[phenixbb] ncs

[Engin Ozkan]

Check out the Atom selection section for examples in the documentation.
http://www.phenix-online.org/documentation/refinement.htm#anch82

Good luck,

Engin

On 6/27/09 12:10 PM, Maia Cherney wrote:
> Hi Engin,
> thank you for your reply. That is exactly what I wanted. I just forgot
> the correct syntax. Actually, I could not find these words in the
> documentaion. I guess, they are very well hidden.
>
> Maia
>
> Engin Ozkan wrote:
>    
>> Am I missing something?  How about this
>>
>> refinement.ncs.restraint_group {
>>     reference = chain A and not (resid 125 or resid 248 or ...)
>>     selection = chain B and not (resid 125 or resid 248 or ...)
>> }
>>
>> as it is in http://www.phenix-online.org/documentation/
>> I don't think this is harder than excluding residues with an "option".
>>
>> Engin
>>
>> On 6/27/09 10:28 AM, Pavel Afonine wrote:
>>
>>      
>>> Hi Maia,
>>>
>>>
>>>
>>>        
>>>> I made all restraint_groups in my parameter file. It's just too many of
>>>> them. I thought that may be there is an option to say exclude residues
>>>> 125, 248 etc.
>>>>
>>>>
>>>>          
>>> No - there is no such command: you need to edit selections manually.
>>>
>>>
>>>
>>>        
>>>> By the way, I have  excessive_distance_limit = None. If I
>>>> change it to some number, how does it work? the violating residues will
>>>> be  excluded or the whole molecule will?
>>>>
>>>>
>>>>
>>>>          
>>> I'm not sure, Ralf knows this better. Ralf, could you comment on this
>>> please?
>>>
>>> My guess, that all this parameter does is it checks the distances
>>> between atoms in NCS copies and if there is a distance larger than
>>> excessive_distance_limit, then phenix.refine stops and tells you this.
>>>
>>> Pavel.
>>>
>>> _______________________________________________
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>>> phenixbb at phenix-online.org
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>>>
>>>
>>>        
>>
>>      
>
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>    


-- 
Engin Özkan
Post-doctoral Scholar
Laboratory of K. Christopher Garcia
Howard Hughes Medical Institute
Dept of Molecular and Cellular Physiology
279 Campus Drive, Beckman Center B173
Stanford School of Medicine
Stanford, CA 94305
ph: (650)-498-7111

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