[chimerax-users] Colab Modelled, but no PDB

[Tom Goddard]

Hi Anthony,

  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 at 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
> 
> <Screen Shot 2022-07-23 at 12.17.14.png>
> 
> 
> 
> 
> _______________________________________________
> ChimeraX-users mailing list
> ChimeraX-users at cgl.ucsf.edu
> Manage subscription:
> https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://www.rbvi.ucsf.edu/pipermail/chimerax-users/attachments/20220723/ce7d9b99/attachment.html>