[Chimera-users] UHBD map, generated with APBS

Elaine Meng meng at cgl.ucsf.edu
Tue Jan 20 15:05:54 PST 2015


Hi Anna,
Issue 1:  reading UHBD grd format.  Chimera does read the binary format from UHBD, for which we use the .grd filename extension: 
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/filetypes.html#esp>
I don't know how the UHBD grid format from your ABPS standalone is different.  The APBS documentation only says "legacy UHBD format" without a full description.  You could try using Chimera menu: Help… Report a Bug, making sure to attach the file and include your email address for feedback if you believe it is the binary UHBD format that Chimera should read.
<http://www.poissonboltzmann.org/docs/file-format-info/>

Problem 2: if you are using Chimera to make a dx file, I guess you are using the APBS tool.  
<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/apbs/apbs.html>
This calculation is not run within Chimera but using an APBS web service provided by the NBCR. This web service may not have all the options of standalone APBS.

I haven't used it myself, but I found a program online that is supposed to convert the formats:
<http://apbs.sourcearchive.com/documentation/1.0.0/dx2uhbd_8c_source.html>
Apparently it is a tool included with the APBS distribution.

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 Jan 20, 2015, at 2:11 AM, "Feldman-Salit, Anna" <anna.feldman-salit at h-its.org> wrote:

> My current "strange" problem:
> 
> I use APBS stand-alone to generate electrostatic potential for a protein in PQR format. What I do is to ask for output in UHBD (GRD not DX) format. Unfortunately, the generated GRD file is not read by CHIMERA, which upsets me... Strange, but VMD seems to be less sensitive to the GRD generated with APBS to visualize the map.
> 
> Another point:
> I am very glad that CHIMERA computes potential. Do you think one could save it not only in DX format? Maybe you could suggest me a way to convert DX to UHBD format?
> 
> Thank you!
> Have a lovely working day!
> 
> Greetings,
> Anna
> 




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