Hi Jim, The AlphaFold predicted model is always saved as best_model.pdb. It would be nice if you could specify a different name when you start the prediction run but that is not available. I made a ChimeraX feature request for that https://www.rbvi.ucsf.edu/trac/ChimeraX/ticket/9128 You can request new features directly with ChimeraX menu entry Help / Report a Bug.... This can be used for both bugs and new feature suggestions. Tom

On Jun 5, 2023, at 11:51 AM, James Raymond <james.raymond@unlv.edu> wrote:

Thank you. I am slowly learning how to use ChimeraX. One other question that I haven't solved yet: when I paste a sequence into the box for structure prediction, is there a way to name it right at the beginning? All my previous jobs are given the same name "best_model".I know I can rename them later, but it would be easier if I could name them at the start. Jim

On Mon, Jun 5, 2023 at 11:30 AM Tom Goddard <goddard@sonic.net <mailto:goddard@sonic.net>> wrote:

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Hi Jim,

The ChimeraX panels are can be dragged and dropped on the main ChimeraX window to allow stacking them. In your case you dragged the AlphaFold Run panel on top of the Log panel. Then it shows the two tabs (AlphaFold Run, Log) at the bottom and you can click on those to switch between them. You can make the AlphaFold Run window free-floating again by showing its tab then dragging the title-bar of the panel out of the main ChimeraX window. All the ChimeraX panels work this way -- they can be made free-floating windows or "docked" in the main window.

Sometimes it is annoying when you drag a ChimeraX window and it tries to drop it on top of another panel. You can tell ChimeraX to not allow dropping the AlphaFold Run window on another panel using the command

ui dockable false "AlphaFold Run"

Tom

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On Jun 2, 2023, at 6:36 PM, James Raymond <james.raymond@unlv.edu <mailto:james.raymond@unlv.edu>> wrote:

Thanks, Tom, I sent another email to say that I think I solved the problem but you didn't see that one.

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Here's a cool protein structure I made today with ChimeraX. I used Yasara to view it. This is so great! Jim

On Fri, Jun 2, 2023 at 4:34 PM Tom Goddard <goddard@sonic.net <mailto:goddard@sonic.net>> wrote:

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Hi Jim,

You kind of shoot yourself in the foot if you close the AlphaFold Run. But Google Colab does not immediately kill your AlphaFold job. So you could reconnect to Google Colab in whatever web browser you normally use (search for Google Colab). When it asks if you want to load some previous notebook say Cancel. Then use Google Colab menu Runtime / Manage Sessions and click on your AlphaFold session that you started from ChimeraX. Then you should see your job still running. When it completes it will ask to download the results. The original ChimeraX window you closed would have downloaded the prediction and opened it in ChimeraX. But now you have Colab in a normal web browser so it will simply download to your ~/Downloads folder (not where ChimeraX usually puts it in ~/Downloads/ChimeraX/AlphaFold/prediction_N) so you would have to open the results.zip and load the predicted structure yourself.

In short don't close the AlphaFold Run window. It isn't quite as bad as opening a terminal, starting a computation, then closing the terminal before it finishes. Since it is running on Google's servers and Google kindly doesn't immediately shut it down, you can rescue it. But it is not intended to work that way.

Tom

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On Jun 2, 2023, at 4:04 PM, James Raymond via ChimeraX-users <chimerax-users@cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu>> wrote:

Dear ChimeraX, I keep losing this window, whenever I click on it or move it. How do I get it back again? thank you Jim

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