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 -- DeLano Scientific LLC Subscriber Support Services mailto:[email protected] -----Original Message----- From: [email protected] [mailto:[email protected]] On Behalf Of Chun Tang Sent: Monday, August 18, 2008 5:43 PM To: [email protected] 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 ------------------------------------------------------------------------- This SF.Net email is sponsored by the Moblin Your Move Developer's challenge Build the coolest Linux based applications with Moblin SDK & win great prizes Grand prize is a trip for two to an Open Source event anywhere in the world http://moblin-contest.org/redirect.php?banner_id=100&url=/ _______________________________________________ PyMOL-users mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/pymol-users
