VMD-L Mailing List

From: Leonardo Trabuco (ltrabuco_at_ks.uiuc.edu)
Date: Thu Apr 05 2007 - 14:55:07 CDT

Hi,

To add a little to what John said, you can convert the map using, e.g.,
mapman (google for it). I'm attaching a converted map which workded
fine.

Cheers,
Leo

On Thu, Apr 05, 2007 at 12:22:23PM -0500, John Stone wrote:
> 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
> 

-- 
Leonardo Trabuco, Ph.D. student
Theoretical and Computational Biophysics Group
University of Illinois at Urbana-Champaign