Hello, I am a newer user of ChimeraX and am having some trouble creating visualizations to characterize a channel of interest. I began by following the procedure outlined in the tutorial "MOLE Channel Coloring by Property" but quickly ran into some issues with my own channel. This led me to try the click-to-execute links for the example in the tutorial and I ran into the same problem. It seems ChimeraX cannot accept .json files that are not Alphafold PAE maps, meaning there is no way to visualize the results of the MOLEsever analysis. I have attempted parsing data from the .json into a usable file format such as a .bild or a .pdb in a separate anaconda kernel, and while I am able to get coordinates for a superimposed visualization, they are not selectable atoms that can be color-coded or manipulated as they are in the procedures following the "open molepore-1bl8.json" command. I know this is because I have not found a way to parse all of the useful data from the .json file into another format, but I do not see exactly how I would go about doing so. Is there a way to get ChimeraX to accept a .json file that is not a PAE plot without the need for parsing data or changing format? Thank you so much for the help!
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
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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participants (3)
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Elaine Meng -
Josh Gonzalez -
Tom Goddard