how to reproduce query result

[orgw]

hi

given a fasta file with multiple proteins,

A:H:L MNASRFLSALVFVLLAGESTAWYYNASSELMTYDEASAYCQRDYTHLVAIQNKEEINYLNSNLKHSPSYYWIGIRKVNNVWIWVGTGKPLTEEAQNWAPGEPNNKQRNEDCVEIYIQRTKDSGMWNDERCNKKKLALCYTASCTNASCSGHGECIETINSYTCKCHPGFLGPNCEQAVTCKPQEHPDYGSLNCSHPFGPFSYNSSCSFGCKRGYLPSSMETTVRCTSSGEWSAPAPACHVVECEALTHPAHGIRKCSSNPGSYPWNTTCTFDCVEGYRRVGAQNLQCTSSGIWDNETPSCKAVTCDAIPQPQNGFVSCSHSTAGELAFKSSCNFTCEQSFTLQGPAQVECSAQGQWTPQIPVCKAVQCEALSAPQQGNMKCLPSASGPFQNGSSCEFSCEEGFELKGSRRLQCGPRGEWDSKKPTCSAVKCDDVPRPQNGVMECAHATTGEFTYKSSCAFQCNEGFSLHGSAQLECTSQGKWTQEVPSCQVVQCPSLDVPGKMNMSCSGTAVFGTVCEFTCPDDWTLNGSAVLTCGATGRWSGMPPTCEAPVSPTRPLVVALSAAGTSLLTSSSLLYLLMRYFRKKAKKFVPASSCQSLQSFENYHVPSYNV:EVALQQSGAELVKPGASVKLSCAASGFTIKDAYMHWVKQKPEQGLEWIGRIDSGSSNTNYDPTFKGKATITADDSSNTAYLQMSSLTSEDTAVYYCARVGLSYWYAMDYWGQGTSVTVSS:DIVMTQSPSSLTVTTGEKVTMTCKSSQSLLNSGAQKNYLTWYQQKPGQSPKLLIYWASTRESGVPDRFTGSGSGTDFTLSISGVQAEDLAVYYCQNNYNYPLTFGAGTKLELK

1. query using colabfold server colabfold_batch test.fasta ./test_output_query --msa-only
2. use local colabfold search and colabfold batch a) search colabfold_search --mmseqs /nfsdata/home/~~~/workspace/ColabFold/mmseqs/bin/mmseqs /nfsdata/home/~~~/workspace/IntFold/plabdab/test.fasta ../../colabfold_db_gpu test_output_search --gpu 1 --db-load-mode 2 b) run colabfold_batch on the results of a) colabfold_batch ./test_output_search ./test_output_batch --msa-only

does not get me the same results from 1). are there any instructions on how to do so?

the server query results in

. ./log.txt ./config.json ./cite.bibtex ./A_H_L_env ./A_H_L_env/out.tar.gz ./A_H_L_env/uniref.a3m ./A_H_L_env/pdb70.m8 ./A_H_L_env/bfd.mgnify30.metaeuk30.smag30.a3m ./A_H_L_env/msa.sh ./A_H_L_pairgreedy ./A_H_L_pairgreedy/out.tar.gz ./A_H_L_pairgreedy/pair.a3m ./A_H_L_pairgreedy/pair.sh ./A_H_L.a3m ./A_H_L_coverage.png ./A_H_L.pickle

and the local version leads to

. ./log.txt ./config.json ./cite.bibtex ./2.pickle ./2.a3m ./2_coverage.png ./1.pickle ./1.a3m ./1_coverage.png ./A_H_L.pickle ./A_H_L.a3m ./A_H_L_coverage.png

the local colab search leads to

. ./A_H_L.a3m ./1.a3m ./2.a3m

[martin-steinegger]

The GPU mode and server differ due to their prefiltering strategies, the server use the CPU version. So, to reproduce the results, please use the CPU version. GPU should be more sensitive.