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reuter-group / webnma3

Fast normal mode calculation and analyses for protein structures
http://apps.cbu.uib.no/webnma3/
GNU General Public License v3.0
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Why is it so slow? #12

Open user456790 opened 3 months ago

user456790 commented 3 months ago

Hi folks,

I submitted a set of proteins (4) in webnma3 a couple of days ago but the hits are still showed up as "submitted". How can I proceed?

Thank you.

Thamy C.

phillippesamer commented 3 months ago

Dear Thamy,

We are really sorry about this delay. We are working to understand what is causing the issue, and trying to get WebNMA up and running as soon as we can. Sorry that we are a bit slow, as we are in the middle of a (1-person) team transition.

Meanwhile, I was hoping that you could use our code from github as it is, and run the exact same software on your computer. I wrote below the steps that we expect the user to follow... For the time being, could you please try that instead?

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  1. [Optional] If you are not using mamba instead of conda, I recommend at least the following for much faster conflict-resolution and environment setup in conda. Just run conda install -n base conda-libmamba-solver conda config --set solver libmamba

  2. Download the repository, e.g. using git clone https://github.com/reuter-group/webnma3.git

  3. Navigate to the new directory that is created, and enter conda env create --file environment.yml

  4. Still on that terminal window, activate the new environment and setup webnma: conda activate webnma3-env python setup.py install

Done! Use the --help flag to get a usage example for each command, e.g. webnma ca --help

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Kind regards, Phillippe