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

Abhinav Kumar abhinavk at slac.stanford.edu
Wed Feb 13 14:34:29 PST 2013


How about using residue CME which is the CYS and BME linked together.
CME is included in the CCP4 monomer library, and so Phenix should accept 
it without a dictionary file.

Thanks,
Abhinav

JCSG at SSRL, SLAC
(650) 926-2992

On 02/13/2013 01:02 PM, Nigel Moriarty wrote:
> Raj
>
> In the more recent versions of PHENIX, phenix.refine can found and 
> link atoms closer than 3 angstrom if you specify intra_chain=True. In 
> the older versions, you can use phenix.ligand_linking to generate the 
> needed files.
>
> Nigel
>
> PS PHENIX does not read SSBOND or LINK records but there is a script 
> to generate the link files from the LINK records.
>
> On Tue, Feb 12, 2013 at 11:56 PM, Sabine Schneider 
> <sabine.schneider at mytum.de <mailto:sabine.schneider at mytum.de>> wrote:
>
>     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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>
>
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>
>
> -- 
> Nigel W. Moriarty
> Building 64R0246B, Physical Biosciences Division
> Lawrence Berkeley National Laboratory
> Berkeley, CA 94720-8235
> Phone : 510-486-5709     Email : NWMoriarty at LBL.gov
> Fax   : 510-486-5909       Web  : CCI.LBL.gov <http://CCI.LBL.gov>

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