I don't think pdbtools has this right now, although it can probably be added with minimal effort. If you're willing and able to edit your model interactively, phenix.pdb_editor is much more flexible (but it's a GUI, so not suitable for automated use). Of course I'm pretty sure Coot can do this too. -Nat On Wed, Feb 26, 2014 at 9:21 PM, Rojan Shrestha wrote:

Hello,

I have found the program phenix.pdbtools. Maybe, it can renumber residues of pdb. I have found the options *renumber_residues* options but I am unable to see the options for starting residues.

I have pdb starts from 1 and want to renumber 1 into 250. Can somebody tell me how to put the option for starting residue?

Regards,

Rojan

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Both CCP4's PDBSET and COOT should do what you want (i.e. offset the numbering by 250) Phil Jeffrey Princeton ________________________________ From: [email protected] [[email protected]] on behalf of Rojan Shrestha [[email protected]] Sent: Thursday, February 27, 2014 12:21 AM To: PHENIX user mailing list Subject: [phenixbb] Option for renumber the pdb Hello, I have found the program phenix.pdbtools. Maybe, it can renumber residues of pdb. I have found the options renumber_residues options but I am unable to see the options for starting residues. I have pdb starts from 1 and want to renumber 1 into 250. Can somebody tell me how to put the option for starting residue? Regards, Rojan

Since you are already in Phenix - How about the option under "Model tools" called "PDB file editor"? When you open this option it asks for a pdb file, and once loaded you can select (click on) your chain.  Click "Edit" from the top bar and select "Renumber residues".  It pops up a box asking how much to increment the numbers by and produces the renumbered pdb file.  (Note - it will accept negative numbers as well) Many other options there too... Kind regards, Christina Christina R. Bourne, Ph.D. Assistant Professor Dept. of Chemistry and Biochemistry University of Oklahoma 101 Stephenson Parkway, SLSRC Rm 2610 Norman, OK 73019 Office +1 (405) 325-5348 Mobile +1 (405) 338-5616 http://faculty-staff.ou.edu/B/Christina.Bourne-1/CRBourne/Welcome.html On Wednesday, February 26, 2014 11:21 PM, Rojan Shrestha wrote: Hello, I have found the program phenix.pdbtools. Maybe, it can renumber residues of pdb. I have found the options renumber_residues options but I am unable to see the options for starting residues. I have pdb starts from 1 and want to renumber 1 into 250. Can somebody tell me how to put the option for starting residue? Regards, Rojan  _______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb