[phenixbb] Autobuild confrusion...which files to use?

Thomas C. Terwilliger terwilliger at lanl.gov
Tue May 4 12:08:48 PDT 2010

Hi Carl,

Yes, as Nat points out the two files contain the same data;
MR.MAP_coeffs.mtz has extracted 2 columns of data from MR.1.mtz and
relabeled columns.  Both should contain all data (regardless of the
resolution limit used in MR).

In autobuild it is useful to provide a starting map from phaser with
sigmaA-weighted coefficients; however if you skip that input then
autobuild will generate a starting map from the model (using a slightly
different algorithm) with resolve.

All the best,
Tom T

>> On Tue, May 4, 2010 at 10:30 AM, Carl Carruthers <caxrl at hotmail.com>
>> wrote:
>>>  using the GUI, i ran AutoMR and got several files, then hit the "Run
>>> AutoBuild" button.  When the AutoBuild panel came up, it automatically
>>> loaded three files from the AutoMR run: the original .mtz used in the
>>> AutoMR
>>> with Data Type as "X-ray data;" MR.mtz with Data Type as "Map Coeffs.";
>>> and
>>> MR.pdb with Data Type as "Start Model."
>>> my question is:  AutoMR lists the file MR.mtz as the Data type "Phased
>>> Data."  the AutoMR run also created a file named MR.MAP_coeffs.mtz with
>>> Data
>>> Type as "Map Coefficients."  Why did AutoBuild load MR.mtz as the "Map
>>> Coeff" instead of the MR.MAP_coeffs.mtz file as the "Map Coeffs?"  which
>>> should i use?
>> I think the map coefficients file is just a subset of the data in MR.mtz.
>>  The main differences in the map file are that the resolution limit used
>> in
>> MR is applied to the entire file including HKL indices, and the PHI column
>> is renamed.  I assume this was done for the benefit of some external
>> program.  I'm not sure if any starting map coefficients are necessary for
>> AutoBuild in this case since the resolution may be limited and the model
>> is
>> provided anyway - it is possible that the GUI is misleading you.
>> Hopefully
>> Tom and/or Randy can clarify.  If you don't get good results from
>> AutoBuild
>> using the default inputs, I would definitely recommend removing MR.mtz and
>> re-trying.
>> -Nat
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