Re: [phenixbb] coot add residue issue

A bit late to the party... :-( Try adding these to your ~/.coot.py set_terminal_residue_do_rigid_body_refine(0) set_add_terminal_residue_do_post_refine(1) Paul. On 20/08/13 20:25, Heather L Condurso wrote:

Thank you all. I do not know what solved my issue but I deleted many UNK residues that though having a lower number came after the end of my chain in the pbd file and now it is working. I had tried real space refine and moved it manually but without avail. Maybe this version of coot 0.6.2-pre-1 is unhappy with pdb from phenix autobuild/refine.

On Tue, Aug 20, 2013 at 3:18 PM, Ursula Schulze-Gahmen mailto:[email protected]> wrote:

Heather,

I am using the stand alone version of coot and I am adding terminal residues all the time. I have the same experience as you do , that the residue is usually added far away from the end of my chain. I then move it into a sensible position relative to the chain end and refine the geometry on coot. I have never seen the residue moving back to its original position. Perhaps try the stand alone version of coot and see if it works there for you.

Ursula

On Tue, Aug 20, 2013 at 11:53 AM, Heather L Condurso mailto:[email protected]> wrote:

Dear all,

I have been trying to add a residue to my model in coot for hours now. The add terminal residue function adds a residue far from the end of my chain and I've tried moving it manually and it keeps going back and it never makes a bond between the two amino acids. Is there a trick in coot or a better way to do this in phenix?

Thanks, Heather Condurso UF-Department of Chemistry

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-- Ursula Schulze-Gahmen, Ph.D. Assistant Researcher UC Berkeley, QB3 356 Stanley Hall #3220 Berkeley, CA 94720-3220

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