Hello –

 

It shouldn’t be too hard for us to develop a conversion script for XPLOR.  Could others on the mailing list indicate whether this would be of use to them as well?

 

Thanks,

__________________________________________________
Nathan Baker
Pacific Northwest National Laboratory
Tel:  509-375-3997

http://signatures.pnl.gov

 

From: Jean-yves Sgro [mailto:jsgro@wisc.edu]
Sent: Wednesday, March 23, 2011 9:58 AM
To: apbs-users@lists.sourceforge.net
Cc: Jean-Yves Sgro
Subject: [Apbs-users] DX to XPLOR file format for electrostatics

 

March 23, 2011

 

Greetings,

I am trying to use a software that requires input of the electrostatic potential map as a .xplor file

http://bilbo.bio.purdue.edu/~viruswww/Rossmann_home/softwares/river_programs/rivem.php

The original paper (Xiao and Rossmann, j. Structural Biology 158(2007) 182-187 mentions that they calculated the map with Delphi. However, looking on the web site for Delphi that format does not seem to be the standard output.


I have clalcuated a .dx file that I was able to open within  UCSF Chimera in the hope that I could re-export it with that format, but that is not an option.


Is there a way to go from a .dx file to a .xplor file describing the electrostatic?


I have looked to what I believe is "everywhere" via Google but I cannot find any information on how one might do that. More confusing is the fact that xplor has multiple file formats, including PDB-like files.


The example file provided by the Riverm software (URL above) is about 200 Mb and has the following format at the top of the file (first line is blank):


     1
qdiffxas: qdiffxs4 with an improved surfacing routine       
     256     -74     182     256    -128     128     256     132     388
0.12800E+03 0.12800E+03 0.12800E+03 0.90000E+02 0.90000E+02 0.90000E+02
ZYX
       0
0.82800E-02 0.80512E-02 0.78926E-02 0.77350E-02 0.75803E-02 0.74275E-02
0.72770E-02 0.71290E-02 0.69833E-02 0.68407E-02 0.67005E-02 0.65627E-02
0.64282E-02 0.62969E-02 0.61677E-02 0.60427E-02 0.59206E-02 0.58022E-02
0.56875E-02 0.55752E-02 0.54681E-02 0.53639E-02 0.52638E-02 0.51684E-02


and continues on for a long long time....

 

Thanks for anyone that can help with this new Format issue, so typical in the computer world.

 

Sincerely

 

Jean-Yves Sgro