[phenixbb] modification of nonbonded geo restraints between symmetry mates

Nigel W Moriarty NWMoriarty at lbl.gov
Tue Feb 3 08:32:19 PST 2009


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.


On 2/3/09 3:10 AM, Alejandro Buschiazzo wrote:
> Dear PHENIX users,
> I wonder what is the 'correct' way of (re)defining geometric restraints 
> among atoms.
> Here's what I need to do : I have several cations that are chelated by 
> protein residues; some of them involve residues from the same monomer, 
> yet others involve atoms from both the ASU monomer as well as crystal 
> neighbors (i.e. symmetry mates).
> I see that in the .geo file, these parameters are taken into account as 
> nonbonded simple and nonbonded asu respectively ... how can I change the 
> ideal distances to get proper Zn+2 coordination bonds for both kind of 
> partners?
> Thank you in advance for your help!

Nigel W. Moriarty
Building 64R0246B, Physical Biosciences Division
Lawrence Berkeley National Laboratory
Berkeley, CA 94720-8235
Phone : 510-486-5709
Fax   : 510-486-5909
Email : NWMoriarty at LBL.gov
Web   : CCI.LBL.gov

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