CS-HM-Rosetta

[Anonymous]

Hello,

i would like to use the CS-HM-Rosetta for homology modelling with chemical shift data. It is stated in the supporting information (http://www.pnas.org/lookup/suppl/doi:10.1073/pnas.1202485109/-/DCSupplemental) that cm_scripts/rosetta_cm.conf needs to be edited before the execution of “cm_scripts/bin/predict_distances.pl sequence.fasta sequence.aln –aln_format grishin –outfile sequence.dist_csts” in order to generate the homology constraints.
Unfortunately i can not find the cm_scripts/rosetta_cm.conf file or the predict_distances.pl in my Rosetta3.4 installation. There is a folder cm_scripts in the homology_modelling_with_end_extension, but it does not contain any of those files.

Thanks in advance,
Philip

[Anonymous]

There is a separate cm_scripts folder lurking in Rosetta-land (not part of Rosetta proper) that I found by digging around on the developer server. The conf file is a non-issue, but the predict_distances script is nontrivial, and it looks like it needs a whole library supporting it. I’ve asked if that’s supposed to be released or not.

[Anonymous]

Hi Philip-
The cm_scripts includes a lot of software we don’t have license to distribute. However, if all you want is to run homology modeling with CS data hold tight. I believe there will be an update to robetta server so you can run with CS-data with the newer hybrid homology modeling protocol within the next month or so.

-TJ

[Anonymous]

Hi guys,

thanks for your fast response. I basically just want to do the homology modelling with CS data and some distance constraints. So the robetta server would be fine, but i thought this would be a nice opportunity to become acquainted with Rosetta and learn how to use it. So i will have to look for another project involving a Rosetta application

Cheers,
Philip

[Anonymous]

Hello,

I would like to use the CS-HM-Rosetta to determine the 3D structure of protein (2lha.fasta sequence file).

I have generated a sequence alignment file in .aln format (from here: http://toolkit.tuebingen.mpg.de/psi_blast), and then, used the following command line :

predict_distances.pl -aln_format grishin 2lha.aln 2lha.fasta

Unfortunately, I have received the following error message:

Can’t locate blast.pm in @INC (@INC contains: /Users/mariuswanko/dev/HH-suite/2LHA/../perl_lib/ /sw/lib/perl5/darwin-thread-multi-2level /sw/lib/perl5 /sw/lib/perl5/darwin /opt/local/lib/perl5/site_perl/5.16.3/darwin-thread-multi-2level /opt/local/lib/perl5/site_perl/5.16.3 /opt/local/lib/perl5/vendor_perl/5.16.3/darwin-thread-multi-2level /opt/local/lib/perl5/vendor_perl/5.16.3 /opt/local/lib/perl5/5.16.3/darwin-thread-multi-2level /opt/local/lib/perl5/5.16.3 /opt/local/lib/perl5/site_perl /opt/local/lib/perl5/vendor_perl .) at predict_distances.pl line 9.

BEGIN failed–compilation aborted at predict_distances.pl line 9.

Someone can help me please?

Thank you in advance for your help.

Marius

[Anonymous]

I believe you need to have BioPerl installed in order to run the predict_distances.pl script. 

[Anonymous]

Thank you.

To run the predict_distances.pl script using Rosetta 3.3, I also need two files: bounds.txt and hhsearch_table.txt located into cm_data. But I don’t have the cm_data directory into the homology_modeling_with_end_extension directory.

It is possible to have these data?

thanks!

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