[Molvis-list] help: SS-bond in Rasmol-2.7.3

Kevin Karplus karplus at soe.ucsc.edu
Tue Mar 14 12:05:21 EST 2006

I don't know how RASMOL determines SSbonds, but my program undertaker
finds 6 disulfides in 1aol:
SS bond: 2.01426 Ang (1aol)C178.SG and (1aol)C184.SG
SS bond: 2.0387 Ang (1aol)C133.SG and (1aol)C146.SG
SS bond: 2.01986 Ang (1aol)C121.SG and (1aol)C141.SG
SS bond: 2.02242 Ang (1aol)C46.SG and (1aol)C98.SG
SS bond: 2.02107 Ang (1aol)C72.SG and (1aol)C87.SG
SS bond: 2.04136 Ang (1aol)C73.SG and (1aol)C83.SG
I'm using a simple SG-SG distance to detect these disulfides, and I
suspect that RASMOL uses a similar mechanism.
The 1aol file does not have crystallographer-provided SSBOND or HBOND
records, just the HELIX and SHEET records.  

Kevin Karplus 	karplus at soe.ucsc.edu	http://www.soe.ucsc.edu/~karplus
Professor of Biomolecular Engineering, University of California, Santa Cruz
Undergraduate and Graduate Director, Bioinformatics
(Senior member, IEEE)	(Board of Directors & Chair of Education Committee, ISCB)
life member (LAB, Adventure Cycling, American Youth Hostels)
Effective Cycling Instructor #218-ck (lapsed)
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