ColabFold

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Index error/ List Index out of range in the Display 3D structure

1

## Expected Behavior I am trying to use the default condition. but I get same error #206 . I get the following error in the Display 3D Structure cell: ---------------------------------------------------------------------------...

yean-woo

AF2 colab error using template

4

## Expected Behavior successful structure prediction by AF2 just using one specific template structure (representing one of the known conformational state, e.g open state, for an ortholog) to put bias...

mahdikalhori

MMseqs2 search results with Taxonomy ID using uniref30_2103 database and colabfold_envdb_202108 database

5

Dear friends, we got some trouble for MSA searching contain Taxonomy ID annotation. ## Expected Behavior We want to search using mmseqs2 with uniref30_2103 database and colabfold_envdb_202108 database. We want...

Starmie21

uniref30_2103 database cannot be untarred

2

trying to download anew the uniref database to include the .dmp file needed for paired MSAs. Using the setup_databases.sh script posted [here](https://colabfold.mmseqs.com/). getting: ``` gzip: stdin: not in gzip format...

listofdina

Singularity installations?

2

Hi, I was wondering if the project could be integrated into a singularity installation of AlphaFold2. If yes, how would one go about achieving it? Best, Pranav

shahpnmlab

colabfold_batch still runs a MSA query even if `--msa-mode single_sequence`

5

## Expected Behavior No query should be sent to the server if `--msa-mode single_sequence` `colabfold_batch --num-recycle 6 --msa-mode single_sequence --model-type AlphaFold2-multimer-v2 --recompile-padding 1 ./{fn} . ` ## Current Behavior Queries...

ajasja

Index error/ List Index out of range in the Display 3D structure

6

## Expected Behavior I am trying to use my own template (single PDB in a mmcif format) with single_sequence (msa_mode). I get the following error in the Display 3D Structure...

yudanshi

Alphafold2 multimer prediction GPU memory related error on google colab pro

1

I am trying to run the alphafold2 notebook on colab pro for multimer prediction of amino acid sequences of total length 1760. While running the prediction cell , I am...

anpanche

Archana

2

Thank you @sokrypton , I could run the msa and get results. While executing Alphfold step, I got the error below, NameError Traceback (most recent call last) [](https://localhost:8080/#) in ()...

anpanche

Aberrant 3D modeling of a multiprotein complex leads to the formation of a covalent interprotein bond Arginine - Leucine

4

I attempted to model a missense mutation in the NUF2 peptide located in the NDC80 protein complex. The substitution of a leucine at position 303 by an arginine in the...

yoannvial