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[EMAIL PROTECTED] wrote on 05/02/2006 01:41:39 PM: > *** For details on how to be removed from this list visit the *** > *** CCP4 home page http://www.ccp4.ac.uk *** > > > Axel Brunger had an X-PLOR script to do exactly this sort of thing with > the Fab fragment of the antibody 26-10 that was one of his molecular > replacement test cases. Rummaging around I see it's called "elbow.inp" > so if you have a working X-PLOR installation you might find it in: > > xplor_3.851/tutorial/xtalmr/elbow.inp > Just a couple of points about this script: - it's also in the X-PLOR manual (page 247) in case you have a copy of that lying around but don't have an X-PLOR installation. - it works perfectly well in CNS, with a couple of minor modifications. I unfortunately can't remember what I modified (and I don't have the file with me anymore) but it was a very short (15 mins) cycle of trying the script, reading the CNS error messages, adjusting things the errors pointed to, and getting it to work. Email me if you need more details and I'll try to remember what I did... - the rotation about the user-specified hinge is relative, not absolute - specifying a rotation angle of 10 degrees adds 10 deg to the elbow angle whatever the angle currently is. You don't even need to know the angle. - if you use this script for its original purpose of adjusting a Fab's elbow angle, watch out for the residue numbering. The script assumes your Fab is numbered sequentially; if you're using Kabat numbering instead, the wrong residues will be chosen for the hinge. - Matt -- Matthew Franklin phone:(917)606-4116 Senior Scientist, ImClone Systems fax:(212)645-2054 180 Varick Street, 6th floor New York, NY 10014 Confidentiality Note: This e-mail, and any attachment to it, contains privileged and confidential information intended only for the use of the individual(s) or entity named on the e-mail. If the reader of this e-mail is not the intended recipient, or the employee or agent responsible for delivering it to the intended recipient, you are hereby notified that reading it is strictly prohibited. If you have received this e-mail in error, please immediately return it to the sender and delete it from your system. Thank you.
