Hi, Noinaj:
Thanks for your suggestion. I feel it is not the assignment problem. I tried
using "cartoon tube" to show the 2nd structure and the strand part can
showed up. Then I painted the molecule according to the secondary structure
by using util.cbss("morphy_01","red","yellow","green") and the strand is
color as "yellow" correctly in the cartoon tube mode. Then I tried another
thing, I copy-pasted the second structure information from the ca trace pdb
to my formal all stoms pdb, the strand showed up correctly. This means these
information are correct. So I guess under the default "cartoon automatic"
mode, pymol can't draw arrow for the strand residues which do not have the
coordinates of N, C, O written in the PDB file. This might be a default
setting of pymol I can't find to turn off or just an internal problem for
"cartoon automatic" mode.
Thank you again.
Tiger
From: "Noinaj" <noi...@uky.edu>
To: "Geng Tian" <gengt...@hotmail.com>,<pymol-users@lists.sourceforge.net>
Subject: Re: [PyMOL] another question about ca trace model.
Date: Tue, 18 Apr 2006 11:06:49 -0400
Tiger,
Unfortunately I don't have much experience with this procedure. But one
thing came to mind, you can manually assign secondary structure within
DEEPVIEW/SWISS PDB Viewer [EDIT]. Not sure how many pdb files you have
generated for the morph, but if nothing else works, you could try manually
assigning secondary structures and see how that works out. Yep, a huge
pain in the buttocks I know, but it should work, in theory.
Best of Luck.
Cheers,
Nick
----- Original Message ----- From: "Geng Tian" <gengt...@hotmail.com>
To: <pymol-users@lists.sourceforge.net>
Sent: Tuesday, April 18, 2006 6:24 AM
Subject: [PyMOL] another question about ca trace model.
Hi, there:
I am trying to make a movie following the intruction at
http://ginsberg.med.virginia.edu/~dcoop/Help/morph.html
From Lsqman, I got a serial of PDB files morphing between two
conformations. These PDB files contain only alpha carbon and non-hydrogen
side-chain atoms. Then I used DSSP to include the secondary structure
information ito the PDB files. In the pymol, after set cartoon_trace, 1
the helix and loop showed up nicely. But all the strands are missing. I
tried several setting about cartoon but just can't get them out. Do you
have any idea how to solve this problem.
Thank you.
Tiger
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