[phenixbb] modification of nonbonded geo restraints between symmetry mates
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:
> 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
>> Thank you in advance for your help!
Alejandro Buschiazzo, PhD
Laboratory of Protein Crystallography
Pasteur Institute of Montevideo
Phone: +5982 5220910 int. 120
Fax: +5982 5224185
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