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Is it possible to read in a homology modeled structure that is not in RCSB pdb using the
`-pdb-file-dir`
argument?
Thanks
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Please work to debug the step1_pdb_process.py script.
Script: https://github.com/lemaslab/CAMP/blob/master/data_prepare/step1_pdb_process.py
Input Data (RCSB PDB) : Download the fasta files fro…
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After finishing #290 , let's look into couplings between GPCRs and arrestins, and add β-arrestin as another protein we couple the odor receptors with and do docking on, then add the dock results of th…
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### Problem to solve
PDB entries with extended Chemical Component Dictionary (CCD) or PDB IDs will be distributed in PDBx/mmCIF format only, as announced by the wwPDB in collaboration with the [PDBx…
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We need a general mechanism to map experiment names to short codes.
Tentative spec: parse `shortcodes.csv` (if provided), which has just two columns: experiment names and shortcodes.
> exp…
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The following code raises `AttributeError: 'PDBFixer' object has no attribute 'missingResidues'`:
```
from pdbfixer import PDBFixer
fixer = PDBFixer("6dyo.pdb")
fixer.findMissingAtoms()
```
…
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```
What steps will reproduce the problem?
1. Running pdb_bfactor with a pdb file that is not deposited in rcsb
2.
3.
What is the expected output? What do you see instead?
What version of the produ…
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getting Uncaught TypeError: molLoop is undefined in console from parsing https://www.rcsb.org/ligand/H20 CIF File
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Hi!
Thanks for the lib :-)
I would like to calculate a similarity score between two PDBs (like rcsb but for any protein combination) . Is there any documentation how to do that with this librar…
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Hi there,
thanks for the script! I am using to generate pdb with missense mutations. It works except for this:
`pymissense O95477 abaca1 --maxacid 2224 --pdbpath 7tc0.pdb --tsv /tmp/alpha.tsv`
…