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Since the Protein Data Bank (PDB) has switched the standard file format from PDB to mmCIF, it is desirable to support [PDBx/mmCIF](http://mmcif.wwpdb.org/pdbx-mmcif-home-page.html) (and PDBML/XML). I …
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**Describe the bug**
(1) pymatgen.Structure.to method silently writes YAML output if the requested structure file type is not in the decision tree.
(2) Writing Protein Data Bank (.pdb) structure f…
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I have an older [TG-1](https://www.internode.on.net/support/guides/internet_access/broadband_adsl/tg-1/).
Do you know of any way to unlock it?
e.g. exploits you have have found in the technicolor we…
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I found inconsistencies for specifying a well-defined identifier in the guides document and I'm wondering which one would you endorse.
In my mind, I'm thinking a structure that's something like thi…
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It would be useful to have more stats on the Scholia homepage,and the following query (from [here](https://github.com/fnielsen/scholia/commit/f826f00e6bb3e1be0ea3e00c29b50e08451891f0#diff-7245b475d8fe…
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e.g. [number of triples in Wikidata](https://query.wikidata.org/#SELECT%20%28count%28%2a%29%20as%20%3Fcounts%29%20WHERE%20%7B%0A%20%20%3Fs%20%3Fp%20%3Fo%20.%0A%20%20%7D)
```SPARQL
SELECT (count(*)…
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I'm hitting some errors when attempting to index the current RefSeq *Homo sapiens* reference genome `GCF_000001405.38_GRCh38.p12` using `bcbio_setup_genome.py`. Is RefSeq currently supported in bcbio?…
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Hi there,
For a project I'm doing, I'm using the RCSB API to get information about the particular chain-level information associated with a given PDB stored in the Data Bank.
For example, using …
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```
Process: Xcode [13306]
Path: /Applications/Xcode.app/Contents/MacOS/Xcode
Identifier: Xcode
Version: 11.3.1 (15715)
Build Info: …
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When applying pdbxyz with the forcefield oplsaa.prm some of the atomtypes don't seem to fit perfectly:
* In amino acid isoleucine the C atom of the CH2 group gets atomtype 80 ("Alkane CH3-") whereas …