[phenixbb] phenix.map_to_object for HA sites

Thomas C. Terwilliger terwilliger at lanl.gov
Thu Dec 16 17:32:52 PST 2010

Hi Michael,

No, I'm afraid map-to-object only moves the whole contents of a PDB file
close to the target object, not individual atoms.

You can use a function in phenix.solve to do the job, however:

#!/bin/csh -f
cp $PHENIX/solve_resolve/ext_ref_files/p21.sym .     # copy symmetry file
to working directory
cell 25.000   25.000   25.000  90.00 100.00  90.00
symfile p21.sym
resolution 200 5
infile(1)  atoms.pdb      !  input file with coordinates to be mapped
infile(2)  object.pdb     !  pdb file with object that we want to be close to
outfile    atoms.mapped   !  atoms mapped close to object
dismin     0.0            !  Only atoms with a closest distance to an atom
dismax 1000.0             !  in object between dismin and dismax will be
                          !  written out. Default= 0 to 1000000.
maptoobject                 !  map them as close to the object as possible


All the best,
Tom T

>> Hi,
>> I have a .pdb with heavy atoms that are dispersed all over the unit
>> cell. I would like to move all of them (about 40) as close as possible
>> to my refined structure. Could phenix.map_to_object do that for all
>> heavy atoms at once, or would I need to do this in an atom by atom manner?
>> Thanks
>> Michael
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