[phenixbb] sculptor modifications

[Gabor Bunkoczi]

Dear Emily,

In addition to the suggestions below, you can run sculptor with verbose (or debug) output, and this will list all modifications made. Unfortunately, this is only available from the command line, try setting --verbosity to VERBOSE or DEBUG (you can use the eff-file generated by the GUI).

BW, Gabor

> -----Original Message-----
> From: phenixbb-bounces at phenix-online.org [mailto:phenixbb-
> bounces at phenix-online.org] On Behalf Of R. D. Oeffner
> Sent: 20 June 2017 23:54
> To: Emilia C. Arturo (Emily); PHENIX user mailing list
> Subject: Re: [phenixbb] sculptor modifications
>
> Hi Emilia,
>
> Sculptor may changes B-factors, morph residues or prune their side chains
> but in general it will not change their coordinates. One way to inspect
> changes is by using diff with the modified and the original file.
>
> Regards,
>
> Rob
>
>
> --
> Robert Oeffner, Ph.D.
> Research Associate, The Read Group
> Department of Haematology,
> Cambridge Institute for Medical Research University of Cambridge
> Cambridge Biomedical Campus Wellcome Trust/MRC Building Hills Road
> Cambridge CB2 0XY
>
> www.cimr.cam.ac.uk/investigators/read/index.html
> tel: +44(0)1223 763234
> -----Original Message-----
> From: Pavel Afonine
> Sent: Tuesday, June 20, 2017 11:26 PM
> To: Emilia C. Arturo (Emily) ; PHENIX user mailing list
> Subject: Re: [phenixbb] sculptor modifications
>
> Hi Emily,
>
> simplest and quickest way would be to load both models into Pymol (or
> Coot) and color one read and the other one blue (or any other combination
> of colors of your preference!). That will give you a quick idea about changes
> in coordinates (note, it may change B factors too, as far as I know..).
>
> Also,
>
> phenix.pdb.hierarchy model.pdb
>
> will give you counts of chains, residues, atoms, etc.
>
> Pavel
>
> On 6/20/17 14:44, Emilia C. Arturo (Emily) wrote:
> > Hello All,
> >
> > Is there a way to identify quickly the changes to a model that
> > Sculptor has made?
> >
> > I am running the Phenix GUI to use Sculptor. I have read through the
> > out-put log file, and understand (mostly) the sculpt protocol as it
> > relates to the circumstances under which modifications to main chain
> > or side chains are made, but it would be nice to see (in a list
> > format, perhaps) what changes (if any...) were made.
> >
> > Regards,
> > Emily.
> >
>
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