[chimerax-users] Job or output file name when running Alphafold in ChimeraX?

[Rayees Mattoo]

Great!!! Appreciate.
Thanks.

Best
Rayees
________________________________
From: Tom Goddard <goddard at sonic.net>
Sent: Tuesday, August 23, 2022 2:02 PM
To: Rayees Mattoo <rmattoo at stanford.edu>
Cc: Dmitry Semchonok via ChimeraX-users <chimerax-users at cgl.ucsf.edu>
Subject: Re: [chimerax-users] Job or output file name when running Alphafold in ChimeraX?

Hi Rayees,

  I added an option to AlphaFold prediction to specify the directory for saving the results.  It will be in tonight's ChimeraX builds (August 24, 2022).  You press the Options button on the ChimeraX AlphaFold panel to use this or use the new "directory" option of the ChimeraX "alphafold predict" command.  The directory you specify does not need to exist, it will be created when you run the prediction.  Thanks for the suggestion.

Tom

[cid:7F3CBD74-6A04-433A-9D15-4582CB15DBB7]

On Aug 21, 2022, at 11:23 AM, Rayees Mattoo via ChimeraX-users <chimerax-users at cgl.ucsf.edu<mailto:chimerax-users at cgl.ucsf.edu>> wrote:

Thanks. I do often rename the Prediction_N directory, Just wanted to avoid that step if there was a possibility. Hope it will be added soon.

Best
Rayees
________________________________
From: Elaine Meng <meng at cgl.ucsf.edu<mailto:meng at cgl.ucsf.edu>>
Sent: Sunday, August 21, 2022 11:19 AM
To: Rayees Mattoo <rmattoo at stanford.edu<mailto:rmattoo at stanford.edu>>
Cc: ChimeraX Users Help <chimerax-users at cgl.ucsf.edu<mailto:chimerax-users at cgl.ucsf.edu>>
Subject: Re: [chimerax-users] Job or output file name when running Alphafold in ChimeraX?

Hi Rayees,
Not currently, but I recently made a ticket with the request to add that feature:

<https://www.rbvi.ucsf.edu/trac/ChimeraX/ticket/7474>

I will put you on the notification list for when changes occur to the ticket.

The workaround currently is to go to the ~/Downloads/ChimeraX/Alphafold/ folder (or equivalent if you are not on a mac) and "manually" rename and/or move the prediction_N folders each time you do a run, while you still remember which one is which.  By manually I mean outside of ChimeraX, by whatever  way you normally move or rename folders on your computer.

Best,
Elaine
-----
Elaine C. Meng, Ph.D.
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco




> On Aug 20, 2022, at 11:54 AM, Rayees Mattoo via ChimeraX-users <chimerax-users at cgl.ucsf.edu<mailto:chimerax-users at cgl.ucsf.edu>> wrote:
>
> Hi,
> Is there a way to name the AlphaFold run job or the output file in ChimeraX?
>
>
> Best
> Rayees
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