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schrodinger / pymol-open-source

Open-source foundation of the user-sponsored PyMOL molecular visualization system.
https://pymol.org/
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Cartoon_trancparency command not working after using it on specific residue ranges #269

Closed TheWizier closed 1 year ago

TheWizier commented 1 year ago

Reproduce: cmd.set("cartoon_transparency", 0.5, "not i. 12-38") cmd set("cartoon_transparency", 1)

Outcome: Second command does nothing. Expected outcome: All cartoons become fully transparent.

JarrettSJohnson commented 1 year ago

This is likely expected since the first command provides a selection which applies the transparency on the atomic level which the second command does not. If you want all parts of all cartoons to be transparent, either unset the setting on the atomic level by applying unset_deep cartoon_transparency (and then perform the second command) or apply transparency on the atomic level by providing a selection which describes all atoms (e.g. set cartoon_transparency, 1.0, (all))

JarrettSJohnson commented 1 year ago

Feel free to reopen if the comment doesn't address your needs.