[phenixbb] input sharp phases into phenix.autosol

Thomas C. Terwilliger terwilliger at lanl.gov
Mon Jun 14 15:51:41 PDT 2010

Hi Michael,

If I understand correctly, you want to take a file that has experimental
phases, density modify it, and autobuild a model.  Plus you want to take
the inverse hand of the phases and do the same thing.

For the first part you have two easy options:

phenix.autobuild      my_exptl_phases.mtz my_seq.dat ha_file=my_ha_file
phenix.build_model my_exptl_phases.mtz my_seq.dat ha_file=my_ha_file

These do more or less the same thing, but build_model is a lot faster (but
not quite as good), and requires version 1.6.2-242 or higher.  For phases
from sharp, you will want to specify the columns of data to be used for FP
SIGFP PHIB FOM HLA HLB HLC HLD for each method above. (The way to specify
these are different in the two methods. For autobuild you just list the
column labels to be used for the above items with labels="myFP mySIGFP
myPHIB myFOM myHLA myHLB myHLC myHLD", and for build_model you specify a
regular labin line: labin="FP=myFP SIGFP=mySIGFP...etc"

For the second part, flipping the hand of a file with experimental
phases...I am not sure if we have a tool for that. Perhaps someone else
can comment.

All best,
Tom T

>> Hi,
>> I hope what I want to do is not considered a crime :-) Is there a way to
>> input phases e.i. from sharp into phenix.autosol (preferably the command
>> line version) to run resolve with both hands and autobuild for a SAD or
>> SIRAS case?
>> Thanks!
>> Michael
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