Re: [PyMOL] APBS problem

[Thomas Holder]

Hi Warren,

run pdb2pqr with the "--whitespace" argument to make sure the columns
are separated with whitespace.

If you still want to adjust the coordinates, you can use the
"alter_state" command in PyMOL.

alter_state 1, all, (x,y,z)=(x+100,y+100,z+100)

http://www.pymolwiki.org/index.php/Alter_State

Cheers,
   Thomas

Warren Gallin wrote, On 08/30/12 06:54:
> Hi,
> 
> I am having trouble running APBS on a structure, and it appears to be
> because some of the coordinates are -100 or more negative.  This
> leads to APBS reading numbers from adjacent columns as concatenated
> strings because there is no space between the columns.
> 
> This is happening either if I use the plugin or run PDB2PQR and APBS
> as stand-alone applications.
> 
> If I can adjust the co-ordinates such that the relative positions of
> the atoms do not change but the coordinates stay greater than -100 I
> think that the problem would be solved.
> 
> Has anyone ever encountered this problem, and is there a simple
> solution in PyMol to adjust the coordinates and then save a simple
> PDB file with the corrected values?
> 
> Thanks,
> 
> Warren Gallin

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

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Re: [PyMOL] Weird behavior of MacPyMOL

[Jason Vertrees]

Hi Mark,

Thanks for the note. We've recorded the bug and will look into it.

Cheers,

-- Jason

On Wed, Aug 29, 2012 at 10:58 PM, Mark Saper  wrote:
> Jason et al.,
>
> I've noticed some strange behavior launching MacPyMOL. I'm running v 1.5.0.4 
> on OSX 10.8.1, but I don't think the version or OS is at fault.  I discovered 
> this problem when opening a session (.pse) file in a folder whose name is 
> "pMM12(His6-EcLpoA(28-678)" (without quotes).  Note the unmatched parenthesis 
> before the "His".
>
> If I launch MacPyMOL by double-clicking the session file in that folder, 
> MacPyMOL launches but detects a syntax error in the file pathname and doesn't 
> open the file.  If I again double-click the same session file again, a new 
> MacPyMOL window opens and the session file is successfully opened!  If I 
> change the name of the enclosing folder to remove the unmatched parenthesis, 
> the problem goes away.  I know this is a consequence of the layered 
> architecture, but I thought you should know about it.
>
> Regards,
> Mark
> _
> Mark A. Saper, Ph.D.
> Associate Professor of Biological Chemistry, University of Michigan
> Ann Arbor MI  48109-1055 U.S.A.
> sa...@umich.edu phone (734) 764-3353 fax (734) 764-3323
>
>
>
>
>
>
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-- 
Jason Vertrees, PhD
PyMOL Product Manager
Schrödinger, LLC

(e) jason.vertr...@schrodinger.com
(o) +1 (603) 374-7120

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