[phenixbb] omit map with twinning?

[Francis E Reyes]

Hi Pavel

Well it seems that Nathaniel Echols tried it with the merohedrally  
twinned porin structure in the examples directory and the density maps  
were not great at all.

>>> http://cci.lbl.gov/~nat/img/phenix/omit_detwinned_sa.png

The OP (Kelly Daughtry) wants an SA omit map on a twinned structure.  
This is something I've struggled with for sometime and could never get  
a decent map.

FR



On Feb 18, 2010, at 12:29 PM, Pavel Afonine wrote:

> Hi Francis,
>
> you can compute SA omit map in phenix.refine right now, regardless  
> whether you have twinning or not. I wrote how you can do it in  
> previous email - just two trivial steps!
>
> Pavel.
>
> On 2/18/10 11:18 AM, Francis E Reyes wrote:
>>> No, I was too impatient to wait for simulated annealing, but I  
>>> started it up when I got here this morning - you're right, it's  
>>> much much worse than the non-SA map, and much worse than anything  
>>> I've seen from the same procedure run on a non-twinned structure.
>>>
>>> http://cci.lbl.gov/~nat/img/phenix/omit_detwinned_sa.png
>>
>>
>> Ah! I was losing sleep thinking I was the only one who had this  
>> issue.
>>
>> Xtal refinement is dominated by three programs (correct me if I'm  
>> wrong). Refmac, phenix.refine, and cns. simulated annealing is  
>> handled by phenix.refine and cns, but twinning is handled  
>> (decently) by refmac and phenix.refine.  Given this, phenix.refine  
>> seems to be the only solution when you have twinning and want to  
>> calculate an sa-omit (unless you decide to "grow a better  
>> crystal"). Therefore, fixing this for phenix would be much needed!
>>
>>
>> FR
>>
>>
>> ---------------------------------------------
>> Francis Reyes M.Sc.
>> 215 UCB
>> University of Colorado at Boulder
>>
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>>
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>>
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---------------------------------------------
Francis Reyes M.Sc.
215 UCB
University of Colorado at Boulder

gpg --keyserver pgp.mit.edu --recv-keys 67BA8D5D

8AE2 F2F4 90F7 9640 28BC  686F 78FD 6669 67BA 8D5D