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[ccp4bb]: Thanks: Toppar and parameter files for Cis-peptide



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Dear colleagues,

Thank you very much for your good suggestions on how to deal with 
cis-peptide refinement! Here, I give a summary on these suggestions and 
hope these suggestions can do great help to those who will meet similar 
difficulties.

Dr. Yibin Xu
Don't have to set up any topology and parameter files in CNS for 
Cis-peptides. Adjust that peptide in right position according to maps, for 
example, you can flip it and use mov-z command in O.

Dr. Kathryn Turton, Dr. Susan Heffron and Dr. Paul Adams
Use the program cis-peptide.inp in CNS to write out a parameter file for 
all cis-peptides in your protein. Then include this cis-peptide.param file 
in the other programs for refinement.

Dr. Remy Loris 
insert a smzll parameter statement in all the refinement scripts as 
follows:
{## cis-peptide ##} {#################}
 parameter
 dihedral ( segid SEGA and name CA and resid 85 ) ( segid SEGA and name C 
and resid 85) ( segid SEGA and name N and resid 86 ) ( segid SEGA and name 
CA and resid 86 ) 1250. 2 180.
 dihedral ( segid SEGB and name CA and resid 85 ) ( segid SEGB and name C 
and resid 85) ( segid SEGB and name N and resid 86 ) ( segid SEGB and name 
CA and resid 86 )           1250. 2 180.
 end


Dr. Edwin Pozharski
Check the link xtal.structure.northwestern.edu/~lists/ 
ccp4list/Apr_01/0035.html or X-PLOR website
http://xplor.csb.yale.edu/xplor-info/xplor-faq/Q.006.html

Dr. William G. Scott and Dr. Holly Heaslet
Use CNS 1.1 or Refmac because it can refine the cis-peptides automatically.

Thank you again for your great help!

Good luck with everything!

Best,

Fan






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