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Error about permission denied when using the docker version. #5
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Hello, First of all, thanks for using SURFMAP (or at least trying to :) ). docker caseUnfortunately I wasn't able to reproduce your error. It might come from running the docker with root privileges but I am not sure of that. You could try following the procedure described here to run docker without root privileges. However, when trying to reproduce your error, I have noticed something wrong: the directory output given after the My additional advises to help you resolving the issue from the docker are:
Also, if you are still facing any issue, could you please share your input pdb file ? I also need to add that using - local running caseFor this case, it appears that you don't have numpy installed in your python library. I thus deduce that you might not have installed required python libraries through the following command: |
Thank you very much for your speedy reply! Indeed the pip3 did the trick. I now have a question regarding interpetation of the results. May I contact you directly? Cheers! Oren |
Archive.zip |
You're welcome and thank you for the archive, I will take a look. You can contact us at the following mails: Please put all of us in copy to increase the speed of your answer(s). Cheers |
So I looked at your archive. From what I saw, I understand that you tried to "find" and map the binding sites of components of a multimeric protein. Unfortunately, SURMAP does not "find" binding sites, it only maps them as long as their residues have already been identified and this information been given in the b-factor column of an edited pdb file by the user. For instance, let's say for simplicity that you know that the residues I, F, and Q of the chain A constitute a binding site. To map those residues with SURFMAP, you will need to edit the pdb file in the following way:
Hope I didn't misunderstand your aim of using SURFMAP here and answer your question. I will try (maybe tomorrow) to make a script to help users modify a pdb file from simplified information on the known residues of a binding site in order to avoid editing "manually" a pdb file, if that could help. |
Thank you very much! Yes we di have the locations of the binding sites, so we need to edit the pdb files we use as input. Your kind suggestion for a script will be very helpful! |
Hello, I am running the following:
Why I get permission denied, even when I use sudo? Cheers! Oren
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