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

Thomas C. Terwilliger terwilliger at lanl.gov
Tue Jun 7 14:25:29 PDT 2011

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
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