VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Thu Apr 05 2007 - 12:22:23 CDT

Angelo,
  The VMD CCP4 plugin currently only supports the newer "image 2000"
specification CCP4 map files. I just checked your map file and it
appears to be one of the older variety files. We plan to add support
for the older MRC and CCP4 map file variations, but for the short term
I would suggest converting your map to the new CCP4 map
format, which is described in detail here (see "image data file format"):
  http://www2.mrc-lmb.cam.ac.uk/image2000.html

You can tell if the file follows the image2000 spec or not based
on whether it contains the "MAP" string at offset 53.

I plan to start working on updating the CCP4 map plugin to support the older
formats after VMD 1.8.6 is released and I've taken care of a few other
comittments that are already on the TODO list.
Anyone interested in testing the updated CCP4 plugin (when it's ready)
should email us at vmd_at_ks.uiuc.edu and I'll contact them when the
new version is available. Once enough people have tested it, we can
provide it in a plugin update release for everyone.

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Thu, Apr 05, 2007 at 12:32:02PM -0400, rossi_at_york.cuny.edu wrote:
> Hello:
>
> There is an emap module in the charmm program which writes out a map file in
> ccp4 binary format.
>
> In a test, I used the pdb file that was for use with the emap module of
> charmm to write out a map file in ccp4 binary format.
>
> The resulting map file is read by the pymol program and produces a plot of
> an isosurface.
>
> However, the same ccp4 binary file is not read in by vmd. A message "unable
> to load molecule" is obtained.
>
> The version of charmm I am using is c32b2 compiled on a debian linux system.
> I am using VMD 1.8.5.
>
> I am attaching both the pdb file and the ccp4 map file. Hopefully, they
> won't be scrubbed.
>
> Thank you in advance for any help in resolving this problem.
>
> Kind regards,
>
> Angelo 

-- 
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