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While using `make-mmcif.py` to read a complete mmCIF file and write it out, it gives an alignment error with the reference sequence.
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'Traceback (most recent call last):\n File "~/make-mmcif.py", …
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As title. Mirror code that Mark has created to setup an independent, minimal working example of the nglview widget on a web-browser.
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The PDB reader does not seem to assign aromaticity correctly for non-protein molecules, see this example which reads in 3 different versions of the small molecule benzamidine:
The .pdb file retrieved…
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I am running 3.0.9 and I keep getting this error when I run a single PDB code or a text file full of them like in the tutorial.
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Hugo >= 0.50 (including master HEAD as of today) exits before finishing building a website when getJSON fails to get a resource.
This problem was earlier filed as Issue #5076 "getJSON etc. should l…
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Hi,
Is it possible to access bond orders from a protein structure via a pdb file, as interpreted by pdbfixer? Do topology objects from a pdb file (without any other input files) infer bond order at a…
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The latest insiders build has lost test discover functionality. The bottom window bar has no "run tests" item displayed. No controls are available to discover tests and provide run/debug options in…
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`pypdb`-related notebooks must be updated since the old API does not work any more due to changes in the RCSB API.
From `pypdb`'s GH page:
> As of November 2020, pypdb is undergoing significantl…
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How can obtain the atoms, which are present in an atomic graph of a protein?
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Hi! I am using the `biozernike` library to perform some comparisons between PDB structures. I would like to do some calculations between subsets of assemblies and get some distance/similarity scores. …