Chun,
Thank you for sending me a couple of specific examples (off list).
The problem appears to be that PyMOL cannot represent "bent" helices with
straight cylinders. In other words, if the underlying secondary structure
definition specifies a continuous helix, then PyMOL will connect the start
of the helix with the end of the helix irrespective of what occurs
inbetween.
The DSSP algorithm is particularly problematic in this way, since it tends
to incorrectly assign helices right through turn regions.
PyMOL's DSS (define secondary structure) algorithm suffer from this problem
(though it may well have other weaknesses), so...
One thing you can do with structures such as "1u7k" is to simply redefine
secondary structure with dss:
fetch 1u7k, async=0
as cartoon
show ribbon
set cartoon_cylindrical_helices
# note problem in the 50's helix
indicate 52-75/ca
# resolved with "dss"
dss
The other approach would be to manually break the helix definition:
dele all
fetch 1u7k, async=0
as cartoon
show ribbon
set cartoon_cylindrical_helices
alter 65/ca, ss='L'
rebuild
Cheers,
Warren
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Subscriber Support Services
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-----Original Message-----
From: pym...@li...
[mailto:pym...@li...] On Behalf Of Chun Tang
Sent: Monday, August 18, 2008 5:43 PM
To: pym...@li...
Subject: [PyMOL] cylindrical representation
Dear all,
I don't know if this has been discussed before.
I noticed that the structure is completely wrong when I have cylindrical
representation of helices turned on. This happens when I have multiple
structures loaded up - rendering of single pdb file seems all right. I am
using version 1.1 on redhat Linux.
Thanks.
Chun
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