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RosettaCommons / RoseTTAFold

This package contains deep learning models and related scripts for RoseTTAFold
MIT License
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no pdb outcome in the pyrosetta run version #50

Open ajian-he opened 3 years ago

ajian-he commented 3 years ago

runs normal, however, there is no pdb file out in the result folder

$ run_pyrosettaver.sh XXX.fasta . Running HHblits Running PSIPRED Running hhsearch Predicting distance and orientations Running parallel RosettaTR.py $ ls hhblits log parallel.fold.list pdb-3track t000.3track.npz t000.atab t000.hhr t000.msa0.a3m t000.msa0.ss2.a3m t000_.ss2 $ ls pdb-3track

any suggestion? run e2e version normal, thanks

liuboeo commented 3 years ago

I also ran into the same problem, besides, side chain information can not be got from e2e script

ajian-he commented 3 years ago

the side chain info is also missing in my e2e run

Rusfell commented 3 years ago

runs normal, however, there is no pdb file out in the result folder

$ run_pyrosettaver.sh XXX.fasta . Running HHblits Running PSIPRED Running hhsearch Predicting distance and orientations Running parallel RosettaTR.py $ ls hhblits log parallel.fold.list pdb-3track t000.3track.npz t000.atab t000.hhr t000.msa0.a3m t000.msa0.ss2.a3m t000_.ss2 $ ls pdb-3track

any suggestion? run e2e version normal, thanks

I also ran into the same problem with my own protein, but ran with the example protein normal.

aputron commented 3 years ago

Have you ensured that PyRosetta has been installed correctly in the folding conda environment? If you view the $WDIR/log/folding.stderr file you'll probably see errors regarding PyRosetta. Follow the instructions here to install and test the running of PyRosetta.

lkj-keeke1 commented 3 years ago

Have you ensured that PyRosetta has been installed correctly in the folding conda environment? If you view the $WDIR/log/folding.stderr file you'll probably see errors regarding PyRosetta. Follow the instructions here to install and test the running of PyRosetta.

You are right, the folding.stderr told me there was no module called ''pyrosetta"😂. Thanks for your help, I'm installing it now and will try again to see if the run_pyrosetta_ver.sh works out this time.

lj734999889 commented 3 years ago

I ran e2e version which was normal. But when I ran Pyrosetta version, it's wrong. The folding.stderr also told me there was no module called ''pyrosetta". However, I have installed Pyrosetta4 via conda in conda-folding folder. I just don't why it doesn't work well.