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.



On Thu, Sep 2, 2010 at 4:35 PM, Noinaj, Nicholas (NIH/NIDDK) [F] <noinajn@niddk.nih.gov> wrote:



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depending on which version of Pymol I use (recently upgraded to 1.3 and noticed this when re-making a figure that was originally made using 1.2r3)!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!


















[ Nicholas Noinaj ]

the Buchanan Lab

Laboratory of Molecular Biology


50 South Drive, Room 4505

Bethesda, MD  20892-8030

1-301-594-9230 (lab)

1-859-893-4789 (cell)



[ the Buchanan Lab ]







This SF.net Dev2Dev email is sponsored by:

Show off your parallel programming skills.
Enter the Intel(R) Threading Challenge 2010.
PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net)
Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net

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)
Bethesda MD 20892-9314 (USPS)