ColabFold
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sokrypton
Making Protein folding accessible to all!
Assumption: Databases not indexed correctly or naming mismatch. Input /apps/prod/COMPCHEM/colabfold/git/ColabFold/MsaServer/databases/uniref30_2103 does not exist -> ? Input /apps/prod/COMPCHEM/colabfold/git/ColabFold/MsaServer/databases/uniref30_2103.idx does not exist -> a file called "uniref30_2103_db.idx" exists ## Expected Behavior fasta...
Built MSA from already downloaded DB_File from [colabfold.mmseqs.com](https://colabfold.mmseqs.com/) using command: ` tar xzvf "uniref30_2103.tar.gz" mmseqs tsv2exprofiledb "uniref30_2103" "uniref30_2103_db" mmseqs createindex "uniref30_2103_db" tmp1 --remove-tmp-files 1 ` However, it went wrong with...
## Expected Behavior to produce 5 models given two sequences (homodimer) ## Current Behavior 2022-08-12 09:35:17,620 Running colabfold 1.3.0 (26de12d3afb5f85d49d0c7db1b9371f034388395) WARNING: You are welcome to use the default MSA server,...
Hi, Would it be possible to combine the partial hallucination and binder hallucination protocols to hallucinate loops or other new structural elements within a given binder scaffold? A trial case...
Hello, I wonder what is the correct format of a3m input for complex. I have succeeded in using an a3m file as an input for monomer prediction, both in the...
## Expected Behavior Hello, I am trying to run batch searches against ColabFoldDB on a SLURM cluster, following the [MSA instructions](https://github.com/sokrypton/ColabFold/tree/26de12d3afb5f85d49d0c7db1b9371f034388395#generating-msas-for-large-scale-structurecomplex-predictions) in the README. ## Current Behavior `colabfold_search` fails at...
What is your question? During the execution of the Local-ColabFold by the following command, it encounters a problem. The error file was attached. $ colabfold_batch --amber --templates --num-recycle 3 --use-gpu-relax...
Hi there, We have plans on running a few hundreds of complexes (some relatively big) and we've been trying to set up a pipeline to run locally on our HPC...
## Expected Behavior Running colabfold (online v1.4 and localcolabfold latest) with custom templates to predict different conformations ## Current Behavior No template is detected with any combination of options in...
## Expected Behavior hopefully being able to use a .pdb with some small modifications ## Current Behavior I removed the chains of a complex of my protein (the only crystal...
