VMD-L Mailing List

From: Rahul Mahajan (mahajanr_at_vcu.edu)
Date: Tue Sep 29 2009 - 21:23:53 CDT

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.