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TurtleTools / caretta

A software-suite to perform multiple protein structure alignment and structure feature extraction.
BSD 3-Clause "New" or "Revised" License
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The third aligned output structure would gone for no reason #15

Closed mapuyi87 closed 1 year ago

mapuyi87 commented 2 years ago

This is a super useful tool that helped me a lot!

However, when I took more than three structures as input, the outputs in the superposed_pdbs would always miss the third one from input. So I guess it's might be a bug.

akdel commented 2 years ago

Hi! Yes this was a bug that is fixed several weeks ago in the master branch, and we will update the release version this week.

For now you can use pip uninstall caretta and then pip install "caretta[GUI] @ git+https://github.com/TurtleTools/caretta.git" from your environment to install it.

mapuyi87 commented 2 years ago

Hi, Thanks for the reply! I just get it re-installed. But the bug is still showing. I lost the third input file in the output folder, just like before.

akdel commented 2 years ago

We pushed the new version with the fix, can you try the new version (0.1.2) with pip?

mapuyi87 commented 2 years ago

Yes I just reinstalled the 0.1.2 version. This time I took 500 pdb files as input to superimpose them. Have done several times and it seems the 8th input file will be missing in the output folder.

akdel commented 2 years ago

We're finding it difficult to replicate this - could you provide us with the PDB IDs of the proteins you are using? Also, is the missing protein present in the cleaned_pdb folder?

mapuyi87 commented 2 years ago

Hi, sorry for the late reply. I was superimposing my own predicted protein structures. Every time I input 500 similar structures and every time there would be one structure missing in the superposed_pdb folder. It seemed random. I had to look for the missing one by eyes. But in the cleaned_pdb folder, there wasn't any structure missing.

mapuyi87 commented 2 years ago

So my strategy was finding the missing one, copying it and adding it as the 501th input, and obtaining 500 ones.

Y4SCH4 commented 2 years ago

I solved the issue by changing the for loop from: for i in range(1, len(self.structures)): to for i in range(len(self.structures)):

Here is the position in the code: https://github.com/TurtleTools/caretta/blob/1e3adb00dd47366475ea9b98b595c448520b45d4/caretta/multiple_alignment.py#L957