[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
>
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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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>
>
>
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