[phenixbb] autosol strategy

Maia Cherney chern at ualberta.ca
Thu May 28 12:42:42 PDT 2009


Thanks Tom, Miguel,
for your help.

I would like you to know that the older version of phenix (1.4-3) works, 
but the newer versions 1.4-4 and 1.4-58 don't recognize some key words. 
The error message is
 
Sorry, unknown file or keyword: peak.data=peak1_p6422.sca


Maia

Miguel Ortiz Lombardia wrote:
> Hi Maia,
>
> If your phases are good enough I think resolve should be able to build 
> at least a good partial model. Otherwise, you can build it manually... 
> Your resolution isn't great, but you may be able to place some 
> secondary structure elements (ARP/wARP 'Quick fold' can also come to 
> help here).
>
> Perhaps another option is to solve your native dataset by molecular 
> replacement using the best map you have from the MAD dataset, then you 
> wouldn't need to build a model in the low resolution MAD data. Molrep 
> and AMoRe can do that, probably Phaser can as well.
>
> Good luck,
>
>
> Miguel
>
> Le 28 mai 09 à 06:12, Maia Cherney a écrit :
>
>>
>> Hi Tom,
>> thank you for your reply. How can I build a model at this resolution
>> 3.3A (anomalous signal 4.2A). Actually, that was my major question. Is
>> it possible to build a model at this resolution? Or how else I can use
>> the phases from the low resolution solution (if I get it) with the high
>> resolution native data?
>>
>> I did not see such a combination in the examples.
>>
>> Maia
>>
>> Thomas C. Terwilliger wrote:
>>> Hi Maia,
>>>
>>> As your datasets are in 2 different space groups, you pretty much 
>>> have to
>>> solve the structure in one space group, then transfer information about
>>> the structure (model) to the other space group.
>>>
>>> So...you want to run an autosol run with the MAD data (or as SAD,
>>> sometimes that works better if you have a lot of decay) to solve the
>>> structure...then you want to build a model if you can in that space 
>>> group.
>>>
>>> Then you have to figure out where that model goes in the high-res
>>> crystal...you'll use phenix.automr  with your model from the low-res
>>> crystal to do that.
>>>
>>> Then you can do cross-crystal averaging with phenix.multi_crystal 
>>> average
>>> to improve the phases (optional). You can also just rebuild the 
>>> model in
>>> the high-res crystal form and you may be done.
>>>
>>> Good luck!
>>> All the best,
>>> -Tom T
>>>
>>>
>>>>> Hi everyone,
>>>>>
>>>>> I have a native set to 2.3A resolution and mercury MAD data in a
>>>>> different space group to 3.3A resolution (anomalous signal to 4.2A).
>>>>>
>>>>> How I can use autosol with the data I have. There is no such example.
>>>>> (Native +MAD)? What is the best strategy in this case?
>>>>>
>>>>> Maia
>>>>>
>>>>>
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>>
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>
> -- 
> Miguel Ortiz Lombardía
> Architecture et Fonction des Macromolécules Biologiques
> UMR6098 ( CNRS, U. de Provence, U. de la Méditerranée )
> Case 932
> 163 Avenue de Luminy
> 13288 Marseille cedex 9
> France
> Tel : +33(0) 491 82 55 93
> Fax: +33(0) 491 26 67 20
> e-mail: miguel.ortiz-lombardia at afmb.univ-mrs.fr
> Web: http://www.pangea.org/mol/spip.php?rubrique2
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