[phenixbb] On Phenix refinement

Andreas Förster docandreas at gmail.com
Fri Feb 20 05:58:15 PST 2015


Hi Smith,

convergence means that the coordinates of your model (and thus R free, 
geometric parameters etc) have stabilized.  Adding further cycles of 
refinement doesn't change anything, i.e. the results of a five-cycle run 
will be indistinguishable from those of a four-cycle run if convergence 
was reached after four cycles.


Andreas (still very much alive)




On 20/02/2015 1:39, Smith Liu wrote:
> Dead Andreas,
> For Phenix refine, will you please tell me the definition of the
> convergence?
>
> I am looking forward to getting your reply.
>
> Smith
>
>
>
>
>
>
> At 2015-02-20 20:02:31, "Andreas Förster" <docandreas at gmail.com> wrote:
>>Hi Smith,
>>
>>refinement shouldn't be done for three macrocycles or five but to
>>convergence.  Do you think you've reached convergence?
>>
>>If your refinement result is unacceptable, as you say, you have to
>>change your strategy or improve your model.
>>
>>Best.
>>
>>
>>Andreas
>>
>>
>>
>>
>>On 20/02/2015 11:56, Smith Liu wrote:
>>> Dear All,
>>>
>>> The default number of cycles for the Phenix refinement graphical
>>> interface is 3 (should be macro-cycles). I have done a refinement with 3
>>> default cycles, and I get the acceptable refinement results. Then I kept
>>> everything same, except I changed the cycles of refinement from 3 to 5,
>>> however the refinement result was ugly which was unacceptable (Rfree
>>> increased).
>>> The Phenix document regards 5 macrocycles refine is fine. For my
>>> situation, do you think the 3 macrocycles refine result is acceptable or
>>> not? If not acceptable, what do you suggest for improvement?
>>>
>>> I am looking forward to getting your reply.
>>>
>>> Smith
>>>
>>>
>>>
>>>
>>>
>>>
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>
>
>


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