It appears that PyMOL is writing out an improperly-formated PDB file here
(the coordinate sections do not start at the correct columns). I'm looking
into it.
Thanks,
-Michael
On Tue, Sep 14, 2010 at 10:42 AM, Afonso Duarte <[email protected]>wrote:
>
> Dear All,
>
> 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 ?
> Best
>
> Afonso
>
>
>
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--
Michael Lerner, Ph.D.
IRTA Postdoctoral Fellow
Laboratory of Computational Biology NIH/NHLBI
5635 Fishers Lane, Room T909, MSC 9314
Rockville, MD 20852 (UPS/FedEx/Reality)
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