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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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