[phenixbb] mr_rosetta - homology search with hhr file - Cannot contact EBI DbFetch

Thomas C. Terwilliger terwilliger at lanl.gov
Wed Jun 8 02:47:22 PDT 2011


Hi Jorge,

In your version of phenix yes, you need a special format for the alignment
files. I just changed it to allow a simple alignment file:

>target
sequence-of-target
>template
sequence-of-template

which is also used by sculptor. This is available in a current nightly
build.  You can then just paste the alignment from hhpred into such a
file.

I hope that helps!
-Tom T


>>>      Thanks, Tom.
>>      Yes,  phenix.mr_model_preparation fails just like phenix.mr_rosetta:
>>
>> "
>> Traceback (most recent call last):
>> File
>> "/usr/local/phenix-1.7.1-743/phaser/phaser/command_line/mr_model_preparation.py",
>> line 9, in <mod ule>
>> mr_model_preparation.run( args = sys.argv[1:], out = sys.stdout )
>> File
>> "/usr/local/phenix-1.7.1-743/phaser/phaser/mr_model_preparation.py",
>> line 255, in run
>> proxy = proxy.DbfetchHTTP( database = "pdb", format = "pdb" )
>> File "/usr/local/phenix-1.7.1-743/phaser/phaser/proxy.py", line 108, in
>> __init__
>> raise RuntimeError, "Cannot contact %s" % str( self )
>> RuntimeError: Cannot contact EBI DbFetch service
>> "
>>
>>      I think I will have to go to phenix sculptor. This seems to require
>> the alignment in ".aln (CLUSTAL format), .pir (PIR-format) and .ali
>> (relaxed PIR-like format)" maybe I could prefer to keep the hhr
>> alignment but I will have to check if there is an easy way to translate
>> one format into the other. Apart from this, phenix.mr_rosetta, seems to
>> require the alignment "MODELLER-style".
>>      Therefore, to keep the alignment as output by hhr (is this wise?
>> Does this use multialignment and maight this be better that pairwise
>> alignment?) I have to translate it to either aln/pir/ali (for phenix
>> sculptor) and then to MODELLER-style for phenix.mr-rosetta.
>>      A suggestion to make this more straight forward?
>>
>> J.
>>
>>> Hi Jorje,
>>>
>>> Yes, you can prepare your model separately from mr_rosetta.  You can do
>>> this (for example) with:
>>>
>>> phenix.mr_model_preparation 3800765_mod_ed.hhr
>>>
>>> If that fails with the same download problem, you can create an
>>> alignment
>>> file and use phenix.sculptor to edit your model.
>>>
>>> Then as you suggest, you can use your edited model directly as a
>>> "search_model" and skip the .hhr files entirely.
>>>
>>> Let me know if that doesn't do it!
>>> All the best,
>>> Tom T
>>>
>>>>> Dear all,
>>>>>
>>>>>
>>>>>       I would like to use mr_rosetta with homolgy search. I followed
>>>>> the
>>>>> instructions at
>>>>> http://www.phenix-online.org/documentation/mr_rosetta.htm , generated
>>>>> the hhr and the fragment files, but at submitting the job I receive
>>>>> the
>>>>> message:
>>>>>
>>>>> ******************* ERROR ENDING ***************
>>>>> Cannot contact EBI DbFetch service
>>>>>
>>>>> ******************* ERROR ENDING ***************
>>>>>
>>>>> after both loading the file 3800765_mod_ed.hhr and generating the log
>>>>> file mr_model_preparation.log.
>>>>>
>>>>>       Concerning this problem, I saw
>>>>> http://www.phenix-online.org/documentation/faqs.htm#anch8 . But I am
>>>>> not
>>>>> behind a proxy and even disabling completely the firewall, the message
>>>>> still appears.
>>>>>       Maybe this is more linux related, I use openSuSE 11.4.
>>>>>       One workaround would be that I write a script to wget the pdb
>>>>> files
>>>>> (listed in .hhr) and select the due chains, putting these in a certain
>>>>> location and indicating in my script where they are. But I am a kind
>>>>> of
>>>>> confused, might
>>>>>
>>>>> search_models=
>>>>>
>>>>> do this. I am not sure I could use a hhr file together with it.
>>>>> Anyway,
>>>>> this might be a desirable solution for me yet I use to run my stuff in
>>>>> a
>>>>> laptop which goes around by.
>>>>>
>>>>>       Thanks,
>>>>>
>>>>> Jorge
>>>>>
>>>>>
>>>>>
>>>>> _______________________________________________
>>>>> phenixbb mailing list
>>>>> phenixbb at phenix-online.org
>>>>> http://phenix-online.org/mailman/listinfo/phenixbb
>>>>>
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>>
>>



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