[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
phenix.solve<<EOD
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
EOD
------------------------------------
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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