[phenixbb] ncs

[Maia Cherney]

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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>>    
>>     
>
>
>