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

Best,
Sabine

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
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