ColabFold

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I added a two lower level routines to plot a single colored protein backbone using matplotlib and plot a single PAE heatmap. These new routines are in colabfold.py and are...

tomgoddard

Couldn't use amber in colabfold_batch, after running colabfold_search

11

Hi, I have followed all the steps on your GitHub using pip install (not localcolabfold), and everything worked fine. I downloaded all the data to my machine, and was able...

lzhangUT

Thanks for the useful tool. What I want to know is the relationship between these five files(***_unrelaxed_rank_2_model_2_scores.json，***_unrelaxed_rank_3_model_4_scores.json，…) and this one file(***_predicted_aligned_error_v1.json). Is this png(***_PAE.png) generated from these five files Thanks...

danboshuiyan

colabfold_search and colabfold_batch takes too long than expected

2

Hi there, Thanks for sharing colabfold. It is greatly appreciated. we followed the exact step on the github using 'Running locally'. we have a virtual machine with 6cCPUs, 112 RAM,...

lzhangUT

CUDA_ERROR_ILLEGAL_ADDRESS: an illegal memory access was encountered while running locally

6

## Expected Behavior Expected model to run correctly on lo ## Current Behavior After updating using the update script presented in the Local Colabfold install github yesterday suddenly I can't...

wlawler45

Relaxation Error Running Locally

3

## Expected Behavior I am unable to use --amber to relax models. ## Current Behavior First model will fold but crash immediately when the relaxation step begins. ## Steps to...

RaymondRuff

Could not predict many-chain complexes

2

## Expected Behavior Use ColabFold to predict two-protein complexes with trimmed sequences (intrachain gaps). ## Current Behavior I am running my fasta file using colabfold_batch, which to my knowledge does...

ishikagovil

ValueError: attempt to get argmax of an empty sequence

7

## Expected Behavior trying to get produced relaxed models of tcr-pmhc complexes running on the terminal (prior to the update it worked) ## Current Behavior In the fasta file contains...

melyssacheung

Could not find CIFs

3

## Expected Behavior Use ColabFold to predict complex including a target and two ligand, on my local computer ## Current Behavior There are 600 sequence in the csv files, where...

danboshuiyan

Thank you for sharing the ColabFold repo, it helps a lot. Are there any relevant APIs or methods that support the extraction of msa from protein sequences alone without structure...

zxzhang8