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Official Release PyMOL v2.3 has been released on February 11, 2019.
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New Plugin ProBiS H2O is a new plugin for identification of conserved waters in protein structures.
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New Script dssr_block is a wrapper for DSSR (3dna) and creates block-shaped nucleic acid cartoons
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Did you know...


Rms computes a RMS fit between two atom selections, but does not tranform the models after performing the fit.


rms (selection), (target-selection)


fit ( mutant and name ca ), ( wildtype and name ca )


To determine the RMS without any fitting, see Rms_Cur

Fit, Rms, Rms_Cur are finicky and only work when all atom identifiers match: segi, chain, resn, name, alt. If they don't then you'll need to use the alter command to change the identifiers to that they do -- typically that means clearing out the SEGI field, renaming chains, and sometimes renumbering.

I tried made two selections A, and D as

PyMOL>sel A, 1gh2 and n. CA and i. 65-99
Selector: selection "A" defined with 35 atoms.
PyMOL>sel D, 1kao and n. CA and i. 64-98
Selector: selection "D" defined with 35 atoms

which as you can see both yield 35 atoms. Now,

rms_cur A, D

won't work, due to the aforementioned reason. To fix this, one needs ..→

A Random PyMOL-generated Cover. See Covers.