[phenixbb] modification of nonbonded geo restraints between symmetry mates

Alejandro Buschiazzo alebus at pasteur.edu.uy
Tue Feb 3 09:26:46 PST 2009

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?)


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!

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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