[phenixbb] how to make covelent link of BME with Cys and refine

Sabine Schneider sabine.schneider at mytum.de
Tue Feb 12 23:56:17 PST 2013

Hello Raj,

do you have the link specified in you PDB file?
Here is an example for an disulphide bond. Usually the link is the line 
above the CRYST1 card.

SSBOND   1 CYS A  123    CYS A  123 1555   8555  2.12


On 02/12/2013 11:21 PM, Rajeshwer Sankhala wrote:
> Hello,
> I can see additional density just next to Cys residues in my protein 
> structure and it looks like BME is covalently linked to cys. I could 
> form a disulfide bond between BME and Cys in "Refmac 5 review 
> restrain" but when i subject it for refinement BME is thrown away (no 
> disulfide bond). I also given Cif file in refinement but it didnot 
> help. I have a feel that i am missing something in cif file. Can 
> anyone suggest step  by step starting from adding BME to making a link 
> with BME (Cys-BME) and then refinement?
> Raj
> _______________________________________________
> phenixbb mailing list
> phenixbb at phenix-online.org
> http://phenix-online.org/mailman/listinfo/phenixbb

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://phenix-online.org/pipermail/phenixbb/attachments/20130213/063a7772/attachment.htm>

More information about the phenixbb mailing list