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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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```
Process: Xcode [13306]
Path: /Applications/Xcode.app/Contents/MacOS/Xcode
Identifier: Xcode
Version: 11.3.1 (15715)
Build Info: …
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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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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 …
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The version of fasta36 (the bioconda fasta3 package) is fasta-36.3.8g dated December, 2017. This version has some bugs that have been corrected in fasta3-36.3.8g dated August, 2018. How can I help g…
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Hi,
I am using latest BioMAJ and BioMAJ2 Galaxy versions and Galaxy v18.05.
For example, Anopheles_gambiae.properties looks like:
```
bwa.name=bwa
bwa.desc=Build bwa index
bwa.type=index
bwa.ex…
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After installing Tinker, I type `pdbxyz` in the `test` folder and input `bdna.pdb`, but get the errror:
```
Enter Protein Data Bank File Name : bdna.pdb
At line 425 of file readpdb.f
Internal Err…
njzjz updated
5 years ago
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Hi, I don't have a strong computer science background so if this is not the place for this question please feel free to delete this or send me to where I should be asking, but I'm trying to use freesa…
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Currently some of the test files reference `x-common//canonical-data.json` with a version number, and a few test files lack any such a reference. Additionally, `x-common` was recently renamed to `prob…