[phenixbb] Autobuild with Model

Terwilliger, Thomas Charles terwilliger at lanl.gov
Mon May 23 18:18:12 PDT 2016

Hi David,

Unfortunately there isn't a way yet in autobuild to completely fix part of the model and try to build another part from scratch.  However one of the steps in autobuild is "build_outside = True" which blanks out the density wherever there is a model and builds into the remainder. This is kind of what you want to do, but it is combined with other building steps.

Another option is to use phenix.cut_out_density using a dummy model for the region that is not built to mark it. Then you can run phenix.map_to_model on the cut out map to build just that part.   Let me know if that works for you!

All the best,
Tom T

From: phenixbb-bounces at phenix-online.org <phenixbb-bounces at phenix-online.org> on behalf of Korasick, David A. <korasickd at missouri.edu>
Sent: Monday, May 23, 2016 2:39 PM
To: phenixbb at phenix-online.org
Subject: [phenixbb] Autobuild with Model

Dear All—

I have a question about the options in a series of Autobuild runs I am attempting. I have a structure that has 8 chains in the asymmetric unit, and one of the chains has very poor density. I ran phenix.refine using a model that lacked this chain, and now I want to run Autobuild to attempt to build in that chain. The issue I am running into is that I want Autobuild to only build into the density where there is no model, but not modify or build in density that is occupied by the model I give it. What are the options I should select to attempt this?

Thank you for your help!

David Korasick
Postdoctoral Fellow
Tanner Lab
University of Missouri-Columbia, Department of Biochemistry
korasickd at missouri.edu

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