VMD-L Mailing List

From: Mahesh Chandrasekhar Gandikota (maheshgandikota_at_niser.ac.in)
Date: Wed May 14 2014 - 09:59:40 CDT

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.
>