[phenixbb] Remove distant restraint between two atoms

Pavel Afonine pafonine at lbl.gov
Thu Mar 3 08:16:01 PST 2016

Hi Wulf,

> I would like to unrestrain the distance between two atoms in a ligand 
> – how can I do this? I found instructions for writing a 
> remove_restraints_selections.params file in the phenix.refine manual, 
> but it does not seem to address bond distances.

bonds are not there indeed. Currently you can do it as following 
(admittedly rather ugly!)...

Edit ligand CIF file to remove the definition of bond in question, then 
run refinement providing this CIF file. If CIF file is part of Phenix 
library, then

a) Find its location:

elbow.where_is_that_cif_file ATP

you will see something like this


b) Copy it to your place

cp /Users/pafonine/phenix_dev/modules/chem_data/mon_lib/a/ATP.cif 

Then edit ATP_edited.cif to remove the bond in question (I guess you 
would want to remove angle too) and give it to phenix.refine along with 
all other inputs.

Let me know how this worked (or didn't) for you!

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