Rms cur: Difference between revisions
Jump to navigation
Jump to search
No edit summary |
(examples) |
||
| (9 intermediate revisions by 4 users not shown) | |||
| Line 1: | Line 1: | ||
=== | [[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 == | ||
* [[align]] | |||
* [[fit]] | |||
* [[rms]] | |||
* [[intra_fit]] | |||
* [[intra_rms]] | |||
* [[intra_rms_cur]] | |||
* [[pair_fit]] | |||
[[Category:Commands| | [[Category:Commands|Rms Cur]] | ||
[[Category:Structure_Alignment|Rms Cur]] | |||
Latest revision as of 02:09, 4 September 2017
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