[phenixbb] coot add residue issue
Paul Emsley
pemsley at mrc-lmb.cam.ac.uk
Wed Aug 21 08:21:36 PDT 2013
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
> <uschulze-gahmen at lbl.gov <mailto:uschulze-gahmen at lbl.gov>> 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
> <condurso at bc.edu <mailto:condurso at bc.edu>> 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
>
> _______________________________________________
> phenixbb mailing list
> phenixbb at phenix-online.org <mailto:phenixbb at phenix-online.org>
> http://phenix-online.org/mailman/listinfo/phenixbb
>
>
>
>
> --
> Ursula Schulze-Gahmen, Ph.D.
> Assistant Researcher
> UC Berkeley, QB3
> 356 Stanley Hall #3220
> Berkeley, CA 94720-3220
>
> _______________________________________________
> phenixbb mailing list
> phenixbb at phenix-online.org <mailto:phenixbb at phenix-online.org>
> http://phenix-online.org/mailman/listinfo/phenixbb
>
>
>
>
> _______________________________________________
> phenixbb mailing list
> phenixbb at phenix-online.org
> http://phenix-online.org/mailman/listinfo/phenixbb
More information about the phenixbb
mailing list