Tom Goddard

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icon company University of California San Francisco icon location Molecular visualization, electron microscopy, and virtual reality.

Results 90 comments of Tom Goddard

alphafold crash causes nvml library mismatch which cannot be resolved. must reinstall ubuntu OS

Hi Ryan, I've run more than 100 consecutive AlphaFold 2.3 jobs on Ubuntu 22.04 and an Nvidia 4090, dimers with total sequence length 500 - 3000 with ColabFold 1.5 using...

alphafold crash causes nvml library mismatch which cannot be resolved. must reinstall ubuntu OS

I didn't make clear, using localcolabfold allows you to run the predictions using a command-line program colabfold-batch without using a Jupyter notebook.

Using rotamers for mutations

Are you sure you ran an AlphaFold prediction? I think it is more likely you fetched a close matching structure from the AlphaFold database which did not have the same...

Add v1.5.3 tag for latest ColabFold

Thanks!

Boltz-2 affinity prediction fails when using a CCD ligand

Thanks! I tested 3 affinity predictions with CCD ligands and all are working now.

Spire DB Download?

Hi @martin-steinegger I also would like to get this spire_ctg10_2401_db database. Without it local colabfold_search and local colabfold msa servers can't use env pairing which is necessary to replicate the...

Spire DB Download?

Thanks!

Spire DB Download?

I downloaded the spire database but didn't have enough disk space to try it. But there were other reasons I gave up on spire. I was interested in getting the...

libmarv initialization error during GPU-accelerated search against ColabFold databases using Docker

Here's another clue about this error CUDA error: initialization error : /work/lib/libmarv/src/marv.cu, line 85 Error: Prefilter died I got it with Nvidia 4090, Driver Version: 575.64.03, CUDA Version: 12.9 using...

libmarv initialization error during GPU-accelerated search against ColabFold databases using Docker

I get this exact same error about 1 in 10 runs of colabfold_search with Nvidia 4090, driver 575.64.03, CUDA Version: 12.9, Ubuntu 24.04 and mmseqs binary release mmseqs-gpu-release18 from the...