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Is there a syntax for loading multiple/split .pdb files? Large structures (e.g. `5XTH`) are not contained in a single .pdb file, but rather multiple ones (either that or a single .cif/.xlm file). I su…
ghost updated
5 years ago
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Does the new Visual Studio 2017 version (the one that just entered RC state) add anything new to the PDB format? Are there any plans to update this repository with any new information in the newer PDB…
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This issue will be left open for all PDBs that have strange errors...
ID: 5nc5
Problem: Biopython loading of mmcif file fails, says duplicated atom name
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User emailed asking whether we support PDB files.
It is more/less undocumented that we open `.map` via MRC. Beyond that I think we are in the realm of other tools like Biopython's `Bio.PDB`. If …
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I'm opening this since I suspect we need more detailed documentation on this topic.
### Discussed in https://github.com/microsoft/WindowsAppSDK/discussions/2001
Originally posted by **AzAgar…
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It seems that Yank only accepts mol2 files as ligands, while in my case I want to use a very short peptide as a ligand for the free energy calculation. It seems that even if I specify a pdb file as li…
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Oftentimes, PDB files are downloaded in `.pdb.gz` format. When a filepath is specified to `read_pdb`, a zipped file should be read correctly and automatically detected using the file extension.
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## Environment Information
Open Babel version: 2.4.1
Operating system and version: Ubuntu 18
## Expected Behavior
When using the command
```
obabel -m -ipdb multi.pdb -opdb -O multi-.pdb
```
…
RMeli updated
3 years ago
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`pdbfixer` seems to produce a highly deformed structure for PDB id code `1AO7`.
You can reproduce this yourself by running the HTML-based `pdbfixer` on `1AO7` to simply build in the hydrogens. For s…
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Similar to PR#1451894, when hydrogens are added to PDB files (or Mol2
files with residues), the hydrogens do not go into residue order. Instead,
they all end up at the end.
-Geoff
Reported by:…