[phenixbb] Failure when calculating a composite omit map

Dale Tronrud det102 at uoxray.uoregon.edu
Mon Jan 7 15:13:03 PST 2008

Hi all,

    I'm trying to calculate a composite omit map so that I can get
a clear view of a troublesome region in my structure.  I have two
copies of everything in the asu so I created some dummy atoms to
mask the region in the A chain and called those atoms chain Y and
another collection to mask the region in the C chain and created a
Z chain for them.  I put these atoms in a file name Mask.pdb

    I attempted to calculate the composite omit map starting from my
MR solution but that fails because Autobuild doesn't like being
given the Fourier coefficients produced by Phaser.

    To work around this problem I decided to ask it to create the
omit map based on the results of my AutoBuild followed the MR.  My
script is:

phenix.autobuild model=AutoBuild_run_12_/overall_best.pdb data=1M50-2.mtz \
   input_refinement_labels="FP SIGFP None None None None None None FreeR_flag" \
                  seq_file=../fmo-ct.pir \
                  resolution=2.2 dmax=20 refinement_resolution=2.2 \
                  cif_def_file_list=/usr/users/dale/geometry/chromophores/bcl_tnt.cif \
                  input_lig_file_list=AutoMR_run_4_/MR.1-Bchl-a.pdb \
                  composite_omit_type=iterative_build_omit omit_region_specification=omit_around_pdb omit_box_pdb=Mask.pdb\
                  omit_res_start_list="1 1" omit_res_end_list="39 30" omit_chain_list="Y Z" \

    Mask.pdb is attached.

    Resolve is unable to create a mask.  The log file, omit_box_id.log
is also attached.

    Resolve creates a temp file named TMP.pdb which I would expect to
contain the contents of my Mask.pdb.  It only contains the first set
of dummy atoms; chain Y.  Then when Resolve reads this file it appears
not to find even those atoms.

    I know Tom is out of reach for quite a while.  Is there someone else
who could help me over this hurdle?

Dale Tronrud
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