[phenixbb] modification of nonbonded geo restraints between symmetry mates

Nigel W Moriarty NWMoriarty at lbl.gov
Tue Feb 3 09:42:09 PST 2009


Alejandro

Currently you have to have LINK records in your model.pdb that contain 
the symmetry details and use

phenix.link_edits

to generate the correct "edits".  I'll have to look into putting the 
smarts into the metal_coordinate code.

Nigel

On 2/3/09 9:26 AM, 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
>>
>> 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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