Hi Tony, Good. I didn't see the sleep issue mentioned in our ChimeraX documentation. We'll add that. Tom

On Feb 6, 2024, at 2:35 PM, Anthony Newcombe <ant.newcombe@gmail.com> wrote:

Ah ok thanks Tom!

My PC does go into sleep mode, I'll turn this off and try again!

Many thanks for the help

Best wishes

Tony

Anthony Newcombe Brook Lodge Lisnacunna Ballinascarthy Clonakilty Cork

On Tue, Feb 6, 2024 at 10:25 PM Tom Goddard <goddard@sonic.net <mailto:goddard@sonic.net>> wrote:

...

Hi Tony,

If you let your computer sleep when the ChimeraX AlphaFold job is run on Google Colab it will probably lose the results. Google intends Colab to be for interactive use. So I suggest setting your computer not to sleep when running a prediction. There is more discussion of AlphaFold prediction not downloading on the ChimeraX mailing list

https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/...

including how you can get the results if Google Colab has not closed the session and deleted them (happens within a few hours).

Tom

...

On Feb 6, 2024, at 5:57 AM, Anthony Newcombe via ChimeraX-users <chimerax-users@cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu>> wrote:

Hello ChimeraX team

I am evaluating ChimeraX (non-commercial use) but have an issue you may be able to help with. When I run a structure prediction:

Tools > structure prediction > AlphaFold

I enter two primary sequences and hit ‘predict’

The simulation completes, but nothing opens in ChimeraX, also there is no data saved in the location below. I have tried alternative locations, but no data is saved

~/Downloads/ChimeraX/AlphaFold/prediction_[N]

Do you know how I obtain saved predicted results ChimeraX? Do I need a paid service for this?

Many thanks

Tony

Anthony Newcombe Brook Lodge Lisnacunna Ballinascarthy Clonakilty Cork _______________________________________________ ChimeraX-users mailing list -- chimerax-users@cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu> To unsubscribe send an email to chimerax-users-leave@cgl.ucsf.edu <mailto:chimerax-users-leave@cgl.ucsf.edu> Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/