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

[Nigel Moriarty]

That will work also.

On Wed, Feb 13, 2013 at 2:34 PM, Abhinav Kumar
<abhinavk at slac.stanford.edu>wrote:

>  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> 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
>
>
>
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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
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