Hi Nick,
Could you send me a specific example of this happening? Feel free to email
it to me off-list if you'd like.
One thing I can think of off-hand is that the most recent version of the
plugin defaults to using more memory for the electrostatics calculation,
which can certainly make a difference for bigger systems.
Thanks,
-Michael
On Thu, Sep 2, 2010 at 4:35 PM, Noinaj, Nicholas (NIH/NIDDK) [F] <
noin...@niddk.nih.gov> wrote:
> Hi,
>
>
>
> I have noticed an 'odd' behavior when calculating electrostatic surface
> potential representations between the APBS Tools (v1.2r3) and APBS Tools2
> (v1.3) where the results are significantly different depending on which
> version of Pymol I use (recently upgraded to 1.3 and noticed this when
> re-making a figure that was originally made using 1.2r3)!
>
>
>
> I am just wondering, has anyone else observed similar behavior? The
> results from v1.3 look more accurate, which worries me somewhat about the
> figures I have previously made using the v1.2r3 APBS plugin! While i am
> happy using v1.3 (which agrees reasonably well with other programs), people
> currently using v1.2r3 or the like might want to investigate further by
> comparing their results to v1.3.
>
>
>
> Thanks in advance for any feedback!
>
>
>
>
>
>
>
>
>
>
>
> Cheers,
>
> Nick
>
>
>
>
>
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>
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>
>
>
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>
>
> --------------------------------
>
>
>
> [ Nicholas Noinaj ]
>
> the Buchanan Lab
>
> Laboratory of Molecular Biology
>
> LMB-NIDDK, NIH
>
> 50 South Drive, Room 4505
>
> Bethesda, MD 20892-8030
>
> 1-301-594-9230 (lab)
>
> 1-859-893-4789 (cell)
>
> noin...@niddk.nih.gov
>
>
>
> [ the Buchanan Lab ]
>
> http://www-mslmb.niddk.nih.gov/buchanan/
>
>
>
>
>
>
>
>
>
>
>
>
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--
Michael Lerner, Ph.D.
IRTA Postdoctoral Fellow
Laboratory of Computational Biology NIH/NHLBI
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