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After successfully installing RF2NA in my linux workstation, I tried to run these commands
```
# run Protein/RNA prediction
../run_RF2NA.sh rna_pred rna_binding_protein.fa R:RNA.fa
# run Protein…
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Dear HHsuite developers and users,
I am using hhblits_omp to search many sequences (above 10,000) against custom database. The searching went well at the beginning. But the memory usage becomes hig…
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Dear RoseTTAFold Team,
Hi, I'm a user!
I tried to predict a large protein (>2500 amino acids) using RoseTTAFold in Linux server.
But, I got this message.
[log/make_msa.stderr]
```
.…
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I use precomputed msas (--use_precomputed_msas) for my work and af2 currently spends most of its time performing HHSearch and HHblits, even though I know it won't find anything.
Is there any flag to …
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Anyone tried building their own databases for hhblits ?
I mean that from a protein fasta file to hhblits database.
I am using this pipeline
ButI am very sorry that it seems that there are lots of…
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Hello! I am running the alphafold2 (non-docker version; Miniconda) in a HPC platform (with Nvidia GPUs), predicting the structure of a protein with about 500 amino acid residues. I am sure that the ha…
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Hello,
I want to generate the input MSA file through hhblits. However, I found the output fasta file include lots of gaps like below:
---------------------------------------------------------------…
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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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Hello.
When running RoseTTAFold-All-Atom using the following input YAML config file, I observed that the inference code returned a `.pdb` file that contains a predicted protein structure with the f…
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ERROR: invalid or damaged sequence database to be searched by hhblits: /home/rpearson/Structure_Prediction_Tools/RaptorX-3DModeling/UniRef30_2020_03_hhsuite
ERROR: failed to run /home/rpearson/Struct…