PDB Tools and CNS formatted structure factors
Is there anyway with the PDB Tools to renumber protein chains? I have a model that doesn't correspond to the actual sequence, off by a couple of residues and just looking for a quick way to change that. Also, which module in Phenix is used to read in and convert CNS formatted ascii structure factors to the mtz read by phenix other then using ccp4. ___________________________________________________________ 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 ___________________________________________________________
Hi Joe, I usually use coot when I renumber sequences or reassign chain IDs. HTH Carsten From: [email protected] [mailto:[email protected]] On Behalf Of Joseph Noel Sent: Wednesday, September 22, 2010 6:39 AM To: [email protected] Subject: [phenixbb] PDB Tools and CNS formatted structure factors Is there anyway with the PDB Tools to renumber protein chains? I have a model that doesn't correspond to the actual sequence, off by a couple of residues and just looking for a quick way to change that. Also, which module in Phenix is used to read in and convert CNS formatted ascii structure factors to the mtz read by phenix other then using ccp4. ___________________________________________________________ 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 ___________________________________________________________
On Wed, Sep 22, 2010 at 3:39 AM, Joseph Noel
Is there anyway with the PDB Tools to renumber protein chains? I have a model that doesn't correspond to the actual sequence, off by a couple of residues and just looking for a quick way to change that. Also, which module in Phenix is used to read in and convert CNS formatted ascii structure factors to the mtz read by phenix other then using ccp4.
The reflection file editor in the GUI is the easiest tool for format
conversions (there are also a couple of command-line utilities like
phenix.reflection_file_converter). However, most of the programs will
quite happily take a CNS file as input (the exception I believe is a
few of the tools which use Resolve directly, like fit_loops or
find_helices_strands). Some of these will export the reflections as
an MTZ file too - for instance, phenix.refine will write out a file
Hi Joseph,
Is there anyway with the PDB Tools to renumber protein chains?
Did you mean "renumber residues in protein chains"? Do you want it protein-specific (that is say DNA/RNA and other non-protein molecules will be ignored)? Anyway, I just added the simplest version of renumbering residues in chains will be available in the next PHENIX version (nightly build): phenix.pdbtools model.pdb renumber_residues=true I can add more functionality as needed/requested.
Also, which module in Phenix is used to read in and convert CNS formatted ascii structure factors to the mtz read by phenix other then using ccp4.
The tool for doing this and more is available from PHENIX GUI and called "Reflection file editor". Pavel.
participants (4)
-
Joseph Noel -
Nathaniel Echols -
Pavel Afonine -
Schubert, Carsten [PRDUS]