From 2b3d217dce7f1714902655329679b2bdd20d2296 Mon Sep 17 00:00:00 2001 From: chrissciwilliams Date: Thu, 14 Oct 2021 09:55:40 -0400 Subject: [PATCH] allow_polymer_cross_special_position flag This pdb_interpretation parameter allows processing of pdb files that otherwise fail. It is likely inappropriate for refinement, but is useful in validation where we seek to accept as many models as possible. --- mmtbx/hydrogens/reduce_hydrogen.py | 1 + 1 file changed, 1 insertion(+) diff --git a/mmtbx/hydrogens/reduce_hydrogen.py b/mmtbx/hydrogens/reduce_hydrogen.py index 533a4ec64d..8ebec6b38e 100644 --- a/mmtbx/hydrogens/reduce_hydrogen.py +++ b/mmtbx/hydrogens/reduce_hydrogen.py @@ -123,6 +123,7 @@ def run(self): p.pdb_interpretation.clash_guard.nonbonded_distance_threshold=None p.pdb_interpretation.use_neutron_distances = self.use_neutron_distances p.pdb_interpretation.proceed_with_excessive_length_bonds=True + p.pdb_interpretation.allow_polymer_cross_special_position=True #p.pdb_interpretation.automatic_linking.link_metals = True t0 = time.time()