VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Tue Nov 11 2003 - 10:56:28 CST

Dear Francesca,
  Rather than using the "readedm" Tcl script, please use the
built-in X-PLOR EDM reader plugin in VMD, it is much much faster
than the Tcl script, and handles several cases that the Tcl script
doesn't handle. Select "EDM" as the file type. If you still have
any problems, please let us know.

Thanks,
  John Stone
  vmd_at_ks.uiuc.edu

On Tue, Nov 11, 2003 at 04:11:11PM +0100, Francesca Mocci wrote:
> Hello!
>
> I have an xplor map file (produced with the program ptraj of the
> amber7 package)
> and I want to display it with vmd.1.8.1
> I downloaded the readedm.txt file from
> http://www.ks.uiuc.edu/Research/vmd/script_library/scripts/readedm/readedm.txt
> I changed its name in readedm.tcl
> and I followed the suggestion for the usage written in the readedm file:
>
> vmd > source readedm.tcl
> vmd > mol load pdb my_structure.pdb
> vmd > readedm my_edm.map
>
> and the following error occurred:
> mol volume: size of data does not match specified sizes
>
> this is the output in the vmd console:
>
> >EDM Reader, opening Light/2na_light.map
> > rdparm generated grid density
> > Grid dimensions: X: 60, Y: 60, Z: 60
> > Grid elements: 216000
> > Grid orientation: a: 30.000, b: 30.000, c: 30.000,
> > alpha: 90.000, beta: 90.000, gamma: 90.000
> > xOrigin, yOrigin, zOrigin: -14.5, -14.5, -14.5
> > xVec: 30.0 0 0
> > yVec: -1.53102359078e-10 30.0 0
> > zVec: -1.53102359078e-10 -1.53102359079e-10 30.0
> > ZYX
> > # of grids in 1 slide: 3600
> > # of grids in 1 line: 6
> > # of lines in 1 slide: 600.0
> > 215964
> > 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000
> >mol volume: size of data does not match specified sizes
>
> It is quite clear that my edm format is not ok for readedm,
> and I tried to change it in several way but with no results..
>
> Did anybody solved this problem for xplor map file
> obtained by means of the program ptraj?
> If not, it can be usefull for me
> to have a look at an xplor map file that is accepted by vmd
> in order to convert mine.
>
> Thanks for your attention,
> Francesca
>
> 

-- 
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