Open amani-acog opened 1 month ago
@amani-acog Have a look at transform_structure
in https://github.com/jvkersch/tmtools/blob/main/tmtools/helpers.py#L6. This will allow you to transform the structure, and you can then write it to another PDB file using BioPython.
For the second question, I'm not sure I understand the specifics. Do you align the different chains, and get one TM score per chain? How do you define the overall TMScore?
Hi, thank you for your response. I am not a domain expert. So I have some doubts that I need to get clarified.
I have explored tmtools from OpenStructures as well, they are providing only one TMScore which is matching with one of your TMScore. I assumed TMScore from openstructures is overall tmscore.
@amani-acog Keep in mind that this library is just a thin wrapper around the original TMalign code, which is not mine. So if you have structural questions about how the library works, it may be better to consult the original code and documentation: https://zhanggroup.org/TM-align/.
TM1
is normalized by the length of the second protein, and similar for `TM2.
Hi, I want to know how to do the following: