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

iulek at interponta.com.br iulek at interponta.com.br
Tue Jun 7 16:28:25 PDT 2011

     Thanks, Tom.
     Yes,  phenix.mr_model_preparation fails just like phenix.mr_rosetta:

Traceback (most recent call last):
"/usr/local/phenix-1.7.1-743/phaser/phaser/command_line/mr_model_preparation.py", line 9, in <mod  
mr_model_preparation.run( args = sys.argv[1:], out = sys.stdout )
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?


> 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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