Sibbe Bakker

Prediction of a small dimer with a ligand

2

### Description I am attempting a prediction of the enolase dimer with its ligand 2PG by running these commands: ``` $ mkdir data $ wget -O "data/2PG.sdf" "https://files.rcsb.org/ligands/download/2PG_ideal.sdf" $ python...

### Description I ran the command ```bash neuralplexer-inference --task=batched_structure_sampling --model-checkpoint results/dependencies/neuralplexer/data/neuralplexermodels_downstream_datasets_predictions/models/complex_structure_prediction.ckpt --out-path resul ts/data/bench_large/6nw5A_mono/ --input-receptor 'data/6nw5A.pdb' --input-ligand 'data/6nw5_CO_A_1.sdf|data/6nw5_CO_A_1.sdf' --sampler langevin_simulated_annealing --n-samples 20 --cuda ``` The resulting model has gaps between...

pLDDT values mssing

2

I managed to run the model using the following command: ```bash apptainer run --nv np.sif neuralplexer-inference --task=batched_structure_sampling --input-receptor 1b8uA.pdb --sampler=langevin_simulated_annealing --cuda --model-checkpoint complex_structure_prediction.ckpt --out-path . --n-samples 16 --chunk-size 4 --num-steps=40...

question about adding namespaces

10

Dear developers, I have been exploring the usage of this tool in my data transformation pipeline. If find it to be quite useful in forming RDF documents. However, I am...

GPU not recognised

6

### Description of the bug I am running my pipeline on a system with a single RTX 4090: ``` nvidia-smi Tue Jun 17 14:43:43 2025 +-----------------------------------------------------------------------------------------+ | NVIDIA-SMI 555.42.06 Driver...

ERROR ~ Error executing process > 'NFCORE_FETCHNGS:SRA:SRA_RUNINFO_TO_FTP (1)'

1

### Description of the bug I am trying to download the transcriptomic data for [PRJNA121473](https://www.ebi.ac.uk/ena/browser/view/PRJNA121473). From the error message I do not understand what I can change to fix my...