[phenixbb] Renumbering while retaining refinement info

[Patrick Loll]

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. <TannerJJ at missouri.edu> 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: phenixbb-bounces at phenix-online.org <mailto:phenixbb-bounces at phenix-online.org> <phenixbb-bounces at phenix-online.org <mailto:phenixbb-bounces at phenix-online.org>> on behalf of Patrick Loll <pjloll at gmail.com <mailto:pjloll at gmail.com>>
> Date: Sunday, October 15, 2023 at 1:22 PM
> To: PHENIX user mailing list <phenixbb at phenix-online.org <mailto:phenixbb at phenix-online.org>>
> Subject: [phenixbb] Renumbering while retaining refinement info
> 
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> 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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Patrick Loll
pjloll at gmail.com



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