Rosetta lack of necessary application

[Anonymous]

Hi

    when i learn denovo_model_building from demos/public/electron_density_structure_refinement.In step 1 and step2 ,they ask for place_fragment_into_density.linuxgccrelease,  cal_overlap_score.static.linuxgccrelease,cal_nonoverlap_score.static.linuxgccrelease.In my rosetta 3.0 i can not find these application.I dont know why,thanks for help

[Anonymous]

Those applications actually shouldn’t be needed anymore. The functionality has been rolled into the denovo_density application itself.

Please see https://faculty.washington.edu/dimaio/files/rosetta_density_tutorial_aug18.pdf  and https://faculty.washington.edu/dimaio/files/rosetta_density_demo_aug18.tgz for updated tutorials.

[Anonymous]

Thank you for your help.The file you offer i had download ,however,it mentions about denovo_density.macosclangrelease that rosetta does not exist.I use denovo_density.linuxgccrelease  instead and get some error in doing A_searsh.sh:

I get all .pdb file — 50 for each pos– but no silent file ,which said

protocols.electron_density.DockIntoDensityMover: Have 100 total solutions after refinement

./A_search.sh: 13: ./A_search.sh: -clust_radius: not found

im sure i set -clust_radiu 3 but it seems does not work

[Anonymous]

Rosetta uses a slightly non-standard way of naming executables. We attach the compilation conditions to the name of the file. So it will be denovo_density.macosclangrelease when compiling on a MacOS machine using the Clang compiler. When compiling on a Linux machine with the GCC compiler it will be denovo_density.linuxgccrelease. — It’s effectively the same program, just named differently. It’s the first part (before the dot) which is the important part. Change the part after the dot as appropriate for your machine.

Regarding the error message, it might be that you have a typo in the file. One thing you want to make sure is that the line endings in the script are correct. For convenience/interpretability, each option in the A_search.sh script is on a separate line. But in order to actually run the command, the options all need to be on a single command. To do this, we use the backslash (“”) at the very end of the line on each line. This tells the shell to treat the next line as a continuation of the line. But for this to happen, there needs to be a backslash at the end of the line and at the *very* end of the line. If there’s any whitespace (spaces, tabs, etc.) after the backslash, it won’t work.

From the error message, I’m guessing either that the backslash on the line before -clust_radius is missing, or there’s extra spaces after it.  (If you added an extra blank line or commented out the line before it, that would also cause the issue.)

(Another thing you can try is running the utility `dos2unix` on the A_search.sh file. “dos” formatted files have extra non-printing whitespace charachters at the end of the line which can mess things up. I don’t think this is the case here, though, as I would expect you to get an error about an earlier option if this was the case.)

 

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