Hi Amita,

  The Google Colab connection will time out if your computer goes to sleep.  Google Colab is an interactive service, so if Colab doesn't hear from the web browser window because your computer is sleeping it will disconnect and kill your alphafold prediction.  So you may want to turn off sleep on your computer.

Tom


On Apr 3, 2024, at 7:08 AM, Amita Mohan <amimohan@sas.upenn.edu> wrote:

Thank you Tom for your quick reply. The Colab works but terminate without reaching to the point of downloading results. It shows the connection fails and if I try to reconnect it gives me error message.

I do also get response from Elaine. I will work on the recommendation and contact you if I will still have issues.


Best,

Amita

On Apr 2, 2024, at 4:17 PM, Tom Goddard <goddard@sonic.net> wrote:

Hi Amita,

  You would need to give a more detailed explanation of what you mean by "Google Colab keep on termination".  Does Google Colab disconnect?  Does an error message from AlphaFold appear?  Does it finish and say "Downloading results..."?

Tom


On Apr 2, 2024, at 12:58 PM, Amita Mohan via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:

Hello,

I would appreciate if you please answer the following questions:

1. I am using chimeraX, and I have a trouble getting results from Alphafold. The Google Colab keep on termination without saving results. Could you please help?

2. I am using hydrogen bond tool, how can I save all the H-bonds in the protein as file containing all the information for the paired residues involved in the H bond. Similarly, I also would like to save the information of residues involved in the protein-protein interactions. 

 I hope to hear from you.

Best,

Amita
Department of Biology
University of Pennsylvania
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