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

Ed. Pozharski epozh001 at umaryland.edu
Wed Feb 13 15:08:42 PST 2013

Excellent point.  The difference between using bme and cme is rather ideological.  I would say that incorporating cme implies that your protein was somehow synthesized with non-canonical amino acid. Usind bme seems more in line with what actually happens - betamercaptoethanol forming disulfide bond with a cysteine.

In practical sense, both things work.  Until IUCr comes up with a convention, one is free to ignore ideological considerations :)

-------- Original message --------
From: Abhinav Kumar <abhinavk at slac.stanford.edu> 
To: phenixbb at phenix-online.org 
Subject: Re: [phenixbb] how to make covelent link of BME with Cys and refine 
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.

(650) 926-2992 

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> 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 refinement?



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Nigel W. Moriarty
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