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

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 : [email protected]
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