[phenixbb] how to make covelent link of BME with Cys and refine
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.
JCSG at SSRL, SLAC
On 02/13/2013 01:02 PM, Nigel Moriarty wrote:
> 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.
> 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
> On 02/12/2013 11:21 PM, Rajeshwer Sankhala wrote:
>> 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
>> phenixbb mailing list
>> phenixbb at phenix-online.org <mailto:phenixbb at phenix-online.org>
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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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