Lucas Reber

Is there a way of obtaining template PDB files locally? And if not is it feasible to obtain the templates of many predictions (>10000) from the msa server given the...

That's great. Is there a way of doing this for a batch of proteins with respective .a3m files and .m8 files?

I am trying to use a fasta file with multiple complexes as an input for colabfold_search. This is my code: ``` module load Miniconda3/22.11.1-1 eval "$(conda shell.bash hook)" conda activate...

Thank you for this example. But how would I use an input file like this? ``` >complex_a MFAWVSVSQSYGVIEILKDIMNKVMGIKKKGTNTGITVEDFEQMGEEEVRQHLHDFLRDKKYLVVMDDVWTVDVWRQIHQIFPNVNNGSRILLTTRNMEVARHAEPWIPPHEPHLLNDTHSLELFCRKAFPANQDVPTELEPLSQKLAKR: MCGGLPLALVVLGGLMSRKDPSYDTWLRVAQSMNWESSGEGQECLGILGLSYNDLPYQLKPCFLYITAFPEDSIIPVSKLARLWIAEGFILEEQRQTMEDTARDWLDELVQRCMIQVVKRSVTRGRVKSIRIHDMLRDFGLLEARKDGFLHVCSTDA >complex_b MVVSSHRVAFHDRINEEVAVSSPHLRTLLGSNLILTNAGRFLNGLNLLRVLDLEGARDLKKLPKQMGNMIHLRYLGLRRTGLKRLPSSIGHLLNLQTLDARGTYISWLPKSFWKIRTLRYVYINILAFLSAPIIG: MDHKNLQALKITWINVDVMDMIRLGGIRFIKNWVTTSDSAEMAYERIFSESFGKSLEKMDSLVSLNMYVKELPKDIFFAHARPLPKLRSLYLGG >complex_c MSFQQQQLPDITQFPPNLTKLILISFHLEQDPMPVLEKLPNLRLLELCGAYHGKSMSC: MSAGGFPRLQHLILEDLYDLEAWRVEVGAMPRLTNLTIRWCGMLKMLPEGLQHVTTVRELKLIDMPREFSDKVRSEDGYKVTHPLHYY ```

@YoshitakaMo Thank you for fixing this. I have noticed another related issue, where the templates that are picked at the beginning of the prediction are different when I use `colabfold_batch`...

@crisdarbellay For 5000 predictions `colabfold_search` takes around 6 h with 16 CPU cores in my tests.

@NickWoodall Thank you for the response. I can see that the template folders that are create by the server compared to the local approach are slightly different. Directory generated by...

@milot-mirdita Do you think that difference will affect the results significantly? Do you have any timeline for when this will be addressed?