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

Nigel Moriarty nwmoriarty at lbl.gov
Wed Feb 13 13:02:59 PST 2013


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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-- 
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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