[phenixbb] Phenix Autobuild

Thomas C. Terwilliger terwilliger at lanl.gov
Tue Aug 3 06:26:46 PDT 2010


Hi Munan Shaik,

Phenix autobuild can read several types of sequence files, but the basic
format is very simple: enter one copy of the sequence of each chain,
separated by a blank line or a line starting with ">"  between chains. 
You can optionally add any lines starting with ">" which will be ignored. 
 So here is an example:

>>> alpha subunit (type 1)
MTMPYYASAEQIMRDRSELARKGIARGRSVVVLTFRDGVLFVAENPSTALHKVSELYDRL
GFAAVGKYNEFENLRRAGIVHADMRGYSYDRRDVTGRSLANAYAQTLGTIFTEQPKPYEV
EICVAEVGRVGSPKAPQLYRITYDGSIVDEQHFVVMGGTTEPIATAMRESYRADLDLEAA
VGIAVNALRQGGAGEGEKRNVDVASLEVAVLDQSRPRRAFRRIAGTALEQLVPAEPAAAS
ESAPEPKPDTETKPADTQD
>>> beta subunit (type 1)
MTADRPALRTGDRDTRLSFGSNLSSFTDYLRGHAPELLPENRIGHRSHSTRGGDGMESGD
LAPHGTTIVALTYKGGVLLAGDRRATQGNLIASRDVEKVYVTDEYSAAGIAGTAGIAIEL
VRLFAVELEHYEKIEGVPLTFDGKANRLASMVRGNLGAAMQGLAVVPLLVGYDLDADDES
RAGRIVSYDVVGGRYEERAGYHAVGSGSLFAKSALKKIYSPDSDEETALRAAIESLYDAA
DDDSATGGPDLTRGIYPTAVTITQAGAVHVSEETTSELARRIVAERTEQGGSAR

Please let me know if that doesn't do it!

All the best,
Tom T






>> Hi everybody,
>> I have a problem with Phenix autobuild. I want to input sequence file
>> together
>> with the pdb and mtz that I got from molecular replacement. But I have no
>> idea
>> which types of sequence files its required. if anybody please help me out.
>>
>>
>> thanks
>> ===================================================
>> Md. Munan Shaik
>> Department of Chemical Biology
>> University of Padova
>> via G. Colombo 03
>> Padova 35131, Italy
>>
>>
>>




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