[phenixbb] restraints_edits.params -- inquiries -- issues

[Oleg Sobolev]

Hi Pascal,

I apologize for the delayed reply. Thank you for bringing this to our
attention.

Regarding GUI, can you please change the extension of the file to just
".params" instead of ".params.cif"? This "cif" ending may confuse the GUI.

Given that there is no way to have residue id > 9999 in PDB format I assume
you are using mmCIF and get something like

  Custom bonds:
Sorry: No atom selected: "chain 0 and resname HOH and resid 13322 and name
O"

when you try to use your parameters in the command line.

We will work on fixing this issue in the near future.

Meanwhile:

For resids and atom numbers > 9999 Phenix uses hybrid 36 encoding:
http://cci.lbl.gov/hybrid_36/
https://github.com/cctbx/cctbx_project/blob/master/iotbx/pdb/hybrid_36.py

Therefore you can try to use this encoding in your parameter file. For
example, "resid 13322" will translate to "resid A2KA".
There are several ways to figure out this encoding:

1. Run phenix.cif_as_pdb <your model.cif> and get PDB file where resids
will be encoded with hybrid36.

2. if you have python with cctbx library:
  from iotbx.pdb.hybrid_36 import hy36encode
  hy36encode(width=4, value=13322)

Other option would be splitting chain with > 10k residues into several
chains with less than 10k residues.

Best regards,
Oleg Sobolev.

On Thu, Mar 23, 2023 at 1:26 PM p.auffinger <p.auffinger at unistra.fr> wrote:

> Hi phenix users,
>
> I started to add restraints to a large ribosomal file
> by using the file (in full) below.
>
> I encountered two issues:
>
> 1)
> The first one is:
> how to use this file in the GUI?
> It seems to get rejected while its accepted
> when I run phenix through the command line.
>
> 2)
> The second is:
> restraints involving water molecules with
> residue numbers > 9999 get rejected.
> Could that limit be overcome through a future
> patch?
>
> ###
> refinement.geometry_restraints.edits {
>   MG_8078   = chain 0 and resname  MG and resid  8078 and name MG
>   W_12641   = chain 0 and resname HOH and resid 12641 and name O
>   bond {
>     action = *add
>     atom_selection_1 = $MG_8078
>     atom_selection_2 = $W_12641
>     symmetry_operation = None
>     distance_ideal = 2.2
>     sigma = 0.1
>     slack = None
>    }
>  }
> ###
>
> Thanks for any thoughts on this,
>
> Pascal
>
>
>
> -----
> Pascal Auffinger
> IBMC/CNRS
> 15 rue René Descartes
> 67084 Strasbourg Cedex
>
> p.auffinger at ibmc-cnrs.unistra.fr
> -----
>
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