It sounds like this question might be more appropriate for the PyMOL list since that is the program which downloads and loads the PDB files.
Chief Scientist for Signature Science
Pacific Northwest National Laboratory
From: Afonso Duarte [mailto:duartenl@...]
Sent: Monday, September 13, 2010 4:18 PM
Subject: [Apbs-users] Problem when running APBS 1.1.0 - protein is misplaced
De: Afonso Duarte <duartenl@...>
Assunto: Problem when running APBS 1.1.0 - protein is misplaced
Data: Segunda-feira, 13 de Setembro de 2010, 12:16
I am running APBS 1.1.0. via the "APBS Tools2" plugin on Pymol 1.3 (either on Linux or Vista).
As usual i fetch a pdb structure and then do a "set grid" and then "run APBS".
This works fine for most of the proteins I am working on, however I found out that in some of the pdbs (downloaded directly from the PDB databank) I get half of the protein outside of the box (pymol_generated). This leads to the calculation of only half of the electrostatics of the molecule...
I am sending in attach a pic of what I get in my screen...
does any body know how to solve this problem ?