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google-deepmind / alphafold

Open source code for AlphaFold.
Apache License 2.0
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HOW to change MSA #877

Open GodPCWANG opened 6 months ago

GodPCWANG commented 6 months ago

I have obtained some pair MSAs through certain strategies. However, I don't know how to integrate them because the MSAs in the folder are all individual MSAs. Can someone help me

tcoates5 commented 6 months ago

A bit more information about what you want to do is needed here. Do you want these other MSAs to be used in place of default MSAs? Do you want both to be used? Some sort of mix of the two? By default, different MSAs are generated for each database.

GodPCWANG commented 6 months ago

thank you for your answer. For the target multimer, I would like to construct a single file of all the paired MSAs generated in different ways to replace the default MSA.

tcoates5 commented 6 months ago

You're welcome! As AF by default reads from several files, I would recommend matching the formatting in at least one of those files, then making "fake" MSA files to replace the others. Then run with the use_precomputed_msas flag turned on.