possible to color the secondary structure
according to the electrostatic surface properties? I have an NMR
titration of
this protein with its partner: I would like to relate the shifts of
the NH backbone with the electrostatic surface.

I looked at the archive but I haven't found an answer.

Thanks in advance,
Marco




Dr.Marco Sette, Ph.D.

Department of Chemical Sciences and Technology
University of Rome, "Tor Vergata"
via della Ricerca Scientifica, 00133, Rome, Italy
e-mail:        se...@un...
Tel.:          +39-0672594424
Fax:           +39-0672594328