VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Fri May 16 2014 - 11:33:40 CDT

Hi,
  So far as I know, the CCP4 map only contains the density map data,
and does not contain the structure solved from the density data. You would
normally load the .map file as well as an associated PDB or similar structure
file to be able to get the coordinates for the atoms. VMD isn't a
crystallography package, so if you don't already have a structure solved
from the density, you need to obtain that first, either from a database
like the PDB, or using one of the many crystallography tools out there.

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Wed, May 14, 2014 at 08:29:40PM +0530, Mahesh Chandrasekhar Gandikota wrote:
> I have a .map file which contains x-ray crystallography data of a
> bacteriophage. The format of the file is CCP4. I can open the file using
> VMD. However, I am unable to get the xyz co-ordinates. It shows the
> following error when I click on the option of saving data in xyz format:
>
> `No timesteps selected; trajectory file will not be written.'
>
> The .map is a big file of 64MB written in binary.
>
> The file I am referring to may be downloaded at:
> ftp://ftp.ebi.ac.uk/pub/databases/emdb/structures/EMD-1086/map/emd_1086.map.gz
>
> Can't we save xyz co-ordinates for CCP4 files? Or is it possible to
> extract any other form of data?
>
> I am new to VMD and these formats.
> Any help would be appreciated.
>
> On Mon, May 12, 2014 at 3:53 PM, Mahesh Chandrasekhar Gandikota
> <maheshgandikota_at_niser.ac.in> wrote:
>
> I have a .map file which contains x-ray crystallography data of a
> bacteriophage. The format of the file is CCP4. I can open the file using
> VMD. However, I am unable to get the xyz co-ordinates. It shows the
> following error when I click on the option of saving data in xyz format:
>
> `No timesteps selected; trajectory file will not be written.'
>
> The .map is a big file of 64MB written in binary.
>
> The file I am referring to may be downloaded at:
> ftp://ftp.ebi.ac.uk/pub/databases/emdb/structures/EMD-1086/map/emd_1086.map.gz
>
> Can't we save xyz co-ordinates for CCP4 files? Or is it possible to
> extract any other form of data?
>
> I am new to VMD and these formats.
> Any help would be appreciated. 

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