[ccp4bb]: Treatment of oxidized Cys in refmac

[Abhinav Kumar <akumar@plexxikon.com>]

***  For details on how to be removed from this list visit the  ***
***          CCP4 home page http://www.ccp4.ac.uk         ***

Hi,

I am trying to refine a structure with some of the Cys residues oxidized
with one/two oxygen atoms. I looked around and found that these modified Cys
are referred to as CSX and CSW. Furthermore, there are minimal descriptions
for CSX and CSW in CCP4 lib.

I tried to refine my model with CSX, but refmac complained that the lib is
not complete.

I tried to use only Oxygen of CSX in a different residue name (say CS1)
leaving Cys residue as normal, use Link between Cys-SG and O-CS1, generate a
library for CS1, and then use refmac to refine. Still, error messages are:
1) CS1 : last atom of the tree absent
2) Subscript out of range on file line 12838... Attempt to access the 0-th
element of variable s2_conn[****]


My question is : what is a clean and easy way to describe and refine
oxidized Cys residues?
 

Thanks
Abhinav
 
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Abhinav Kumar, Ph. D.
 
Plexxikon, Inc.
91 Bolivar Dr. Suite A        Tel: 510.647.4021
Berkeley, CA -  94710         Fax: 510.548.4785
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~