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Hello,
We have a custom viewer that labels certain parts of the protein using `plugin.managers.structure.measurement.addLabel`. We would like to have more control over making this label visible/col…
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Hi all
I'm interested in generating contact maps from the ESM2 attention heads as described in the following github notebook:
https://github.com/facebookresearch/esm/blob/main/examples/contact_predi…
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Hello!
I have a query concerning a specific aspect of protein-ligand systems. In cases where both the protein and ligand are identical, but the final conformation varies due to sampling of the protei…
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Currently there are two issues with the current structure of the schema that I would like to address.
First, the CanonicalAllele and Protein SequenceConsequence both exist and are more or less iden…
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Hello,
First of all again, many thanks for developing this great tool. I open this issue because I wanted to know which probability cutoff is recomended, in your opinion, as a minimum to trust a 3…
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Thanks for the very interesting work and the code!
I wanted to try to get the Protein MPNN CMLM model running on one of the example PDB files.
I copied the code from the Readme, but appear to ha…
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Issue Description:
I encountered a CUDA out of memory error when trying to predict a protein containing 1200 amino acids. It's worth noting that I did not encounter this issue when running the pro…
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We have built a mutant library for cucumber and have completed resequencing some of the individual plants, finding a number of proteins with non-synonymous mutations. We have translated these proteins…
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Environment:
GPU: NVIDIA RTX 3060 12GB
PyTorch Version: 2.3.1+cu118
CUDA Version: 11.8
OS: Linux Ubuntu
Python Version: 3.10.13
Amino acid : 651
I am encountering a CUDA Out of Memory erro…
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* PIGT version:
* Python version: 3.10
* Operating System: Linux
### Description
I am trying to generate a protein-ligand complex for a small protein (536 residues) and got `torch.cuda.OutOfMe…