Biotite dssp not running! Subprocess error: code 6

[padix-key]

Discussed in https://github.com/biotite-dev/biotite/discussions/606

^{Originally posted by **intomybioverse** June 22, 2024} Hello everyone. I am trying to run the biotite secondary structure analysis program in wsl to study the secondary structure of a protein after md simulation. The website link for the python code is provided below. [Secondary structure of protein during an MD simulation using Biotite] ([Secondary structure during an MD simulation — Biotite 0.41.0 documentation ](https://www.biotite-python.org/examples/gallery/structure/trajectory_sse.html)) However, I am getting the following error: Traceback (most recent call last): File “/home/sobs/AvrPto/6M/trajectory_sse.py”, line 43, in app.join() File “/home/sobs/.local/biotite_env/lib/python3.10/site-packages/biotite/application/application.py”, line 63, in wrapper return func(*args, **kwargs) File “/home/sobs/.local/biotite_env/lib/python3.10/site-packages/biotite/application/localapp.py”, line 257, in join self.evaluate() File “/home/sobs/.local/biotite_env/lib/python3.10/site-packages/biotite/application/dssp/app.py”, line 90, in evaluate super().evaluate() File “/home/sobs/.local/biotite_env/lib/python3.10/site-packages/biotite/application/localapp.py”, line 278, in evaluate raise SubprocessError( subprocess.SubprocessError: ‘mkdssp’ returned with exit code -6: mkdssp: ./src/CifParser.cpp:330: cif::SacParser::CIFToken cif::SacParser::getNextToken(): Assertion `mTokenValue.length() >= 3’ failed. I am using python3.10 for this program, biotite has been installed, it has a sub-package dssp. Additionally, I have installed dssp as well. Yet, I am getting this error. Can you please help out?

[padix-key]

Thanks for the report. However it is hard to pinpoint the cause remotely. Hence here a few questions:

• Which Biotite version are you using? There is a potentially important CIF file fix in Biotite 0.41: #586
• Does it work for you with the original data from https://www.biotite-python.org/examples/gallery/structure/trajectory_sse.html?
• Could you check if it also fails when you input the template AtomArray directly to DsspApp, i.e. the one loaded from templ_file_path.
• If it does not fail for the template, does it fail already for the first frame of the trajectory?

[intomybioverse]

1. Yes, I am using Biotite 0.41. Name: biotite Version: 0.41.1 Summary: A comprehensive library for computational molecular biology Home-page: Author: The Biotite contributors...

How to fix the CIF file issue?

2. No even with lysozyme_md.pdb and lysozyme_md.xtc I am getting the same error.

3. "Could you check if it also fails when you input the template AtomArray directly to DsspApp, i.e. the one loaded from templ_file_path." Can you please explain what I should do regarding this?

4. Yes, it fails for the only first frame too.

[padix-key]

No even with lysozyme_md.pdb and lysozyme_md.xtc I am getting the same error.

OK, your data seems not to be the problem then.

Can you please explain what I should do regarding this?

In this case we can skip this. The other possible culprits are WSL and the DSSP version. I just recognized that there are newer DSSP versions, that do not exist on Conda yet. If installed from environment.yml DSSP 2.2.1 is installed, which seems to work fine.

Could you check your mkdssp version? If it deviates from 2.2.1 could you install 2.2.1 (e.g. via Conda) and check if it works?

[intomybioverse]

I tried getting dssp-2.2.1 through environment.yml using conda, but I am getting this error.

(myenv) sobs@BEE:~/miniconda3/envs$ conda env create -f environment.yml Channels:

• conda-forge
• defaults
• bioconda Platform: linux-64 Collecting package metadata (repodata.json): done Solving environment: failed

PackagesNotFoundError: The following packages are not available from current channels:

• dssp==2.2.1

Current channels:

• https://conda.anaconda.org/conda-forge/linux-64
• https://repo.anaconda.com/pkgs/main/linux-64
• https://repo.anaconda.com/pkgs/r/linux-64
• https://conda.anaconda.org/bioconda/linux-64

To search for alternate channels that may provide the conda package you're looking for, navigate to

https://anaconda.org

and use the search bar at the top of the page.

I have downloaded the dssp=2.2.1 package from https://src.fedoraproject.org/repo/pkgs/dssp/dssp-2.2.1.tgz/ but while installing it i got this error message.

(myenv) sobs@BEE:~/.local/biotite_env/dssp-2.2.1$ make compiling obj/mkdssp.o In file included from src/structure.h:8, from src/mkdssp.cpp:27: src/primitives-3d.h:12:10: fatal error: boost/tr1/tuple.hpp: No such file or directory 12 | #include <boost/tr1/tuple.hpp> | ^~~~~ compilation terminated. make: *** [makefile:64: obj/mkdssp.o] Error 1

How should I proceed now?

[padix-key]

You can install it with Conda from the salilab channel (https://anaconda.org/salilab/dssp):

conda install -c salilab "dssp=2.2.1"

However, the salilab channel is part of environment.yaml, so it should be installable this way. Hopefully the direct installation via the command above works.

[intomybioverse]

Yes, it is working now. Thanks.

[padix-key]

Great! Still the DsspApp interface should be made compatible with newer DSSP versions as well. Hence, I will create a follow-up issue.

[padix-key]

Do you know which DSSP version you used before?