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Hi Francisco,
Thanks so much for taking the time to develop these great tutorials.
In my project I am comparing two groups of species (Entero co-colonizers vs co-excluders) and have identified a…
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EUKulele stopped at the BUSCO step for me
Error message:
`BUSCO run either did not complete successfully, or returned no matches for sample`
I checked the log files and these are the outputs from…
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Apparently REVIGO has changed format of the file that is obtained by pressing Export results to text table (CSV) in the web interface. Colum `representative` in revigo.csv file now lists GO ids inste…
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Hello ParmEd developers,
I want to give a try to define all the solute molecules as one molecule in the topology, to fix a NPT issue, but I got to know from Amber mailing list that the command com…
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With the following script, I expect to obtain a PDB file `help.pdb` containing a single frame of the trajectory (the one with index 5):
```python
import pytraj as pt
print(pt.__version__)
tr…
RMeli updated
4 years ago
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We need a new CLI analysis tool (which can also be run via the Python API) to analyze simulations set up via the perses CLI.
It should provide three major outputs:
1. **Optimal predictions:** The …
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**Is your feature request related to a problem?**
Part of the problem that causes the Race to Infinity is when two lines (representing Rez links) cross over each other.
But if it's true that link X…
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Thank you for sharing your code!
I am trying to train openfold, but the problem of loss being NAN persists, and the whole training hangs when this problem occurs.
I downloaded the code in early …
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In some cases, a Reactome pathway doesn't have any reactions that are directly associated with it. Instead it has a collection of subpathways under it. In those cases, the parent gets imported as a si…
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The authors present an implementation for a numerical solver specifically design to tackle continuum electrostatics models. Specifically, the authors present a solver for the Poisson-Boltzmann equatio…