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### Setup
I am reporting a problem with Biopython version 1.79, Python version 3.10.6, and operating
system as follows:
3.10.6 (main, Aug 10 2022, 11:40:04) [GCC 11.3.0]
CPython
Linux-5.15.0-…
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Related to #2688
There are three API entry points that can be used to suggest fixes for errors
This works both for allele descriptions and protein modification coordinates, but they have to be …
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Hello,
I have noticed that eventhough you can select chains as :A, it seems not to be possible to select by segid (MDAnalysis) or segname (vmd) like PROA. This would be usefull since psfs don't see…
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When running QC/QA, the first thing that is done is a pairwise alignment. The quality of this alignment can have a big impact of the result. The setting of gap score and gap extend penalties should be…
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The previous entanglement contains GN and GC data. Our group using model V4 and Fragment F1 only.
The `FX` is not the model, it is fragment of sequence in the full sequence.
For human proteins lo…
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The basic version would basically just be a matrix visualizer, but there are lots of nice visualization extensions possible like interactive highlighting, comparing two maps across the diagonal of the…
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Hi,
So I found a bug with mdtraj.rmsd that when it is computing RMSD of a specific trajectory with a frame of itself, the coordinates saved in the trajectory will be changed. I have included all t…
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Get SMILES for PubChem Compount (here for aspirin CID 2244):
* https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/fastidentity/cid/2244/JSON
Get AA sequence for a protein (check the sequence key)…
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Quantitative Behavior of Mass Spectrometers
To apply the theory we learnt in the last chapters of this unit to quantitative analyses with mass spectrometers, we need to think about the limitations th…
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If some pairs are broken, could analyze_results.py still work, suppose e.g. if only FXR_12_FXR_88 pair of the tutorial is broken, e.g. system is unstable, only intermediate pdbs are written and gromac…