RosettaCommons / RosettaCommons/rosetta
rna_cluster issue: Structures within same cluster have RMSD higher than cutoff
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- Dominant language
- C++
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Description
Hi,
I am using rna_cluster to cluster top 1% of structures after FARFAR2 run.
rna_cluster.mpi.linuxgccrelease -in:file:silent ../simple_cycle.out -out:file:silent clustered.out -nstruct 2000 -cluster:radius 5
After that structures from same cluster (confirmed with nclust id) were extracted from clustered.out with extract_pdbs command. However, their RMSD is higher than 5 Angstrom (~15 Angstrom).
This was confirmed with Pymol, Gromac's gmx rms command as well.
Is this bug or Is something missing in rna_cluster command line?
Best,
Mandar
Contributor guide
First steps
- Read the whole issue, then the project's contributing guide.
- Comment on the issue to say you are picking it up — it saves two people doing the same work.
- Fork the repository and make your change on a branch.
- Open a pull request that references the issue number.
Research direction
Start by reproducing the rna_cluster command with the supplied silent file and comparing the resulting same-cluster structures using the reported RMSD tools. Read the rna_cluster and extract_pdbs documentation and relevant entry points to determine whether the cluster radius uses a different RMSD definition or requires another option. Done means identifying the cause of the discrepancy and documenting or correcting the behavior.
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Assessment
- Tech stack
- cpp
- Domain
- bioinformatics
- Issue type
- Bug
- Difficulty
- 4/5
- Estimated time
- 3-5 days
- Activity status
- Stale
- Clarity
- Needs clarification
- Newbie friendliness
- 25/100