The calculation is done exactly the same for Windows and MAc. A friend of mine did the calculation for me (before I have the plugin  set up on my Mac) and sent me the Pymol  pse file, which includes the pdb file and the map file. All I did was opening his pse file on my computer, clicking "update" under visualization and the resulting surface is very different from what the windows generates (the one he sent me). First, at the same display level, say -10 to 10, Mac gives almost all faint picture (mostly white) while windows gives a vivid pictures. Second, the Mac picture seems to have lost much resolution, it gives large blobs of red and blue and not much fine features.

I did use the pdb2pqr sever with default setting to do all the calculations and then used my Pymol to display the surface.  I have also done the calculation under Pymol on my Mac. In all three cases (Windows, server, Mac), the surfaces are the same, i.e. they are all different from the surface generated from Windows. So I suspect the problem is not the APBS calculation, rather Pymol itself or the interface between Pymol and APBS tools2. I tried to see if there are certain settings (coloring scheme etc) change the display, but have not found anything that solve the problem.

I don't have the windows input file, but I can send the server and Mac input file if you think it will help.



On Dec 11, 2012, at 8:13 AM, <>

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Today's Topics:

  1. Re:  electrostatic potential not properly displayed on Mac OS
     10.6.8 (Baker, Nathan)


Message: 1
Date: Tue, 11 Dec 2012 06:09:23 -0800
From: "Baker, Nathan" <>
Subject: Re: [apbs-users] electrostatic potential not properly
displayed on Mac OS 10.6.8
To: "Yao, Xiaolan" <>,
"" <>
Content-Type: text/plain; charset="us-ascii"

Hello -

Can you please send the input files generated by PyMOL for the Windows and Mac calculations?


Nathan Baker
Pacific Northwest National Laboratory
Tel:  +1-509-375-3997<>

From: Yao, Xiaolan []
Sent: Monday, December 10, 2012 3:20 PM
Subject: [apbs-users] electrostatic potential not properly displayed on Mac OS 10.6.8


I recently installed Pymol 1.5 with APBS plugin using Macports. The program runs fine but I don't think it is giving the right output.  Using the same pdb and the same map file, the surface plot generated on Mac is very different from the one generated from Windows.  I attached the two surface plots here. Any suggestions on how to fix is greatly appreciated.


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End of apbs-users Digest, Vol 78, Issue 11