Comments (3)
Currently the predicted contact maps for proteins with no structure are outputs of the compare stage. I know it seems somewhat illogical to run 'compare' and collect its outputs for a protein with no structure, but if we change this then we'll have contact maps in two different locations, which also seems illogical and will get confusing. Plus, the user won't necessarily know if they have a structure before they execute the pipeline.
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@thomashopf Debbie mentioned that you two had discussed this today - are there any special considerations?
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Yes we discussed this a while ago when I was still in Boston... I made very much the same arguments as you, Anna, so I am not sure if this is worth having (then again, I doesn't cost us that much)
Essentially, this could use the very same code used in the compare stage, that would just need to be moved to another place (like the visualize submodule).
The bigger problem would be to have predicted secondary structure on the plots (unless we use Perry's method for that by default)... at the moment, psipred is only run in the fold stage, and I would really like to keep it out align/couplings/compare for runtime and installation simplicity reasons.
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Related Issues (20)
- Add statistics about filtered sequences to output
- Add alignment summary: organisms HOT 1
- Add 2ndary structure pred. from ECs
- Unable to download the database files using evcouplings_dbupdate HOT 2
- Unable to perform the de novo protein structure prediction. HOT 2
- Possible error in complex mixture model scoring HOT 1
- Non-alphabet characters aren't counted as gaps when computing sequence coverage
- Low quality mutational landscape HOT 1
- Code for running jackhmmer to produce MSA, and postprocess to get A2M.file HOT 1
- Running EVComplex with own database
- lack of explicit separator in read_csv in /mutate/protocol.py HOT 3
- Incompatible .model file from EVCouplings web server HOT 4
- Is hhfilter necessary? HOT 2
- EVcouplings not compatible with Python 3.10 version HOT 3
- Incorporate hhpred for pdb search in compare stage
- Evcouplings_dbupdate ResourceError HOT 5
- Troubleshooting Help HOT 2
- EVmutation vs DeepSequence HOT 1
- Feat request: Alphafold within EVCouplings HOT 3
- KeyError: 'samples' using complex pipeline HOT 3
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