[phenixbb] question about SAD+MR

Thomas C. Terwilliger terwilliger at lanl.gov
Fri Jul 24 09:40:48 PDT 2009

Hi Qun,
I'm sorry for the problem! That error message means that autosol made a
mistake, not that you are missing something.  I am hoping that perhaps you
are not using a very recent version phenix. Can you possibly try updating
with a recent "nightly build" from the phenix web site and see if that
fixes this problem?  If it does not, please let me know and I will fix it.
All the best,
Tom T

>> Dear all,
>> I have a Se-Met SAD data which diffracted to 2.8A (peak wavelength). The
>> space group is P1.
>> The map from SAD autosol and autobuild still gives crappy map, I can only
>> see one continous alpha-helix density with all other density fragmented
>> and
>> difficult to identify. I suppose it is because of high mosaicity (1.5),
>> low
>> data redundency, and some radiation damage.
>>  Now I want to use mocular replace (sequence identify ~0.26) plus SAD data
>> to give better map.
>> 1. The result from MR is shown below and the density is poor as the sole
>> SAD
>> map:
>> REMARK Log-Likelihood Gain:   121.374
>> REMARK  RFZ=3.4 TFZ=100.0 PAK=0 LLG=29 RFZ=3.7 TFZ=5.4 PAK=0 LLG=69
>> RFZ=6.1
>> TFZ=4.0 PAK=0 LLG=97 RFZ=5.6 TFZ=5.0 PAK=0 LLG=118 LLG=121
>> 2. I then tried to combine MR model and SAD data set
>> phenix.autosol seq_file=zntb-sd.seq sites=14 atom_type=Se
>> data=output-peak.sca sg="P1" cell="44.355 56.687 58.451 61.061 82.013
>> 82.740" resolution=3.0 input_partpdb_file=AutoMR_run_1_/MR.1.pdb
>> The program failed to run with such error message:
>> Failed to carry out AutoSol_score_ha_solutions:
>> [Errno 2] No such file or directory:
>> 'AutoSol_run_3_/TEMP0/phaser_mtz.hand.mtz'
>> I do not know where to get this phaser.mtz.hand.mtz file or how to
>> generate
>> it. Does anyone know?
>> --
>> Qun Wan
>> Department of Pharmacology, Case Western Reserve University
>> 10900 Euclid Avenue, Cleveland, OH 44106
>> email: qunwan1 at gmail.com
>> lab phone: 216-368-3337
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