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    • #1525


        i would like to use the CS-HM-Rosetta for homology modelling with chemical shift data. It is stated in the supporting information ( that cm_scripts/rosetta_cm.conf needs to be edited before the execution of “cm_scripts/bin/ 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 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,

      • #8461

          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.

        • #8462

            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.


          • #8463

              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 :)


            • #11416


                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:, and then, used the following command line :

       -aln_format grishin 2lha.aln 2lha.fasta

                Unfortunately, I have received the following error message:

                Can’t locate 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 line 9.

                BEGIN failed–compilation aborted at line 9.

                Someone can help me please?

                Thank you in advance for your help.


              • #11420

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

                • #11424

                    Thank you.

                    To run the 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?


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