View Channels from MOLEonline

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.

B-factor Coloring

Atomic B-factor values are read from PDB and mmCIF input files and assigned as attributes that can be shown with coloring and used in atom specification. This example shows B-factor variation within a structure of the HIV-1 protease bound to an inhibitor (PDB 4hvp). For complete image setup, including positioning, color key, and label, see the command file bfactor.cxc.

Additional color key examples can be found in tutorials: Coloring by Electrostatic Potential, Coloring by Sequence Conservation

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