TICA on backbone atoms

[qasimpars]

Hi,

I am trying to do TICA on backbone atoms but I couldn't find the commands for that. Could please tell me how I can do the TICA only on backbone atoms? Do the following commands do the TICA on backbone torsions?

arrays = []
feat = pyemma.coordinates.featurizer(pdb)
feat.add_backbone_torsions()
data = pyemma.coordinates.load(files, features=feat)

Regards

[clonker]

The snipped you posted extracts backbone torsions from trajectory files. This data can be passed into TICA through the corresponding API.

[qasimpars]

Hi,

I want to do TICA on the distances of backbone atoms not on backbone torsions. Is that possible? If yes, how can I do that?

Best,

[clonker]

Ah right. It is possible, you have to select the appropriate atoms and compute distances on them through a featurizer. Please see this tutorial.

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