AlphaFold predictions on Google Colab of 1200 amino acids often fail as you can see from test cases on this web page
https://www.rbvi.ucsf.edu/chimerax/data/alphafold-jan2022/afspeed.html
With free Google Colab you often get a very old Nvidia K80 GPU with 12 Gbytes of memory. With Colab Pro ($10/month) I usually get an Nvidia P100 GPU with 16 Gbytes of memory which can handle slightly bigger proteins. You can check what GPU you got by pressing the "+ Code" button on the Google Colab window, then entering the command "!nvidia-smi" and pressing the play button, which gives output like this
Sat Jul 23 23:28:55 2022
+-----------------------------------------------------------------------------+
| NVIDIA-SMI 460.32.03 Driver Version: 460.32.03 CUDA Version: 11.2 |
|-------------------------------+----------------------+----------------------+
| GPU Name Persistence-M| Bus-Id Disp.A | Volatile Uncorr. ECC |
| Fan Temp Perf Pwr:Usage/Cap| Memory-Usage | GPU-Util Compute M. |
| | | MIG M. |
|===============================+======================+======================|
| 0 Tesla P100-PCIE... Off | 00000000:00:04.0 Off | 0 |
| N/A 38C P0 34W / 250W | 16259MiB / 16280MiB | 0% Default |
| | | N/A |
+-------------------------------+----------------------+----------------------+
To download a completed model after an AlphaFold error (typically out of memory), click on Files in the Google Colab window, then click on the predicted structure, "af1182_unrelaxed_model_1.pdb" in your image, and click the "..." to the right of the file and choose Download from the menu that appears. The file will then appear on your local computer in
~/Downloads/ChimeraX/AlphaFold/prediction_1
I'll see if I can add to the ChimeraX ColabFold output the GPU and also make it automatically download partial results in case an error occurs.
Tom
On Jul 23, 2022, at 4:41 AM, Anthony Morgan via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Dear All,
I’m new to Chimera X and to Colab Alphafold (AF), hope you can help please.
- I’m running Chimera X 1.4 on a Macbook Air.
- I want the predicted structure of a fairly large protein (1182 residues).
- When I first ran Colabfold_predict, it terminated after 90 min (RAM issue).
- I re-ran the same sequence *without * Energy Minimization.
- After 20 mins, it successfully returned the first model (see attached), but ran into RAM issues again.
Two questions:
- There is no ‘Prediction’ folder in my Downloads, so how can I download the *.pdb file of model #1 that it clearly has generated?
- If I cannot do this, will an upgrade to Colab Pro solve this issue for this size of protein?
Thanks for advice.
Kind regards,
Anthony
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