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

[iulek at interponta.com.br]

That must make things easier for me, say, to prepare a single script  
to use, eg, the 10 best alignments from the hhr file.
If I understand well, the "simple alignment file" proposed below must  
suite both sculptor and mr_rosetta.
Many thanks. I will go to download the latest nightly build.

J.
> 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
>>>>>>
>>>> _______________________________________________
>>>> phenixbb mailing list
>>>> phenixbb at phenix-online.org
>>>> http://phenix-online.org/mailman/listinfo/phenixbb
>>>>
>>>
>