Dear all,
I found that thread in my search of what ideal values for metal Phenix is
using. I tried to use that command "phenix.pdb_interpretation model.pdb
write_geo_files=true" for my pdb file, and I get all the values for most atoms,
like:
>>bond pdb=" CB LEU B 332 " segid="B "
pdb=" CG LEU B 332 " segid="B "
ideal model delta sigma weight residual
1.530 1.511 0.019 2.00e-02 2.50e+03 9.40e-01
>>
but for Mg ions i did not find the ideal value:
>>
nonbonded pdb=" O HOH C 405 "
pdb="MG MG M 1 "
model vdw
1.906 3.250
>>
Can I specify some keywords to get it also for Mg?
I looked through phenix folders and I found energy_lib.cif file. There are the
following records for Mg:
MG NPA metal 500.000 2.090 .
MG NPB metal 500.000 2.090 .
MG OHA metal 500.000 2.150 . # ?
MG OHB metal 500.000 2.150 . # ?
MG OHC metal 500.000 2.150 . # ?
MG O metal 500.000 2.180 . # ?
Do I understand correctly, that these are actually the default values? If I use
Phenix with default parameters, then distances will tend to become ideal?
Especially at low resolution when X-ray weight is low?
And what does mean, that for Mg there is no standard deviation of the bonds (.
# ? is placed instead)? How phenix will handle it? will it assign some default
esd?
I appreciate any comments! Thanks a lot!!
With best regards,
Ivan Shabalin, Ph.D.
Research Associate at Minor Lab, University of Virginia
4-224 Jordan Hall, 1340 Jefferson Park Ave.
Charlottesville, VA 22908
