[phenixbb] Rebuild in place - Phenix AutoBuild

Randy Read rjr27 at cam.ac.uk
Tue Sep 15 11:04:21 PDT 2020

That’s a great question!

By default, sculptor produces a model that has the target sequence, even though a lot of side chains might be missing.  AutoBuild looks at the sequence, says it’s basically correct, and decides by default that the rebuild_in_place option should be turned on.  If your original template was not really closely related, this can really hamper model building.  I tend to turn off rebuild_in_place if the model is going to require much improvement (or filling in of missing pieces) and then let it be turned on by default later on once things are basically right.  I would guess that somewhere between 50% and 30% identity, you would want to switch from allowing rebuild_in_place to not allowing it.

Best wishes,

Randy Read
Randy J. Read
Department of Haematology, University of Cambridge
Cambridge Institute for Medical Research     Tel: +44 1223 336500
The Keith Peters Building                               Fax: +44 1223 336827
Hills Road                                                       E-mail: rjr27 at cam.ac.uk
Cambridge CB2 0XY, U.K.                              www-structmed.cimr.cam.ac.uk

> On 15 Sep 2020, at 18:26, Emad Alharbi <emad.alharbi at york.ac.uk> wrote:
> Dear Phenix developers,
> I have a question about using 'Rebuild in place' feature in Phenix AutoBuild. Which is recommended when you build MR case, set this feature to false or use the default option? I mean by saying default option to let Phenix AutoBuild decide. 
> Thank you!   
> ------------------------------
> Emad Alharbi
> Research Student
> Department of Computer Science
> University of York,UK.
> _______________________________________________
> phenixbb mailing list
> phenixbb at phenix-online.org
> http://phenix-online.org/mailman/listinfo/phenixbb
> Unsubscribe: phenixbb-leave at phenix-online.org

More information about the phenixbb mailing list