[chimerax-users] Hi. I have a question about Chimera X program

[Tom Goddard]

Hi KDY,

  If you predict a sequence with AlphaFold using ChimeraX then that sequence is sent to Google Colab.  You would have to investigate the privacy policy of Google Colab to know how private your data is.  The UCSF developers of ChimeraX have no access to your sequence.

  Free Google Colab offers limited disk space,  I get 73 Gbytes and 45 Gbytes are used by just the OS and AlphaFold software.  With Colab Pro service ($10/month) I get 157 Gbytes of disk space.  To delete all your files in the current Colab session you can use Colab menu Runtime / Factory reset runtime.  Of course you would want to download any results you want to keep first.

  AlphaFold on Google Colab typically takes 1 hour to run on a short sequence of 100 amino acids, and 3 hours on a longer sequence of 1000 amino acids.  I do not know of any way to make it run faster.

  ChimeraX Google Colab allows running only one AlphaFold prediction at a time.  This is because Google Colab just gives you one virtual machine.  If you try to connect twice, for example using two copies of ChimeraX, they end up getting the same Colab virtual machine.  People describe online tricks to try to get two Colab virtual machines but I have not tried that.

  Google offers Colab Pro and Pro+ service

	https://colab.research.google.com/signup <https://colab.research.google.com/signup>

That will give you more disk space, more time per day on their virtual machines before being kicked off, and possibly better GPUs.  I use Colab Pro since the free service only allows about 2 hours of use per day which is only enough for one run.

	Tom

> On Sep 24, 2021, at 1:11 AM, dongyoung kim via ChimeraX-users <chimerax-users at cgl.ucsf.edu> wrote:
> 
> Hi. I'm researching protein 3D structure to develop the new drug.
> 
> In recent, I'm using the Alphafold function in Chimera X daily version.
> 
> I have 4 questions.
> 
> First, if I use Alphafold to predict my important project data, is it keep secure privately?
> I want to keep my data secret. It shouldn't be open to anybody without me. 
> 
> Second, when I using Alphafold in ChimeraX, I faced some error messages that mean 'Not enough disk volume. please remove past data.'. I'm not familiar with google colab...how can I manage the disk to remove past data or expand disk volume? 
> 
> Third, how can I improve the speed of alphafold prediction? ChimeraX shows some resources like ram, disk. 
> 
> fourth, I want to operate simultaneously Alphafold prediction to predict 2 or more structures. Is it possible? 
> 
> 
> If there need some pay to improve the second, third, fourth question, please let me know methods.
> Many thanks.
> 
> -from KDY
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