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Dear Blaabjerg et al,
First of all, thanks for making the code available!
I am currently in the process of porting your model to a framework we're building for black box functions related to protein optimization, and I noticed something: the version on the interactive Colab notebook you use is the previous one instead of this one. Funnily, the previous one was easier to set-up for me (given that you don't use dssp
in extract_environments.py
).
I was wondering: is this by design? What was the main rationale for updating the code?
The vaex package currently does not have support for Python 3.11: vaexio/vaex#2368
Perhaps in the meantime it would be possible to switch the use of vaex:
_2022_ML-ddG-Blaabjerg/src/run_pipeline.py
Line 477 in 969e21f
RaSP-log.txt
Hello,
Thank you for sharing this package - it looks really exciting and looking forward to testing it out a bit.
Unfortunately, when I try to install the dependencies with conda, I keep running into UnsatisfiableError problems - the main issue seems to be __glibc
though I'm not sure - I've included the full output in the attached file.
Here's the command I'm using:
conda create -n rasp python=3.6 pyyaml=5.3.1 pandas=1.1.4 scipy=1.5.3 numpy=1.17.3 scikit-learn=0.24.0 mpl-scatter-density=0.7 pdbfixer=1.5 pytorch=1.2.0 cudatoolkit=10.0 biopython=1.72 openmm=7.3.1 matplotlib=3.1.1 seaborn=0.11.2 ptitprince=0.2.5 dssp=3.0.0 vaex=4.5.0 -c salilab -c omnia -c conda-forge -c anaconda -c defaults
And what seems to me to be the relevant output:
The following specifications were found to be incompatible with your system:
- feature:/linux-64::__glibc==2.17=0
- feature:|@/linux-64::__glibc==2.17=0
- biopython=1.72 -> libgcc-ng[version='>=7.3.0'] -> __glibc[version='>=2.17']
- cudatoolkit=10.0 -> libgcc-ng[version='>=10.3.0'] -> __glibc[version='>=2.17']
- dssp=3.0.0 -> libgcc-ng[version='>=11.2.0'] -> __glibc[version='>=2.17']
- matplotlib=3.1.1 -> libgcc-ng[version='>=7.3.0'] -> __glibc[version='>=2.17']
- numpy=1.17.3 -> libgcc-ng[version='>=7.3.0'] -> __glibc[version='>=2.17']
- pandas=1.1.4 -> libgcc-ng[version='>=7.5.0'] -> __glibc[version='>=2.17']
- pdbfixer=1.5 -> openmm[version='>=7.2.0'] -> __glibc[version='>=2.17|>=2.17,<3.0.a0']
- ptitprince=0.2.5 -> libgcc-ng[version='>=9.4.0'] -> __glibc[version='>=2.17']
- python=3.6 -> libgcc-ng[version='>=9.4.0'] -> __glibc[version='>=2.17']
- pyyaml=5.3.1 -> libgcc-ng[version='>=9.3.0'] -> __glibc[version='>=2.17']
- scikit-learn=0.24.0 -> libgcc-ng[version='>=9.3.0'] -> __glibc[version='>=2.17']
- scipy=1.5.3 -> libgcc-ng[version='>=9.4.0'] -> __glibc[version='>=2.17']
Your installed version is: 2.17
Do you have an environment.yml file available for the environment? I'm wondering if installing that way would make a difference at all. I'll also try installing with miniconda and/or mambaforge as well.
RHEL 7.9, anaconda3/2022.05 (conda 4.13.0)
Thanks for this great tool.
I succesfully ran the Colab notebook on 2024-01-08.
However, I've have been trying to re-run again since then but it the cell Retrieve RaSP files and parameters
does not work. This is the error message:
---> Github data imported!
----> reduce installed
mv: cannot stat 'ds_models': No such file or directory
mv: cannot stat 'cavity_models': No such file or directory
mv: cannot move '/content/colab_additional/best_model_path.txt' to '/content/output/cavity_models/': Not a directory
mv: cannot move '/content/colab_additional/clean_pdb.py' to '/content/src/pdb_parser_scripts/': No such file or directory
mv: cannot move '/content/colab_additional/helpers.py' to '/content/src/': Not a directory
bash: line 41: cd: src/pdb_parser_scripts: No such file or directory
Cloning into 'reduce'...
mv: cannot move '/content/colab_additional/reduce' to '/content/src/pdb_parser_scripts/reduce/': No such file or directory
chmod: cannot access '/content/src/pdb_parser_scripts/reduce/reduce': No such file or directory
Is it perhaps related to Github sunsetting SVN support on Jan 8th 2024? https://github.blog/changelog/2024-01-08-subversion-has-been-sunset/
Hi!
Thanks for sharing this method, I'm really looking forward to testing it.
I'm trying to use the colab notebook with default settings ie just pressing "rull all" (with a T4 GPU). The notebook crashes at "PRELIMINARY OPERATIONS: Retrieve parameters and RaSP files". Any help getting it working would be appreciated, thanks!
best wishes,
Nick
Hello! I am appreciated your job and want to use your software to calculate the stability of algal protein by the PDB file. Could you offer a process to help me? Thank you and best wishes.
I want to do protein stability prediction for my 3D structures. I followed the same steps as you mentioned in your READMe file but i am facing problem while running the script. Can you please explain how could i replace the data with my own? And also i am not able to install VAEX with the given commands by conda as well as with pip.
As far as I can tell, Bio.PDB.DSSP requires DSSP from http://swift.cmbi.ru.nl/gv/dssp/, which appears currently unavailable.
_2022_ML-ddG-Blaabjerg/src/pdb_parser_scripts/extract_environments.py
Lines 71 to 75 in 969e21f
It seems we could use pydssp as a replacement, which claims to have most of the functionality of the original dssp, with a few minor changes: https://pypi.org/project/pydssp/
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