search

openmm / pdbfixer

PDBFixer fixes problems in PDB files
Other
461 stars 115 forks source link

How to select a model? #186

Closed Ruibin-Liu closed 4 years ago

Ruibin-Liu commented 5 years ago

It's stated explicitly that pdbfixer can 'Select a single position for atoms with multiple alternate positions listed', but I don't see an option to do that in the APIs. I followed the manual and used 2kul as an example. The output pdb file only contains the first model. I want to use the 10th model, but how?

peastman commented 5 years ago

Those are different things. A single model can have alternate positions for particular atoms. That's what it's talking about. Separately from that, a file can contain multiple models, usually representing either a simulation trajectory or an ensemble of NMR models. PDBFixer always just uses the first model. If you want a different one, it's probably simplest to just create a file containing only the one model you want.