[phenixbb] Restraints file for a new amino acid residue

Pavel Afonine pafonine at lbl.gov
Fri Aug 13 13:44:47 PDT 2010

  Hi Joe,

hm... it's getting a bit complicated. Could you please send me the PDB 
file (or its part containing the residue in question plus a couple of 
residues on both ends)? I need to reproduce this problem myself to be 
able to explain what's happening and how to deal with this.

I guess you need to import a CIF file for modified residues into COOT so 
it can rotate about torsions.


On 8/13/10 11:26 AM, Joseph Noel wrote:
> Thanks all for the advice. Basically that is what I have been doing. 
> It is actually an oxidized cysteine to sulfenic acid. I am refining 
> the site as alternative conformers with the normal Cys, the single 
> oxidation state to sulfenic acid (CSO) and the double to sulfinic acid 
> (CSD). I know that CSO is in the phenix library but it adds hydrogens 
> to the amino group every time I run elbow or ready set. I then I have 
> to edit the PDB file to delete the hydrogen or Phenix will not refine. 
> I also have problems in COOT. It will not let me move the residues 
> torsional angles. I have checked other structures in the PDB and the 
> density fits perfectly with the structures of many such oxidized 
> systems but for some reason Phenix is giving me some problems. I was 
> going to create a "new" residue and explicitly define the oxygen as 
> charged rather then protonated since the pKa of sulfenic acid is quite 
> low. Maybe the problems all stem from refining this particular 
> position with three alternative "conformers", each conformer of which 
> is chemically distinct. For now, I have CSO labeled as convention BCSO 
> for conformer B. Cys is ACYS.
> Joe
> ___________________________________________________________
> Joseph P. Noel, Ph.D.
> Investigator, Howard Hughes Medical Institute
> Professor, The Jack H. Skirball Center for Chemical Biology and Proteomics
> The Salk Institute for Biological Studies
> 10010 North Torrey Pines Road
> La Jolla, CA  92037 USA
> Phone: (858) 453-4100 extension 1442
> Cell: (858) 349-4700
> Fax: (858) 597-0855
> E-mail: noel at salk.edu <mailto:noel at salk.edu>
> Web Site (Salk): http://www.salk.edu/faculty/faculty_details.php?id=37
> Web Site (HHMI): http://hhmi.org/research/investigators/noel.html
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