The protein crystal structure I am refining has a redox modification: cysteine sulfenic acid (S-hydroxy cysteine). How do I go about including parameters for this modification in phenix refine? I have found parameters on HIC-UP (under CSO) but these are for XPLOR/ CNS. Many thanks in advance for suggestions, Jenny Martin University of Queensland
Hi Jenny, You need a cif file for phenix.refine, which you can obtain with phenix.ready_set. You may want to review the resulting parameters and change them manually if necessary. Let us know if you're having trouble generating the cif file. If you send us the CFO residue from the pdb file we can try to help more. Ralf
Jenny You don't need to do anything. The restraints for CSO are in the PHENIX distribution $PHENIX/chem_data/mon_lib/c/CSO.cif If you model corresponds correctly, you should have no trouble running refinement. Running phenix.ready_set (as Ralf mentioned) is still a good idea because it will check that you have the correct CSO residue and it will add hydrogens. Nigel On 4/3/10 6:07 PM, Prof Jennifer Martin (IMB) wrote:
The protein crystal structure I am refining has a redox modification: cysteine sulfenic acid (S-hydroxy cysteine). How do I go about including parameters for this modification in phenix refine? I have found parameters on HIC-UP (under CSO) but these are for XPLOR/CNS.
Many thanks in advance for suggestions,
Jenny Martin University of Queensland _______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb
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participants (3)
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Nigel W Moriarty -
Prof Jennifer Martin (IMB) -
Ralf W. Grosse-Kunstleve