[phenixbb] DEN refinement and reference model

[Jeff Headd]

Hi Luca,

Glad you were able to find the solution. In the future there will be more
flexible handling of chain IDs and segIDs, but for now what you've done is
the best fix.

Jeff


On Tue, Jan 8, 2013 at 8:07 AM, Luca Pellegrini <lp212 at cam.ac.uk> wrote:

> Ok, fixed -
>
> Eugene Valkov suggested using phenix.pdbtools with flags:
>
> set_seg_id_to_chain_id=True (Sets the segID field to the chain ID).
>
> or
>
> clear_seg_id=True (Erases the segID field.)
>
> I tried the second flag on both working and reference models, and now
> phenix.den_refine is running.
>
> Luca
>
> On 8 Jan 2013, at 12:34, Luca Pellegrini wrote:
>
> > Phenix.den_refine (1.8.1-1168) stops and complains that:
> >
> > "Sorry: Reference model contains SEGIDs that do not match the working
> model."
> >
> > I have four chains in both working and reference model, ordered in the
> same way (A to D). Chains A and C are the same molecule, and chains B and D
> are also the same. Can you please advice? Some of the chains in the
> reference model contain more residues, is this a problem?
> >
> > Thanks for your help.
> >
> > Luca
> >
> >
> > Luca Pellegrini
> > Department of Biochemistry
> > University of Cambridge
> > 80 Tennis Court Road
> > Cambridge CB2 1GA - UK
> >
> > Email: lp212 at cam.ac.uk
> > Tel: 0044-1223-760469
> > Fax: 0044-1223-766002
> > Sanger building, room 3.59
> >
> >
> >
> >
> >
> >
> >
> > _______________________________________________
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> > phenixbb at phenix-online.org
> > http://phenix-online.org/mailman/listinfo/phenixbb
>
> Luca Pellegrini
> Department of Biochemistry
> University of Cambridge
> 80 Tennis Court Road
> Cambridge CB2 1GA - UK
>
> Email: lp212 at cam.ac.uk
> Tel: 0044-1223-760469
> Fax: 0044-1223-766002
> Sanger building, room 3.59
>
>
>
>
>
>
>
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> phenixbb mailing list
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