tcoates5

When I had similar problems, it was because I had not properly downloaded/unpacked uniprot.fasta. I remember that the reason it happened is that with how slowly some of the downloads...

So the multimer AlphaFold uses a couple databases that monomer does not, including uniprot.fasta and PDB seqres (as mentioned in the README). Therefore, your problem is _most likely_ one of...

I recently ran the multimer prediction on an antibody, the overall score was about .9, the per residue scores were in the normal range though (average about 90)

As far as I can tell, yes, it seems to just be off by that factor of 100

You can go through the pdb files and see the per-residue confidence (stored as the b-factor). In general that seems to do a better job of really explaining the confidence...

Pretty sure that they mean that the RSA was calculated on structures from the AlphaFold Protein Structure Database. However, there are many tools for calculating RSA, such as PyMOL, Rosetta...

Based on those specs, you can probably run AlphaFold with reduced databases on your local computer, though if you do not have a dedicated graphics card it will probably be...

Assuming you have a dedicated graphics card and do not need high speed results, you could also run with full databases on the HDD

I would also like to be able to run the CPU intensive operations (MSA and templates) separately from the GPU intensive (inference) steps. As Augustin-Zidek added the feature request label,...

That loadout looks like it should run very well, though there are a few points that seem like they have more than AF2 is likely to really leverage. I would...