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Hey:)
I am trying to use the following function for ConformerEnsemble_from_CREST:
ce.prune_rmsd(method = "obrms-batch")
It gives me the following error:
PermissionError: [Errno 13] Permission d…
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Hi I have an issue referencing supplementary figures in the below code
This is how the figure environment is defined
```\begin{figure}
\includegraphics{fig2.pdf}
\caption{
Illustration …
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Hi,
in the documentation ( https://ringtail.readthedocs.io/en/stable/index.html )
in the **command line interface section** there is the following statement:
_"Be cautious when adding results from …
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Currently, the yank documentation says: "The RMSD restraints must also be applied in the solvent phase of the calculation if they are on in the decoupled state, but this is not implemented yet."
An…
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Dear Developers,
I wonder whether you can let an option compute RMSD just for one component of coordinate (e.g., z-component)?
It is necessary in some cases we need to evaluate RMSD for one comp…
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I forget, but is our MDTraj RMSD stuff now sufficiently general to stop using LPRMSD here?
I guess the key factor is aligning to a subset of atoms, then calculating RMSD based on a possibly different…
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Given a newly implemented parallelization (https://docs.mdanalysis.org/dev/documentation_pages/analysis/parallelization.html), implement it for all classes in `analysis.hole2` module. You may use `ana…
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I am working with a system composed of one protein and a ligand. When I open the docking results generated by GaudiMM with gaudiview and I try to cluster them this error appears:
```
Traceback (in…
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Currently, if any molecules shift from one side of the box to the other during minimization, then the RMSD becomes incorrectly large, as the proper minimum image convention is not used.
We need to …
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Here's a "fun" one: when using Coot my map contour will only adjust if I scroll very, very slowly. Here is a relevant section of the log:
```
pushing statusbar text: Map 0 contour_level 0.463 n-…