VMD-L Mailing List

From: Yi Shang (mirandaisbest_at_gmail.com)
Date: Fri Oct 02 2009 - 10:39:21 CDT

Hi Rahul,
When you save coordinates, make sure to choose the mask right ("selected
atoms" option, make sure you are chosing "all" if you want to get another
pdb file only with coordinates changed).
If this still doesn't help. Try to make 2 seperate pdb files out of your
original one (each corresponds to one of your structures). Then you align
those two structures and save 2 pdb files.I have been doing this, I didn't
meet any problem.

On Tue, Sep 29, 2009 at 10:23 PM, Rahul Mahajan <mahajanr_at_vcu.edu> wrote:

> I am trying to align two structures contained in a single pdb file and then
> to save the aligned coordinates into a new file. Viewing the structures as
> "trace" or "cartoons" displays properly before doing the alignment and
> continues to display properly after the alignment, beautifully showing
> cartoons/traces of the two structures properly aligned. I save the aligned
> coordinates as a pdb file newmol.pdb using the "save coordinates" function
> (I have tried several other formats as well). The problem is when I reopen
> newmol.pdb (in the same vmd session or in a new session) the "trace" or
> "cartoons" views no longer display properly and only show a few strands of
> my molecule. Viewing with "lines", "points", "bonds", "licorice" etc shows
> all the atoms to be present in the correct positions and with correct
> connections.
>
> How can I save the aligned coordinates so that they continue to display
> correctly with "trace" or "cartoons" when reopened? If I compare the pdb
> file of the structures before alignment and the written pdb file after
> alignment, the files are identical except for the xyz coordinates of one of
> the structures are changed after alignment. There is no extra information
> (connect/secondary structure information) in the first file compared to the
> second. In fact the structure that was the reference for the alignment (and
> was not moved) is identical in the two pdb files, and yet it still displays
> incorrectly in the pdb file from after the alignment.
>
> I would appreciate any ideas. Thanks in advance.
> 

-- 
Miranda