[phenixbb] sculptor modifications

R. D. Oeffner rdo20 at cam.ac.uk
Tue Jun 20 15:53:43 PDT 2017

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.



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

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..).


phenix.pdb.hierarchy model.pdb

will give you counts of chains, residues, atoms, etc.


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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