[phenixbb] automr : [1] MAP_COEFFS [2] output pdb's of ensemble

Randy Read rjr27 at cam.ac.uk
Tue Nov 16 09:27:43 PST 2010


I was a bit tied up last week, so I only managed to take a look at this today.  It turns out that there's a small bug with the handling of the MAP_COEFFS files, but the same information is present in the FWT/PHWT columns of the MR.n.mtz files, which are indeed produced correctly by AutoMR runs.  So you should be able to get the maps you need from those files.

On the second point, there was a time when we put all the members of an ensemble into the output PDB file, separating them by MODEL/ENDMDL records.  This worked fine if there was only one ensemble in the solution, but there's no way in the current PDB format to have different multiple models for different components.  We thought about splitting them over different PDB files, but that seemed like a logistical nightmare, so we settled on choosing the best representative for each component, as a compromise.  However, this is something we're thinking about (e.g. AutoBuild might benefit from having pieces from all the members of an ensemble to choose from).  In the meantime, as you say, you can run pdbset (or phenix.pdbtools) to transform the individual models.



On 12 Nov 2010, at 15:38, Bryan Lepore wrote:

> dev-572
> [1]
> in automr, i do not understand why only the last MR.MAP_COEFFS.n.mtz
> is written- e.g. i don't get 1-9 if 10 models are requested as output.
> (MR.[1-n].mtz are written ok).
> [2]
> when using an ensemble, i gather that the output is *hardwired* for
> the best rmsd model - i.e. there are no keywords to write out all
> parts of the ensemble. (i know i can run pdbset for them, but
> anyways...)
> -Bryan
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Randy J. Read
Department of Haematology, University of Cambridge
Cambridge Institute for Medical Research      Tel: + 44 1223 336500
Wellcome Trust/MRC Building                   Fax: + 44 1223 336827
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Cambridge CB2 0XY, U.K.                       www-structmed.cimr.cam.ac.uk

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