Job or output file name when running Alphafold in ChimeraX?
Hi, Is there a way to name the AlphaFold run job or the output file in ChimeraX? Best Rayees
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@cgl.ucsf.edu> wrote:
Hi, Is there a way to name the AlphaFold run job or the output file in ChimeraX?
Best Rayees _______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
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@cgl.ucsf.edu> Sent: Sunday, August 21, 2022 11:19 AM To: Rayees Mattoo <rmattoo@stanford.edu> Cc: ChimeraX Users Help <chimerax-users@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@cgl.ucsf.edu> wrote:
Hi, Is there a way to name the AlphaFold run job or the output file in ChimeraX?
Best Rayees _______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
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
On Aug 21, 2022, at 11:23 AM, Rayees Mattoo via ChimeraX-users <chimerax-users@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@cgl.ucsf.edu> Sent: Sunday, August 21, 2022 11:19 AM To: Rayees Mattoo <rmattoo@stanford.edu> Cc: ChimeraX Users Help <chimerax-users@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 <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@cgl.ucsf.edu> wrote:
Hi, Is there a way to name the AlphaFold run job or the output file in ChimeraX?
Best Rayees _______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users <https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users>
_______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
Great!!! Appreciate. Thanks. Best Rayees ________________________________ From: Tom Goddard <goddard@sonic.net> Sent: Tuesday, August 23, 2022 2:02 PM To: Rayees Mattoo <rmattoo@stanford.edu> Cc: Dmitry Semchonok via ChimeraX-users <chimerax-users@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@cgl.ucsf.edu<mailto:chimerax-users@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@cgl.ucsf.edu<mailto:meng@cgl.ucsf.edu>> Sent: Sunday, August 21, 2022 11:19 AM To: Rayees Mattoo <rmattoo@stanford.edu<mailto:rmattoo@stanford.edu>> Cc: ChimeraX Users Help <chimerax-users@cgl.ucsf.edu<mailto:chimerax-users@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@cgl.ucsf.edu<mailto:chimerax-users@cgl.ucsf.edu>> wrote:
Hi, Is there a way to name the AlphaFold run job or the output file in ChimeraX?
Best Rayees _______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu<mailto:ChimeraX-users@cgl.ucsf.edu> Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
_______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu<mailto:ChimeraX-users@cgl.ucsf.edu> Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
participants (3)
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Elaine Meng -
Rayees Mattoo -
Tom Goddard