[phenixbb] Re: Metal distance parameters used by phenix.metal_coordination

Thanks Nigel, I understand your concerns and do not mind modifying a single file in the phenix folder given that we are working on ribosomes meaning that the restraint file contains about 3000 single restraints. The restraint distances we would like to use are generated by the Cat_Wiz scripts and are the following d(Mg…O/N) = 2.07/2.19 Å. The Cat_Wiz paper is going to appear very soon in NAR and describes the entire process. https://www.biorxiv.org/content/10.1101/2024.04.07.588377v1 Thanks for looking at setting a user provided file that would be a nice addition to Phenix. Other than that, in the present case Using Mopac that is a nice feature of Phenix will not help in our case. Best, Pascal

Le 23 févr. 2026 à 01:06, Nigel Moriarty a écrit :

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 http://cci.lbl.gov/ ORCID : orcid.org/0000-0001-8857-9464 https://orcid.org/0000-0001-8857-9464

On Sun, Feb 22, 2026 at 5:39 AM mailto:[email protected]> wrote:

...

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] mailto:[email protected] To unsubscribe send an email to [email protected] mailto:[email protected] Unsubscribe: phenixbb-leave@%(host_name)s

----- Pascal Auffinger IBMC/CNRS 2, Allée Konrad Roentgen 67084 Strasbourg Cedex [email protected] -----