[phenixbb] DTT mediated disulfide crosslink across a crystallographic two-fold!

Pavel Afonine pafonine at lbl.gov
Tue Aug 3 18:05:57 PDT 2010

  Hi Joe,

I think all you need is summarized here:


Please let us know if you still have any questions.

ReadySet creates a CIF file wich has nothing to do with the occupancies, 
symmetry etc... It just defines the geometry of your DTT. So, create a 
CIF file for DTT (if you really need it - I thought it is standard thing 
and might be already in the library) and run the refinement following 
the tips in the link above.


On 8/3/10 5:54 PM, Joseph Noel wrote:
> Hi Phenix Users,
> I have found a beautifully ordered DTT molecule stretching across a 
> crystallographic two-fold and linking two symmetry related cysteine 
> side chains. Since part of this molecule sits on across the two-fold 
> (special position) I will specify the occupancy as 0.5. I am hoping to 
> get some information on how easy (or how difficult) it is to specify 
> this arrangement in Phenix for refinement since it is covalent and 
> sitting across a crystallographic two-fold (and presumably stabilizing 
> the lattice). Will ReadySet build the appropriate CIF file if I build 
> the DTT into the density and give it a 0.5 occupancy?
> 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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