violation lists & DGII comparisons

Garry W. Buchko gw_buchko at
Wed Sep 18 15:10:20 EST 1996

Because dealing with MSI/BIOSYM is worst than buying a used car from 
an ex-O.J.-lawyer turned politician, I have recently been making the 
switch-over from DGII to Xplor.  Two basic questions.

1)  Any general comments about the "quality" of peptide structures 
(40-mers, using only NOE based distance restraints) generated by the 
two methods and how to best "mimick" DGII conditions with Xplor (DGII:  
Tetrangle smooth/4D embed/anneal by heat to 200K and then sigmoidal 
cooling to 0K over 10000 step (0.2 psec/step)).  I have been 
generating Xplor structures with similar convergence by:1) 
Full-Embedding, 2) DGSA (2000K for 1000 steps followed by 5000 steps 
of cooling to 100K) and 3) Refine: (200K initial and cool in 10000 
steps to 1K).  The latter refine part makes a substantial difference.  
Using "gentle_refine" (200 K and cool for 10000 steps) instead of 
"refine" also does a descent job.  Is such an overall Xplor approach 
reasonable or foolish? 

2)  NOE violations.  The "accept" program lists the NOE violations 
(eg: greater than 0.1 A from the distance bounds) for each structure 
together.  Is there an Xplor program, or does anyone have a program, 
that will list all the violations for each NOE restraint for each 
structure together? (Eg: for a group of structures, list the 
violations for a specific NOE restraint in all the structures 
together....similar to the violation list that NMR-Arch generated?).



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