[phenixbb] insert ligand restraints in real space refinement

Oleg Sobolev osobolev at lbl.gov
Fri Mar 27 15:41:37 PDT 2020

Hi Valerie,

The functionality you are mentioning is obsolete for some time now.
Therefore I would recommend updating to recent Phenix release or nightly,
especially for real-space refine.

If you already have restraints for your ligand, they should be sufficient.
If not, you can make them using eLBOW.

There is a video tutorial about how to find and change parameters in
phenix.refine (real-space is very similar):

Generally, in Phil notation '*' marks selected options.

Please get back to us if you have more questions.

Best regards,
Oleg Sobolev.

On Fri, Mar 27, 2020 at 5:42 AM Valerie Biou <valerie.biou at ibpc.fr> wrote:

> Hello
> I am trying to impose restraints on my lipid ligand during real space
> refinement. I found the command
> refinement.geometry_restraints.edits.scale_restraints {
>   atom_selection = "resname LLP"
>   scale = 2.5
>   apply_to = *bond *angle dihedral chirality
> I have 2 questions
> 1) can those lines be called from the GUI and where? if not, how can I
> insert them in a previous command file?
> 2) what do the * stand for? is it to activate or cancel the selection of
> an item?
> sorry if those questions have been asked before, I can't find the command
> to browse the bb archive.
> All the best,
> Valérie
> _______________________________________________
> phenixbb mailing list
> phenixbb at phenix-online.org
> http://phenix-online.org/mailman/listinfo/phenixbb
> Unsubscribe: phenixbb-leave at phenix-online.org
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://phenix-online.org/pipermail/phenixbb/attachments/20200327/148d963d/attachment.htm>

More information about the phenixbb mailing list