With out seeing logs from your Colab virtual matchine that ran AlphaFold I can't say why it didn't download. It could be the Google Colab session closed to a timeout and so the results were lost.

To try to recover the results, if your ChimeraX AlphaFold Run window is up, in the left hand column there is a folder icon that shows the files on the virtual machine including all the ones produced by AlphaFold. If the job completed successfully there would be a results.zip file that you could download from there. But the Colab session times out after some time (hours) and in that case Google has deleted it all. If your ChimeraX is closed or the AlphaFold Run window is closed you can still go to Google Colab in any web browser and rejoin your Colab session started by ChimeraX if it has not been closed by Google.

On Oct 12, 2023, at 3:34 PM, Luz Cristina Vallejo Garcia via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:

Hi there!

I have a problem using ChimeraX. I tried to use the aphafold2 tool to predict a large protein structure. The process to predict the structure of my protein was successfully completed, but the downloading of my results failed. I observed that the folder for the prediction was created but is empty. So my questions are:
Why did the program fail to download my results?
Is there a possibility to obtain my results without to re-run the process?
Thanks in advance

Cris Vallejo
IBt, UNAM, México

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