Hi again Chimera Team,
I have a large macromolecular structure, and I want to, at random, substitute some of the separate models for a variant form.
Is it possible to do this through chimera, e.g. via python? It seems to me it would basically be a case of:
- enumerate the list of open models
chimera.openModels.list() returns a list of all open models (including volume models, etc.); to get a list of just the molecular models:
from chimera import openModels, Molecule
mols = openModels.list(modelTypes=[Molecule])
The Python
random module is used for choosing things at random.
- either open a new model, fit it to that model, then close the old one, or somehow get the old models co-ords, close it, then open the new one in its place from a specified file path
Off the top of my head it seems easiest to open the new model, use
MatchMaker to match it on the old one, and then close the old one. So, suppose you had your random old model in a variable named
old_model, then you would use code something this to replace it:
from chimera import openModels, runCommand
opened_models = openModels.open(“path-to-model-file”)
new_model = opened_models[0]
runCommand(“matchmaker #%d #%d” % (old_model.id, new_model.id))
runCommand(“close %d” % old_model.id)
—Eric
Eric Pettersen
UCSF Computer Graphics Lab