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: [email protected] [mailto:phenixbb- [email protected]] 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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