VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Fri Apr 20 2007 - 21:07:01 CDT

Cesar,
  If you're using the binary ("unformatted") Delphi format, you'll
need to use grdplugin to load them. Since you got an error trying
the grd plugin, it seems that there's a limitation or weakness in the
implementation of the grdplugin reader. If you can send me the delphi
map I'll have a look at this. What version of Delphi made the map file?
Someone else recently ran into trouble loading a binary delphi map, I'm
still waiting for details on their Delphi version etc as well.
Anyway, if the map file is small enough to gzip and email to me,
please send it to me that way, otherwise you could post it in the
VMD Public project BioFS area in the "testfiles" directory:
  http://www.ks.uiuc.edu/Research/vmd/alpha/

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Fri, Apr 20, 2007 at 08:36:48PM -0300, Cesar Luis Avila wrote:
> Dear all,
> I was wondering if PHI maps calculated with delphi could be seen using
> VMD. I had no problem in the past with maps calculated with APBS, but
> with delphi I have tried both standard and GRASP formated phi maps
> (generated with delphi) and none could be loaded with any of delphi file
> types. Here are some of the errors reported by the different plugins.
> -------
> ERROR) Unable to open file with plugin of type delphibig
> Unexpected end-of-file.
> Couldn't read fort.14
> -------
> graspplugin) First characters of file don't look like a GRASP file
> ERROR) Reading raw graphics failed.
> -----------
> Unable to open file with plugin of type grd
> Error: non-cube grid
> ----------
>
> The box is composed of 155 grid points per side.
> The output file from delphi seems to be in binary format.
> Any suggestion on how to generate the phi map for later use with vmd?
> I am using lastest stable version of vmd 1.8.6
> Regards
> Cesar 

-- 
NIH Resource for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
Email: johns_at_ks.uiuc.edu                 Phone: 217-244-3349
  WWW: http://www.ks.uiuc.edu/~johns/      Fax: 217-244-6078