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: [email protected] [mailto:[email protected]] Sent: Saturday, March 03, 2007 11:40 AM To: [email protected] 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: [email protected] Tel.: +39-0672594424 Fax: +39-0672594328
