Re: [ccp4bb]: Treatment of oxidized Cys in refmac

[Garib N Murshudov <garib@ysbl.york.ac.uk>]

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In general there are three ways of using modified residues

1) Use original residue and add modification on them and use MODRES record in 
the header. Modification should be defined in the library (user's library). 
It is good for one or two atom additions.

2) Use link record to add a group and define link in the dictionary. Use link 
record. Link can handle complicated chemistry. It is my favourite as it 
leaves original residue in the pdb.

3) Define residue in the dictionary and use it. If it is amino acid then it 
should have type L-peptide. For others like sugar, RNA/DNA there are types 
also.

Some of the residues in the library have minimum description. I.e. only list 
of atoms, bonds and bond orders. When refmac sees them it creates complete 
description and asks user to check and if satisfied to use it.


Regards
Garib



On Monday 16 Sep 2002 10:53 pm, Abhinav Kumar wrote:
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> ***          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
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-- 
Garib N. Murshudov, Chemistr Department, University of York
Tel: (01904) 328252