[Chimera-users] APBS file format

Tom Goddard goddard at sonic.net
Tue Jun 5 12:10:47 PDT 2012

The APBS electrostatic potential grid file format (suffix .dx) is from 
IBM's Visualization Data Explorer and also used by an open source 
program based on that software called OpenDX.  It is documented in the 
APBS manual here:



> Begin forwarded message:
>> *From: *Nikolay Igorovich Rodionov
>> *Date: *May 21, 2012 12:43:34 PM PDT
>> *To: *Eric Pettersen
>> *Subject: **RE: [Chimera-users] ESP calculations*
>> Thank you both,
>> Can either of you tell me how the information in a volume data set is 
>> organized? I am looking at a .dx file that I created using APBS which 
>> I would assume to be very similar to the volumetric data sets created 
>> by Chimera. What does each column of data represent? Is there any way 
>> for me to sort the ESP data based on position using Excel or Matlab? 
>> I am only concerned with ESP data for one region of molecule.  If you 
>> could point me in the direction of some good documentation on this 
>> file type it would be great.
> I don't know, so I'm forwarding this out to chimera-users land, where 
> someone might have an answer...
> --Eric
>> Thanks again,
>> Nikolay Rodionov
>> -----Original Message-----
>> From: Eric Pettersen
>> Sent: Monday, May 21, 2012 2:57 PM
>> To: chimera-users at cgl.ucsf.edu <mailto:chimera-users at cgl.ucsf.edu> BB
>> Cc: Nikolay Igorovich Rodionov
>> Subject: Re: [Chimera-users] ESP calculations
>> Also, if you compute a volume, you can use the "Values at Atom 
>> Positions" tool to, um, get the values at atom positions (say, a 
>> ligand), if that's relevant to what you're doing.
>> --Eric
>> On May 21, 2012, at 9:09 AM, Elaine Meng wrote:
>>> Hi Nikolay,
>>> You can generate a grid of values with the "Compute grid" option of
>>> Coulombic Surface Coloring (or corresponding option of the "coulombic"
>>> command).  The grid is a volume data set, and when it is generated the
>>> Volume Viewer  and Surface Color dialogs will automatically appear.
>>> <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/coulombic/co
>>> ulombic.html
>>> <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/coulombic/co
>>> ulombic.html#volume
>>> You can save the grid to a file with the FIle menu of Volume Viewer.
>>> <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/volumeviewer
>>> /framevolumeviewer.html
>>> As for the values at each point of the surface, I don't know of a way
>>> to write these all to a file, but in Surface Color if you click the
>>> Options button and then turn on the option to "Report value at mouse
>>> position" it will report the values in the status line at the bottom
>>> of the Chimera window when you click into the graphics window and then
>>> mouse over the surface. I just noticed that to make this work it is
>>> necessary to recolor the surface first by clicking the Color button on
>>> this dialog, which may be a bug, but that's the workaround!
>>> <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/surfcolor/su
>>> rfcolor.html
>>> If you have the grid file saved you can reopen it in Chimera later and
>>> use it in Surface Color without rerunning the ESP calculation.
>>> However, keep in mind that Coulombic ESP is more for qualitative
>>> purposes of visualization or making comparisons between related
>>> structures than for absolute quantitative accuracy.  For example, you
>>> could easily make all the ESP values half as large simply by doubling
>>> the dielectric constant used in their calculation, as shown in the
>>> equation in the Coulombic Surface Coloring manual page.
>>> I hope this helps,
>>> Elaine
>>> ----------
>>> Elaine C. Meng, Ph.D.
>>> UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department
>>> of Pharmaceutical Chemistry University of California, San Francisco
>>> On May 21, 2012, at 8:05 AM, Nikolay Igorovich Rodionov wrote:
>>>> Hi all,
>>>> I was wondering if there was a way to get an output data file
>>>> regarding ESP coloring and calculations based on Coulomb's law. The
>>>> visualization is great but I would also like to quantify the data.
>>>> Thank you,
>>>> Nikolay Rodionov
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