Re: [phenixbb] Renumbering while retaining refinement info

Thanks Jack! Although I’m finding that Coot isn’t writing the refinement info in the output file either… (this is for deposition, so I need the refinement data). Maybe I need to try a newer version.

On 15 Oct 2023, at 3:36 PM, Tanner, John J. wrote:

External.

Hi Pat,

Coot has a tool to shift the residue numbers by a positive or negative increment. See Edit…Renumber Residues.

Best Regards,

Jack

From: [email protected] mailto:[email protected] mailto:[email protected]> on behalf of Patrick Loll mailto:[email protected]> Date: Sunday, October 15, 2023 at 1:22 PM To: PHENIX user mailing list mailto:[email protected]> Subject: [phenixbb] Renumbering while retaining refinement info

WARNING: This message has originated from an External Source. This may be a phishing expedition that can result in unauthorized access to our IT System. Please use proper judgment and caution when opening attachments, clicking links, or responding to this email. Hello all,

I've finished refining a handful of related structures, but now I need to renumber the residues to reflect the fact that I’m working with a truncated construct (like a dope I didn’t do this at the outset). However, when I run PDB Tools, it does not write the refinement information into the output CIF.

Is there a way to get around this, other than re-running the final cycle of refinement with the renumbered coordinates (or entering the refinement info by hand? This would be easy in the PDB format, but not so much in mmCIF).

Cheers,

Pat

__________________________________

Patrick J. Loll, PhD (he, him, his) Professor of Biochemistry & Molecular Biology Drexel University College of Medicine Room 10-102 New College Building 245 N. 15th St. Philadelphia, PA 19102-1192 USA

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