[phenixbb] clash_guard failure
Bock, Tobias
Tobias.Bock at helmholtz-hzi.de
Wed Apr 20 22:40:47 PDT 2016
Dear colleagues,
I am trying to refine a protein-DNA complex. In this structure, 2 DNA double strands are present with 50% occupancy (or similar occupancy’s) and overlap at certain positions. Phenix.refine crashed due to a nonbonded interaction distance issue. To fix that, I tried to exclude the DNA strands using:
pdb_interpretation {
custom_nonbonded_symmetry_exclusions="chain E"
custom_nonbonded_symmetry_exclusions="chain F"
}
Nevertheless, phenix.refine crashed with the same error message. Changing the “nonbonded_distance_threshold” works, but results in terrible statistics (since this applies for the complete structure, I guess).
Is there a way to exclude only the DNA strands (in regard to the clash guard) or a similar approach to refine the structure?
Thank you in advance for your help,
Tobias
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