thanks Thomas.
Actually the "Windows" image is generated with solvent accessible surface.

Xiaolan




On Dec 14, 2012, at 6:10 AM, <apbs-users-request@lists.sourceforge.net>
 <apbs-users-request@lists.sourceforge.net> wrote:

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Today's Topics:

  1. Re:  apbs-users Digest, Vol 78, Issue 11 (Thomas Holder)


----------------------------------------------------------------------

Message: 1
Date: Thu, 13 Dec 2012 17:42:44 +0100
From: Thomas Holder <thomas.holder@schrodinger.com>
Subject: Re: [apbs-users] apbs-users Digest, Vol 78, Issue 11
To: apbs-users@lists.sourceforge.net
Cc: Jason Vertrees <jason.vertrees@schrodinger.com>
Message-ID: <50CA0584.1080503@schrodinger.com>
Content-Type: text/plain; charset=ISO-8859-1

Hi Xiaolan,

from your two screenshots I guess that the "Windows" image is not
generated with "Color by potential on solvent accessible surface", which
is the second checkbox in the "Molecular Surface" panel of the PyMOL
APBS Plugin and corresponds to the surface_ramp_above_mode setting.

Cheers,
 Thomas

Yao, Xiaolan wrote, On 12/11/12 16:34:
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.

Thanks.

Xiaolan


On Dec 11, 2012, at 8:13 AM,
<apbs-users-request@lists.sourceforge.net
<mailto:apbs-users-request@lists.sourceforge.net>> wrote:

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When replying, please edit your Subject line so it is more
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Today's Topics:

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


----------------------------------------------------------------------



Message: 1
Date: Tue, 11 Dec 2012 06:09:23 -0800 From: "Baker, Nathan"
<Nathan.Baker@pnnl.gov> Subject: Re: [apbs-users] electrostatic
potential not properly displayed on MacOS 10.6.8 To: "Yao, Xiaolan"
<yaoxia@umkc.edu>,
"apbs-users@lists.sourceforge.net"<apbs-users@lists.sourceforge.net>


Message-ID:
<28EDF831672B644C9E370B53D001F507012CAD3ECC2D@EMAIL05.pnl.gov>
Content-Type: text/plain; charset="us-ascii"

Hello -

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

Thanks,

__________________________________________________ Nathan Baker
Pacific Northwest National Laboratory Tel:  +1-509-375-3997
http://nabaker.me<http://nabaker.me/>

From: Yao, Xiaolan [mailto:yaoxia@umkc.edu] Sent: Monday, December
10, 2012 3:20 PM To: apbs-users@lists.sourceforge.net Subject:
[apbs-users] electrostatic potential not properly displayed on Mac
OS 10.6.8

Hello

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.

THanks!
[cid:image001.png@01CDD77F.36768D90][cid:image002.png@01CDD77F.36768D90]



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--
Thomas Holder
PyMOL Developer
Schr?dinger Contractor



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