ikk6

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  • in reply to: Download docking visualization #23046
    ikk6
    Keymaster

    Hello.
    Webina mimics Autodock Vina’s behavior by producing the only output file which contains the original receptor and ligand docked. You can access the file on the output tab after a successful run. I just checked that we don’t have a bug there. It’s not the ligand file that you can download. It should be the complex.
    I hope this helps.
    Best regards,
    Yuri
    P.S. I want to highlight, that "mimic" might not be the right term. Webina is actually AutoDock Vina compiled for Web assembly. Webina simply outputs whatever Vina produces. It doesn’t alter the resulting file in any way.

    in reply to: issue with adding material #17356
    ikk6
    Keymaster

    It was me who has actually updated blenmol for 2.8 Haven’t tested it for 2.9 yet. Will look at the issue soon. Does it happen for any proteins or could you please provide some specific pdb(s)?
    Best regards,
    Yuri

    in reply to: Autogrow4: tutorial failure #16942
    ikk6
    Keymaster

    I wouldn’t suggest doing this, to begin with. Yet if no other solution is available, I would assume it makes sense to change the perms before the files are accessed. For example, in:
    /home/witte.t/autogrow4/autogrow/plotting/generate_line_plot.py
    You could add
    import os
    after line 8
    Then, after line 86 (after the loop for rank_file in ranked_file:)
    os.chmod(rank_file , 0777)
    Disclaimer: I’m not the author of autogrow project. This all looks like a poor man’s solution. Ideally would be to deal with the OS setup, so that the files would be accessible with no tweaks.
    Let’s try and call someone else to help you.

    in reply to: Autogrow4: tutorial failure #16835
    ikk6
    Keymaster

    Still looks like a permission error to me. It’s either the ranked file(s) that was not created or it’s empty. Would you mind checking?
    ls -lR | grep "_ranked.smi"

    in reply to: Autogrow4: tutorial failure #16747
    ikk6
    Keymaster

    hello. What are the permissions of the receptor.pdb? I.e.
    ls -l /home/witte.t/autogrow4/tutorial/PARP/4r6eA_PARP1_prepared.pdb

    in reply to: Computer Requirements #16349
    ikk6
    Keymaster

    Yes, there’s docker image if you don’t want to deal with installation. It should run on any major platform.

Viewing 6 posts - 1 through 6 (of 6 total)