[Chimera-users] APBS output format

[Elaine Meng]

Since it is the APBS format, I could only suggest asking the APBS developers or looking at their documentation.
<http://www.poissonboltzmann.org/apbs/>

Many formats are not well documented anywhere, but I don't know if that is true of this format in particular.

In Chimera, the options would be to 

(a) examine the code to read this format. This is beyond my knowledge, and no use unless you can understand code, but here is some info on where to look
<http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/volumeviewer/volumeviewer.html#newformats>

(b) write out the data in a different format for which you can find a description.  Output format choices: MRC, NetCDF, Chimera map, or BRIX format. 
<http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/volume.html#output>

Some additional info on volume formats:
<http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/filetypes.html#volume>

Elaine


On May 23, 2012, at 1:18 PM, Eric Pettersen wrote:

> Begin forwarded message:
> 
>> From: Nikolay Igorovich Rodionov <nirodion at syr.edu>
>> Date: May 21, 2012 12:43:34 PM PDT
>> To: Eric Pettersen <pett at cgl.ucsf.edu>
>> 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
>>