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Database . does not exist

7

Hi, I'm encountering an issue while trying to run colabfold_search. I would appreciate any suggestions you might have for resolving it. Thank you in advance! “colabfold_search test.fasta ./colabfold_db/ test --af3-json...

biochristmas

Required DB's for GPU Server setup

2

**Main question is** -What Is a must to be downloaded to the local disk for `gpuserver` mode setup ? regarding [Optional GPU server for enhanced performance](https://github.com/sokrypton/ColabFold?tab=readme-ov-file#optional-gpu-server-for-enhanced-performance) -> I'm confused as...

eyal-converge

how to reproduce query result

1

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...

orgw

Error: credential propagation was unsuccessful

1

--------------------------------------------------------------------------- MessageError Traceback (most recent call last) [/tmp/ipython-input-4-4085076963.py](https://localhost:8080/#) in () 38 from google.colab import auth 39 from oauth2client.client import GoogleCredentials ---> 40 auth.authenticate_user() 41 gauth = GoogleAuth() 42 gauth.credentials =...

mmmannan

--- **Body:** Hi ColabFold/MMseqs team, I'm encountering an error when running `colabfold_search` with local MMseqs2 databases. Here's the command I'm using: ```bash colabfold_search \ --mmseqs /home/junyu/project/mmseqs2/mmseqs/bin/mmseqs \ /home/junyu/project/sym/motif_sym/paper_design/c/c3/MPNN_results/seqs/C3_idx_0_len_240.fa \ /media/junyu/WinDATA/colab_database...

JoreyYan

Currently, if "save_all" is selected, only single representation of 256 dimensions is returned. However, in the official alphafold repository, if return_representation is set to true, single representation of 384 dimensions...

Ericzhang1

BioEmu Colab Notebook Dependency Installation Error + Workaround

1

It seems that a change in Google Colab's environment affected the dependency installation in the BioEmu notebook. In any case, I was able to run the model by replacing the...

diegoeduardok

Hello, I am trying out boltz2 and in the first step it submits a request to the colabfold API to generate an MSA (endpoint `ticket/msa`). However, whilst some of the...

ChenfuShi

`colabfold_search` fails GPU search

5

### TL;DR -> `colabfold_search` fails search on "GPU" DB setup **Error** ``` INFO:colabfold.mmseqs.search:Running mmseqs align /home/ec2-user/result/prof_res /home/ec2-user/msa-work/db/uniref30_2302_db_seq /home/ec2-user/result/res_exp /home/ec2-user/result/res_exp_realign --db-load-mode 0 -e 10 --max-accept 100000 --threads 64 --alt-ali 10 -a...

eyal-converge

ColabFold fails to predict protein complex (invalid literal for int() with base 10: 'DUMMY' at MSA step)

8

Dear ColabFold Team, I am trying to model the human Get1-Get3 complex using the entire length of Get3 and part of the Get1 protein (348 and 59 residues, as given...

ks-2025