Hello ChimeraX Team, Can you add option to snapshot command like transparentBackground and height to allow more customization of this convenient tool? Thank you, Matt Matt J. Jaremko, Ph.D. (He|Him) Senior Scientist | Protein & Structural Chemistry Merck Research Labs | 126 E Lincoln Ave | 80B 1012 | Rahway, NJ 07065 Cell: 808.741.6277 | Email: matt.jaremko@merck.com<mailto:matt.jaremko@merck.com> This e-mail message, together with any attachments, contains information of Merck & Co., Inc. (126 East Lincoln Ave., P.O. Box 2000, Rahway, NJ USA 07065) and/or its affiliates, that may be confidential, proprietary copyrighted and/or legally privileged. (Direct contact information for affiliates is available at - Contact us - MSD<https://www.msd.com/contact-us/>.) It is intended solely for the use of the individual or entity named on this message. If you are not the intended recipient, and have received this message in error, please notify us immediately by reply e-mail and then delete it from your system.
Hi Matt, I guess you mean you want the Snapshot toolbar icon to do something different. Currently it uses the current ChimeraX window size for saving an image, and it does not make the background transparent. In general toolbar icon behavior is not customizable. The place that the Snapshot button saves its files is customizable using the snapshot command. I am not keen on adding other rarely useful customizations to how the Snapshot button works. You could make a command alias that saves images the way you want alias snap save ~/Desktop/image.png transparentBackground true height 1000 If you wanted that to always be available when you start ChimeraX you could put it in Settings / Startup / "Execute these commands at startup" and Save those settings. If you wanted a button to do custom things like this you could use the ChimeraX buttonpanel command to create a user interface panel with custom buttons that run whatever command you want, and those can appear every time you start. https://www.cgl.ucsf.edu/chimerax/docs/user/commands/buttonpanel.html You could perhaps replace the "sx" keyboard shortcut with Python code to change the behavior. Or you could write some Python code to add your own custom toolbar button. Tom
On Apr 25, 2024, at 6:57 AM, Jaremko, Matt Joseph via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hello ChimeraX Team,
Can you add option to snapshot command like transparentBackground and height to allow more customization of this convenient tool?
Thank you, Matt
Matt J. Jaremko, Ph.D. (He|Him) Senior Scientist | Protein & Structural Chemistry Merck Research Labs | 126 E Lincoln Ave | 80B 1012 | Rahway, NJ 07065 Cell: 808.741.6277 | Email: matt.jaremko@merck.com <mailto:matt.jaremko@merck.com>
This e-mail message, together with any attachments, contains information of Merck & Co., Inc. (126 East Lincoln Ave., P.O. Box 2000, Rahway, NJ USA 07065) and/or its affiliates, that may be confidential, proprietary copyrighted and/or legally privileged. (Direct contact information for affiliates is available at - Contact us - MSD <https://www.msd.com/contact-us/>.) It is intended solely for the use of the individual or entity named on this message. If you are not the intended recipient, and have received this message in error, please notify us immediately by reply e-mail and then delete it from your system.
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Wow, thanks for all the customizable options here Tom! I like the buttonpanel feature, I wasn’t aware of that. I like the snapshot feature because it doesn’t overwrite previous images and I can specify the location to save with directory option. So this alias you’ve created will overwrite the image every time: alias snap save ~/Desktop/image.png transparentBackground true height 1000 Is there any other way to use the sequential numbering for output files without using snapshot? The python method also sounds interesting. Do you have some template I can use to get started with this approach? Thank you! Matt From: Tom Goddard <goddard@sonic.net> Date: Thursday, April 25, 2024 at 8:01 PM To: Jaremko, Matt Joseph <matt.jaremko@merck.com> Cc: chimerax-users@cgl.ucsf.edu <chimerax-users@cgl.ucsf.edu> Subject: Re: [chimerax-users] Add options to snapshot command You don't often get email from goddard@sonic.net. Learn why this is important<https://aka.ms/LearnAboutSenderIdentification> EXTERNAL EMAIL– Use caution with any links or file attachments. Hi Matt, I guess you mean you want the Snapshot toolbar icon to do something different. Currently it uses the current ChimeraX window size for saving an image, and it does not make the background transparent. In general toolbar icon behavior is not customizable. The place that the Snapshot button saves its files is customizable using the snapshot command. I am not keen on adding other rarely useful customizations to how the Snapshot button works. You could make a command alias that saves images the way you want alias snap save ~/Desktop/image.png transparentBackground true height 1000 If you wanted that to always be available when you start ChimeraX you could put it in Settings / Startup / "Execute these commands at startup" and Save those settings. If you wanted a button to do custom things like this you could use the ChimeraX buttonpanel command to create a user interface panel with custom buttons that run whatever command you want, and those can appear every time you start. https://www.cgl.ucsf.edu/chimerax/docs/user/commands/buttonpanel.html You could perhaps replace the "sx" keyboard shortcut with Python code to change the behavior. Or you could write some Python code to add your own custom toolbar button. Tom On Apr 25, 2024, at 6:57 AM, Jaremko, Matt Joseph via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote: Hello ChimeraX Team, Can you add option to snapshot command like transparentBackground and height to allow more customization of this convenient tool? Thank you, Matt Matt J. Jaremko, Ph.D. (He|Him) Senior Scientist | Protein & Structural Chemistry Merck Research Labs | 126 E Lincoln Ave | 80B 1012 | Rahway, NJ 07065 Cell: 808.741.6277 | Email: matt.jaremko@merck.com<mailto:matt.jaremko@merck.com> This e-mail message, together with any attachments, contains information of Merck & Co., Inc. (126 East Lincoln Ave., P.O. Box 2000, Rahway, NJ USA 07065) and/or its affiliates, that may be confidential, proprietary copyrighted and/or legally privileged. (Direct contact information for affiliates is available at - Contact us - MSD<https://www.msd.com/contact-us/>.) It is intended solely for the use of the individual or entity named on this message. If you are not the intended recipient, and have received this message in error, please notify us immediately by reply e-mail and then delete it from your system. _______________________________________________ ChimeraX-users mailing list -- chimerax-users@cgl.ucsf.edu<mailto:chimerax-users@cgl.ucsf.edu> To unsubscribe send an email to chimerax-users-leave@cgl.ucsf.edu<mailto:chimerax-users-leave@cgl.ucsf.edu> Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/ This e-mail message, together with any attachments, contains information of Merck & Co., Inc. (126 East Lincoln Ave., P.O. Box 2000, Rahway, NJ USA 07065) and/or its affiliates, that may be confidential, proprietary copyrighted and/or legally privileged. (Direct contact information for affiliates is available at - Contact us - MSD<https://www.msd.com/contact-us/>.) It is intended solely for the use of the individual or entity named on this message. If you are not the intended recipient, and have received this message in error, please notify us immediately by reply e-mail and then delete it from your system.
Hi Matt, Aliases can be defined to take arguments ($1,$2) so you could have an alias with your options included but that you would still have to give the output filename with. See <https://rbvi.ucsf.edu/chimerax/docs/user/commands/alias.html> alias snap save ~/Desktop/$1.png transparentBackground true height 1000 and then to use it, snap image1 snap image2 Another idea if you need a constant single command (e.g. for buttonpanel) is that you could make it raise the file browser to specify output, e.g. alias snapb save browse transparentBackground true height 1000 ...then you could just use snapb ... but then you would have to specify the output name in the browser window. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Resource for Biocomputing, Visualization, and Informatics Department of Pharmaceutical Chemistry University of California, San Francisco
On Apr 26, 2024, at 5:35 AM, Jaremko, Matt Joseph via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Wow, thanks for all the customizable options here Tom!
I like the buttonpanel feature, I wasn’t aware of that.
I like the snapshot feature because it doesn’t overwrite previous images and I can specify the location to save with directory option. So this alias you’ve created will overwrite the image every time:
alias snap save ~/Desktop/image.png transparentBackground true height 1000
Is there any other way to use the sequential numbering for output files without using snapshot?
The python method also sounds interesting. Do you have some template I can use to get started with this approach?
Thank you! Matt
From: Tom Goddard <goddard@sonic.net> Date: Thursday, April 25, 2024 at 8:01 PM To: Jaremko, Matt Joseph <matt.jaremko@merck.com> Cc: chimerax-users@cgl.ucsf.edu <chimerax-users@cgl.ucsf.edu> Subject: Re: [chimerax-users] Add options to snapshot command
You don't often get email from goddard@sonic.net. Learn why this is important EXTERNAL EMAIL– Use caution with any links or file attachments. Hi Matt,
I guess you mean you want the Snapshot toolbar icon to do something different. Currently it uses the current ChimeraX window size for saving an image, and it does not make the background transparent. In general toolbar icon behavior is not customizable. The place that the Snapshot button saves its files is customizable using the snapshot command. I am not keen on adding other rarely useful customizations to how the Snapshot button works. You could make a command alias that saves images the way you want
alias snap save ~/Desktop/image.png transparentBackground true height 1000
If you wanted that to always be available when you start ChimeraX you could put it in Settings / Startup / "Execute these commands at startup" and Save those settings. If you wanted a button to do custom things like this you could use the ChimeraX buttonpanel command to create a user interface panel with custom buttons that run whatever command you want, and those can appear every time you start.
https://www.cgl.ucsf.edu/chimerax/docs/user/commands/buttonpanel.html
You could perhaps replace the "sx" keyboard shortcut with Python code to change the behavior. Or you could write some Python code to add your own custom toolbar button.
Tom
On Apr 25, 2024, at 6:57 AM, Jaremko, Matt Joseph via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hello ChimeraX Team,
Can you add option to snapshot command like transparentBackground and height to allow more customization of this convenient tool?
Thank you, Matt
Matt J. Jaremko, Ph.D. (He|Him) Senior Scientist | Protein & Structural Chemistry Merck Research Labs | 126 E Lincoln Ave | 80B 1012 | Rahway, NJ 07065 Cell: 808.741.6277 | Email: matt.jaremko@merck.com
This e-mail message, together with any attachments, contains information of Merck & Co., Inc. (126 East Lincoln Ave., P.O. Box 2000, Rahway, NJ USA 07065) and/or its affiliates, that may be confidential, proprietary copyrighted and/or legally privileged. (Direct contact information for affiliates is available at - Contact us - MSD.) It is intended solely for the use of the individual or entity named on this message. If you are not the intended recipient, and have received this message in error, please notify us immediately by reply e-mail and then delete it from your system.
_______________________________________________ ChimeraX-users mailing list -- chimerax-users@cgl.ucsf.edu To unsubscribe send an email to chimerax-users-leave@cgl.ucsf.edu Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/
This e-mail message, together with any attachments, contains information of Merck & Co., Inc. (126 East Lincoln Ave., P.O. Box 2000, Rahway, NJ USA 07065) and/or its affiliates, that may be confidential, proprietary copyrighted and/or legally privileged. (Direct contact information for affiliates is available at - Contact us - MSD.) It is intended solely for the use of the individual or entity named on this message. If you are not the intended recipient, and have received this message in error, please notify us immediately by reply e-mail and then delete it from your system.
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participants (3)
-
Elaine Meng -
Jaremko, Matt Joseph -
Tom Goddard