Restraints file for a new amino acid residue
Hi All, How does one create a new CIF file using Elbow for a non-natural amino acid not found yet in the PDB? I know how to carry it out for the isolated residue readily (but of course thinks it is isolated and doesn't include the necessary peptide bonding) but how does one ensure the correct backbone restraints for it are included since it is not isolated but part of the chain? 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: [email protected] Web Site (Salk): http://www.salk.edu/faculty/faculty_details.php?id=37 Web Site (HHMI): http://hhmi.org/research/investigators/noel.html ___________________________________________________________
Joe
The only things you need for phenix.refine to link a non-standard
amino acid into the peptide chain is
a) The backbone atoms must be named according to the convention - CA, C, N, O
b) The cartesian coordinates need to be reasonable so a bond can be
formed between residues
c) In older versions, the restraints file needs to have a double bond
between C and O.
To get a restraints file, if you have the non-standard amino acid in
the model PDB, you can do several different things depending on you
needs. Using eLBOW directly
phenix.elbow --residue NSA model.pdb
or
phenix.elbow --do-all model.pdb
You can also get a similar results from ReadySet!
phenix.ready_set model.pdb
ReadySet! does some more correcting of atom names. If you have any
trouble let me know and I'll take a look at you specified situation.
Nigel
On Fri, Aug 13, 2010 at 9:38 AM, Joseph Noel
Hi All, How does one create a new CIF file using Elbow for a non-natural amino acid not found yet in the PDB? I know how to carry it out for the isolated residue readily (but of course thinks it is isolated and doesn't include the necessary peptide bonding) but how does one ensure the correct backbone restraints for it are included since it is not isolated but part of the chain? 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: [email protected]
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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-- Nigel W. Moriarty Building 64R0246B, Physical Biosciences Division Lawrence Berkeley National Laboratory Berkeley, CA 94720-8235 Phone : 510-486-5709 Email : [email protected] Fax : 510-486-5909 Web : CCI.LBL.gov
On Fri, Aug 13, 2010 at 10:02 AM, Nigel Moriarty
To get a restraints file, if you have the non-standard amino acid in the model PDB, you can do several different things depending on you needs. Using eLBOW directly
phenix.elbow --residue NSA model.pdb phenix.elbow --do-all model.pdb
FYI, in the GUI, this is equivalent to running eLBOW with these parameters: Chemical file input: model.pdb Residue selection in PDB file: NSA I am working on documentation today, so I will try to add something about generating restraints in the GUI. You can also get a similar results from ReadySet!
phenix.ready_set model.pdb
. . . which can be automatically run from the toolbar button in phenix.refine, and will automatically add the resulting CIF file to the input list when finished. -Nat
participants (3)
-
Joseph Noel -
Nathaniel Echols -
Nigel Moriarty