[phenixbb] how to create /refine a protein with a modified residue

Nigel Moriarty nwmoriarty at lbl.gov
Thu May 13 11:48:40 PDT 2010


You can run ReadySet! thus

phenix.ready_set model.pdb

to, among other things, generate a restraints file for any
non-standard residues.  Simply pass this to phenix.refine.


On Thu, May 13, 2010 at 11:36 AM, vincent Chaptal
<vchaptal at mednet.ucla.edu> wrote:
> Dear phenixbb,
> i have a protein on which a cysteine has been modified and I can't find
> a way to refine my structure with it.
> this seams like a fairly easy problem as a lot of people are refining
> structures with post-translational modifications, but i can't find the
> info on how to do it.
> Could someone point me to a web page explaining it?
> If i understand correctly, i have to create the modified residue, create
> the restraints, and define it as a L-peptide. Is that correct?
> thanks a lot
> vincent
> --
> Vincent Chaptal
> Dept. of Physiology at UCLA
> http://www.physiology.ucla.edu/Labs/Abramson/index.html
> <http://www.physiology.ucla.edu/Labs/Abramson/index.html/>
> Phone: 1-310-206-1399
> IMPORTANT WARNING:  This email (and any attachments) is only intended for
> the use of the person or entity to which it is addressed, and may contain
> information that is privileged and confidential.  You, the recipient, are
> obligated to maintain it in a safe, secure and confidential manner.
>  Unauthorized redisclosure or failure to maintain confidentiality may
> subject you to federal and state penalties. If you are not the intended
> recipient, please immediately notify us by return email, and delete this
> message from your computer.
> _______________________________________________
> phenixbb mailing list
> phenixbb at phenix-online.org
> http://phenix-online.org/mailman/listinfo/phenixbb

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

More information about the phenixbb mailing list