Hi Amita, Google Colab can predict sequences of about 2000 amino acids with a free google account -- the limit is set by the GPU memory which tends to be 12-16 Gbytes on the old Nvidia GPUs free Google Colab gives you (K8, T4, V100). You can also pay Google Colab to get GPUs with more memory that can handle up to about 5000 amino acids, but such a prediction can take 24 hours and cost about $50. I don't know anything about cosmic2 alphafold. Tom

On Apr 3, 2024, at 11:03 AM, Amita Mohan <amimohan@sas.upenn.edu> wrote:

Is there a limit on amino acid used for prediction?

Also does cosmic2 alpha fold is different from google Colab alpha fold prediction?

Best,

Amita

Sent from my iPhone

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On Apr 3, 2024, at 1:52 PM, Tom Goddard <goddard@sonic.net> wrote:

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

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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

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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

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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 _______________________________________________ ChimeraX-users mailing list -- chimerax-users@cgl.ucsf.edu To unsubscribe send an email to chimerax-users-leave@cgl.ucsf.edu Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/