All atoms not represented in model_*.pdb files (MacOSX)

Issue #68 new
nick
created an issue

Ran example code:

$ CABSdock –i 2FVJ:A –p HKLVQLLTTT:CHHHHHHHCC

Using OSX version 10.11.6 and CABSdock build CABS-0.9.13.tar.gz. The link provided to download gfortran on the source page was a dead link, so gfortran (6.1) was downloaded from source https://gcc.gnu.org/wiki/GFortranBinaries for El Capitan (OSX 10.11). Python 2.7 was verified, but installation of nose, tornado, and matplotlib showed conflicts with the root version of python and had to be installed for local user using pip with extension --user or with sudo -H.

Output was generally successful, but the final 10 models (model_*.pdb files) did not show all atom representations. This could be verified opening up the files in a text editor. Only one atom was represented for each amino acid residue.

Comments (2)

  1. Mateusz Kurciński

    Make sure you have modeller installed and that you can import the modeller module in python. Without it, the CABSdock will always produce models in the Calpha representation only. To install modeller go to https://salilab.org/modeller/ and follow the instructions. To verify if the modeller is installed properly start the python console and type

    import modeller
    

    and hit enter. If you get no errors, you are good to go. If that doesn't solve your problem, please run CABSdock again with --verbose 4 option and paste the log messages here.

  2. nick reporter

    Thanks for the reply. I didn't realize there was a requirement to obtain a license for Modeller. That must be the problem.

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