[phenixbb] how to make covelent link of BME with Cys and refine
nwmoriarty at lbl.gov
Wed Feb 13 13:02:59 PST 2013
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> 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
> 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 refinement?
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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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