[phenixbb] modification of nonbonded geo restraints between symmetry mates

Alejandro Buschiazzo alebus at pasteur.edu.uy
Tue Feb 3 09:37:52 PST 2009

sorry to  bother!  

...of course it was silly : the 'shared' Zn atoms are on special 
positions, so I guess the best way to go is to refine their positions 
with 0.5 occupancy and that's it (the bond distance with the symmetric 
of course already being taken into account on the ASU's contents!)



Alejandro Buschiazzo wrote:
> Thank you Nigel!
> I'll try this immediately.
> ...in the meantime, I still have a question for you  : will this handle 
> as well the coordination with atoms on symmetry-related protein 
> neighbors? (don't see those in the elbow.edits that 
> phenix.metal_coordination generates...or am I missing something silly here?)
> ale
> Nigel W Moriarty wrote:
>> Alejandro
>> There are a number of options.  The most direct is to use
>> phenix.metal_coordination --use-default-bondlengths=1 model.pdb
>> to get an "edits" file which contains a number of bond and angle 
>> directives for phenix.refine.  Without the --use-default-bondlengths 
>> option, the bonds in the model.pdb are used as ideal distances.  With 
>> the option, the ideal values are quantum chemical calculated distances.
>> Always look in the edits file to make sure it contains the restraints 
>> you want.  You can remove some (angles are the most likely candidates) 
>> and add if desired.
>> You can also run
>> phenix.ready_set model.pdb
>> which will generate the "edits" file and add hydrogens to your model.
>> Nigel

Alejandro Buschiazzo, PhD
Research Scientist
Laboratory of Protein Crystallography
Pasteur Institute of Montevideo
Mataojo 2020
Montevideo 11400

Phone: +5982 5220910 int. 120
Fax:   +5982 5224185

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