<html><head><meta http-equiv="Content-Type" content="text/html; charset=utf-8"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;" class="">Hi Anthony,<div class=""><br class=""></div><div class=""> AlphaFold predictions on Google Colab of 1200 amino acids often fail as you can see from test cases on this web page</div><div class=""><br class=""></div><div class=""><span class="Apple-tab-span" style="white-space:pre"> </span><a href="https://www.rbvi.ucsf.edu/chimerax/data/alphafold-jan2022/afspeed.html" class="">https://www.rbvi.ucsf.edu/chimerax/data/alphafold-jan2022/afspeed.html</a><br class=""><div><br class=""></div><div>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</div><div><br class=""></div><div><span style="color: rgb(33, 33, 33); font-family: monospace; font-size: 14px; font-variant-ligatures: normal; orphans: 2; white-space: pre; widows: 2; background-color: rgb(255, 255, 255); text-decoration-thickness: initial;" class="">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 |
+-------------------------------+----------------------+----------------------+
<br class=""></span></div><div> 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 </div><div><br class=""></div><div><span class="Apple-tab-span" style="white-space:pre"> </span>~/Downloads/ChimeraX/AlphaFold/prediction_1</div><div><br class=""></div><div> 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.</div><div><br class=""></div><div><span class="Apple-tab-span" style="white-space:pre"> </span>Tom</div><div><br class=""></div><div><br class=""><blockquote type="cite" class=""><div class="">On Jul 23, 2022, at 4:41 AM, Anthony Morgan via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:</div><br class="Apple-interchange-newline"><div class="">
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Dear All,
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<div class="">I’m new to Chimera X and to Colab Alphafold (AF), hope you can help please.</div>
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<li class="">I’m running Chimera X 1.4 on a Macbook Air.</li><li class="">I want the predicted structure of a fairly large protein (<b class="">1182</b> residues).</li><li class="">When I first ran Colabfold_predict, it terminated after 90 min (RAM issue).</li><li class="">I re-ran the same sequence *<i class="">without </i><span style="font-style: normal;" class="">*</span><i class=""> </i><span style="font-style: normal;" class="">Energy Minimization.</span></li><li class=""><span style="font-style: normal;" class="">After 20 mins, it successfully returned the first model (see attached), but ran into RAM issues again.</span></li></ul>
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<div class="">Two questions:</div>
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<li class="">There is no ‘Prediction’ folder in my Downloads, so how can I download the *.pdb file of model #1 that it clearly has generated?</li><li class="">If I cannot do this, will an upgrade to Colab Pro solve this issue for this size of protein?</li></ul>
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<div class="">Thanks for advice.</div>
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<div class="">Kind regards,</div>
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<div class="">Anthony</div>
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