Hi Josh, ChimeraX only looks at the file extension ".json" to guess what file type it is. As Elaine mentioned I changed the default for ".json" to assume AlphaFold predicted aligned error instead of MOLE channel data because the former is more often used. And the solution is to use the "format mole" option as Elaine said open mole_channels.json format mole In the future maybe we will change the ChimeraX json file reader so it inspects the first line of the file to figure out what kind of data it contains. Tom
On Jun 24, 2024, at 8:44 AM, Elaine Meng via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hi Josh, Due to recent changes in ChimeraX, you now need to add "format mole" to the "open" command and it will work as it should. For example, "open browse format mole" instead of just "open browse" as shown in the tutorial, or "open yourfilenamehere.json format mole" if you're just opening the file directly instead of browsing to it.
I submitted a bug report, ticket #15486, including your email address so you will get notifications if anything happens with it. I submitted it before I realized that opening the file would still work if you just include "format mole," so maybe it's not really a bug.
In the meanwhile I will change the tutorial to include "format mole" in the open command. Best, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Resource for Biocomputing, Visualization, and Informatics Department of Pharmaceutical Chemistry University of California, San Francisco
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