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Official Release PyMOL v2.5 has been released on May 10, 2021.
Python 3 New Python 3 compatibility guide for scripts and plugins
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New Plugin PICv is a new plugin for clustering protein-protein interactions and visualization with available data from PDBe
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Plugin Update MOLE 2.5 is an updated version of channel analysis software in PyMOL
New Script dssr_block is a wrapper for DSSR (3dna) and creates block-shaped nucleic acid cartoons
Older News See Older News.
Did you know...

Mesh negative visible

If the mesh_negative_visible setting is on, then an isomesh at iso level 3.0 will in addition show the -3.0 contour. The color of the negative contour is defined by the mesh_negative_color setting. The color of the positive contour is defined with the color command, or with the mesh_color setting.

The surface_negative_visible and surface_negative_color settings control the same behavior for isosurface objects.

Since PyMOL 1.8.4 the negative color can be controlled from the color menu ("C > negative > ...").


Show the +/- 3 sigma iso-level mesh ("wire-frame") of a difference density map.

fetch 1ubq, diffmap, type=fofc, async=0
isomesh diffmesh, diffmap, 3.0
color green, diffmesh
set mesh_negative_color, red
set mesh_negative_visible

Same, but with a closed surface:

fetch 1ubq, diffmap, type=fofc, async=0
isosurface diffsurf, diffmap, 3.0
color green, diffsurf
set surface_negative_color, red
set surface_negative_visible

Color Menu

<gallery heights="250px" ..→

A Random PyMOL-generated Cover. See Covers.