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PDB-REDO / dssp

Application to assign secondary structure to proteins
BSD 2-Clause "Simplified" License
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Succeed to use command lane but fail to use python script from Bio.PDB.DSSP import DSSP #87

Open HaoDingg opened 2 months ago

HaoDingg commented 2 months ago

Hi, I found version 4.0.4 (which is the version I can use sudo apt-get install to install) has a huge bug, it will read some X AA into ! on DSSP file and the length has been changed. I found the bug was solved in the newest version, so I tried to install and use it in my python code. My situation now is that I can use command line mkdssp to use it correctly but for the python code, it shows: mkdssp: error while loading shared libraries: libboost_filesystem.so.1.73.0: cannot open shared object file: No such file or directory I have installed 1.74.0 and add it to ~/.bashrc, also tried to add a soft link to it but none works. Any suggestions?

mohitpandey92 commented 2 months ago

I am struggling with the same issue on a Ubuntu system. Could you share the changes you made to your ~/.bashrc ? Also, what is the operating system that you are using?

HaoDingg commented 1 month ago

I am using Ubuntu22.04 and add this two lanes in bashrc export LD_LIBRARY_PATH=/lib/x86_64-linux-gnu:$LD_LIBRARY_PATH export LD_LIBRARY_PATH=/usr/lib/x86_64-linux-gnu$LD_LIBRARY_PATH but this doesn't work.

this is the path where the libboost are located. I strangely succeed in using DSSP with python code by some strange efforts. I use conda to install DSSP of several versions and it shows error (I forgot which error exactly, something missing) Then I removed DSSP with conda( with dssp 4.4.7 installed in Ubuntu) and can use DSSP with python scripts.

But my coworker just use conda to install an old version of DSSP(3.0.0)and succeeded to use it with python scripts. This way seems easier.

I am struggling with the same issue on a Ubuntu system. Could you share the changes you made to your ~/.bashrc ? Also, what is the operating system that you are using?

mohitpandey92 commented 1 month ago

Ah, that's good to know. Thank you for your response! @HaoDingg