[phenixbb] fwd: phenix.autobuild- multiple models.

Thomas C. Terwilliger terwilliger at lanl.gov
Wed Mar 4 13:01:02 PST 2009

Hi Michael,

In fact phenix.autobuild already is merging the models at some level, as
it uses models from prior cycles as part of the input to each cycle.
However if you want to do a simple merge of a bunch of model you can use

consider_main_chain_list= None This keyword lets you name any number of
                                PDB files to consider as templates for
                                model-building. Every time models are built,
                                the contents of these files will be merged
                                with them and the best parts will be kept.
                                NOTE: this only uses the main-chain atoms of
                                your PDB files.

All the best,
Tom T

(The server bounced this message for some reason.)

> From: Michael Karl Uhl <michael.uhl at uni-graz.at>
> Date: March 3, 2009 11:55:16 PM PST
> To: phenixbb at phenix-online.org
> Subject: phenix.autobuild- multiple models
> Reply-To: michael.uhl at a-b.at
> Hello,
> I have not registered for this list until now, but have a very
> urgent question concerning phenix.autobuild and multiple models as
> input. Is there a possibility to merge models generated by different
> phenix.autobuild runs. I have several overall_best-structure and
> want to merge them into one single overall_best structure. I have
> found the keyword "merge_models= True" but it does not really work
> (Sorry, unknown file or keyword: merge_models=True). How should I
> make the input in this case?
> Thanks a lot,
> Michael Uhl.

Nathaniel Echols
Lawrence Berkeley Lab
NEchols at lbl.gov

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