[phenixbb] autosol strategy

Maia Cherney chern at ualberta.ca
Thu May 28 13:06:11 PDT 2009


Hi Tom,

how do I determine the number of heavy sites? I gave 2 as in your 
example, but it can be more. Should I try several different numbers?

Maia

Maia Cherney wrote:
> 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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>>>>
>>>>         
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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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