Rms cur

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rms_cur computes the RMS difference between two atom selections without performing any fitting.

By default, only matching atoms in both selections will be used for the fit (same chain, residue number, atoms names etc.). Alternate location mess up the match!

Usage

rms_cur mobile, target [, mobile_state [, target_state [, quiet [, matchmaker [, cutoff [, cycles [, object ]]]]]]]

Arguments

See fit.

Examples

Example 1: Identical Identifiers

Alternate location mess up the match, so remove them first.

fetch 1p36 1kw7, async=0
remove not alt ""+"A"
rms_cur 1p36, 1kw7

Example 2: Homologues

Use align or super to create an alignment object (without fitting) and then use the alignment object in the atom selection and turn off identifier matching with matchmaker=-1.

fetch 1oky 1t46, async=0

# create alignment object
align 1oky, 1t46, cycles=0, transform=0, object=aln

# RMSD of alignment object
rms_cur 1oky & aln, 1t46 & aln, matchmaker=-1

See Also