UCSF ChimeraX
UCSF ChimeraX (or simply ChimeraX)
is the next-generation molecular visualization program from the
Resource for Biocomputing,
Visualization, and Informatics (RBVI),
following UCSF Chimera.
ChimeraX can be downloaded free of charge
for academic, government, nonprofit, and personal use.
Commercial users, please see
ChimeraX commercial licensing.
ChimeraX is developed with support from National Institutes of Health R01-GM129325.
ChimeraX on Bluesky:
@chimerax.ucsf.edu
The MOLEonline Server
calculates channels in protein structures and provides several types
of analyses. Results can be downloaded in several different formats, including
JSON.
A JSON file downloaded from the
MOLEonline Server
can be opened in ChimeraX version 1.5 and newer.
A sphere model is generated for each channel in the file, and if the file
contains more than one channel, a
slider interface
will appear for flipping through them one by one.
Since the channels are individual models in ChimeraX,
it is also easy to view more than one at the same time, change their colors,
etc. using the
Model Panel
and/or commands.
For image setup, see the command file
2dkh-mole.cxc
and data file
2dkh-channels.json.
See also the MOLE Channel Coloring by Property tutorial.
More features...
KCNQ1 is the pore-forming subunit of a cardiac potassium channel.
It binds to calmodulin, and mutations in either of these proteins
can cause congenital long QT syndrome, a dangerous
propensity for irregular heartbeats.
In the image, a structure of the KCNQ1/calmodulin complex
(PDB 5vms)
has been assembled into the native tetrameric form with the
sym command.
The view is from the cytoplasmic side, with
KCNQ1 shown as surfaces, calmodulin as cartoons, and calcium ions as balls.
A pastel palette
from ColorBrewer
has been used to color the surfaces, darkened with
color modify
for the cartoons, and “rotated” 45° in hue for the ions.
See the command file colormod.cxc.
More images...