Pascal
The value are buried in a file in the installation. I suggest you edit the
output files as you see fit.
However, I do like the idea of reading a user provided file for the values
so will look into it.
There is also an option to calculate the distances using Mopac which is now
distributed with Phenix. The Quantum Interface (QI) module can calculate
the bond lengths. It's a work in progress so if you have a particular
model, send it to me directly and I will get you the results.
Cheers
Nigel
---
Nigel W. Moriarty
Building 91, Molecular Biophysics and Integrated Bioimaging
Lawrence Berkeley National Laboratory
Berkeley, CA 94720-8235
Email : [email protected]
Web : CCI.LBL.gov
ORCID : orcid.org/0000-0001-8857-9464
On Sun, Feb 22, 2026 at 5:39 AM
Hi,
We used phenix.metal_coordination to generate metal restraints and it works well. My question is in which file can I find the distances (ideal) used by this program.
refinement.geometry_restraints.edits { bond { action = *add atom_selection_1 = name MG and chain V and resname MG and resseq 258 atom_selection_2 = name O and chain Y and resname HOH and resseq A1A8 distance_ideal = 2.140000 sigma = 0.190 } }
refinement.geometry_restraints.edits { bond { action = *add atom_selection_1 = name MG and chain V and resname MG and resseq 258 atom_selection_2 = name N7 and chain a and resname G and resseq 1190 distance_ideal = 1.895092 sigma = 0.050 } }
refinement.geometry_restraints.edits { bond { action = *add atom_selection_1 = name MG and chain V and resname MG and resseq 258 atom_selection_2 = name O and chain Y and resname HOH and resseq 2831 distance_ideal = 2.140000 sigma = 0.190
In this example, the Mg...O ideal distance is 2.14 and we would prefer to use 2.07 Same for Mg...N distances of 1.895092 that should be changed to 2.19
Thanks for letting us know if there is a parameter file for this or even better, an option to use distance values extracted from the input cif file.
Pascal _______________________________________________ phenixbb mailing list -- [email protected] To unsubscribe send an email to [email protected] Unsubscribe: phenixbb-leave@%(host_name)s