Hi, I'm having issues with coloring a surface by volume. When I compare the two volumes I don't get the larger volume completely colored and even when I set 'Color outside volume' to match the same color as the 0 value which in this case is the blue it still renders grey. Can you help me with which step I'm messing up? Thanks. Bryan Hansen Computational Biologist / Electron Microscopist NIH/NIAID/RTB/RML/EMU Rocky Mountain Laboratories 903 S. 4th St Hamilton, MT 59840 406.363.9202 *********************************************************** The information in this e-mail and any of its attachments is confidential and may contain sensitive information.It should not be used by anyone who is not the original intended recipient. If you have received this e-mail in error, please inform the sender and delete it from your mailbox or any other storage devices. National Institute of Allergy and Infectious Diseases shall not accept liability for any statements made that are sender's own and not expressly made on behalf of the NIAID by one of its representatives. ***********************************************************
Hi Bryan, Thanks for reporting the problem. I see the "Color outside volume" option of the Surface Color panel does nothing. Apparently I forgot to implement it when I ported it from Chimera to ChimeraX. I have now implemented it in the ChimeraX daily builds dated January 24, 2025 and newer. I also added an "outsideColor" option to the "color sample", "color gradient", and "color electrostatic" commands. The default outsideColor is gray (#808080). Tom
On Jan 23, 2025, at 2:55 PM, Hansen, Bryan (NIH/NIAID) [E] via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hi,
I’m having issues with coloring a surface by volume. When I compare the two volumes I don’t get the larger volume completely colored and even when I set ‘Color outside volume’ to match the same color as the 0 value which in this case is the blue it still renders grey. Can you help me with which step I’m messing up? Thanks.
Bryan Hansen Computational Biologist / Electron Microscopist NIH/NIAID/RTB/RML/EMU Rocky Mountain Laboratories 903 S. 4th St Hamilton, MT 59840 406.363.9202
*********************************************************** The information in this e-mail and any of its attachments is confidential and may contain sensitive information.It should not be used by anyone who is not the original intended recipient. If you have received this e-mail in error, please inform the sender and delete it from your mailbox or any other storage devices. National Institute of Allergy and Infectious Diseases shall not accept liability for any statements made that are sender's own and not expressly made on behalf of the NIAID by one of its representatives. ***********************************************************
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Great! Thanks so much. I’ll grab that daily build and try again. Bryan *********************************************************** The information in this e-mail and any of its attachments is confidential and may contain sensitive information.It should not be used by anyone who is not the original intended recipient. If you have received this e-mail in error, please inform the sender and delete it from your mailbox or any other storage devices. National Institute of Allergy and Infectious Diseases shall not accept liability for any statements made that are sender's own and not expressly made on behalf of the NIAID by one of its representatives. *********************************************************** From: Tom Goddard <goddard@sonic.net> Sent: Thursday, January 23, 2025 5:24 PM To: Hansen, Bryan (NIH/NIAID) [E] <hansenbry@niaid.nih.gov> Cc: chimerax-users@cgl.ucsf.edu Subject: [EXTERNAL] Re: [chimerax-users] Surface Color Hi Bryan, Thanks for reporting the problem. I see the "Color outside volume" option of the Surface Color panel does nothing. Apparently I forgot to implement it when I ported it from Chimera to ChimeraX. I have now implemented it in the ChimeraX daily builds dated January 24, 2025 and newer. I also added an "outsideColor" option to the "color sample", "color gradient", and "color electrostatic" commands. The default outsideColor is gray (#808080). Tom On Jan 23, 2025, at 2:55 PM, Hansen, Bryan (NIH/NIAID) [E] via ChimeraX-users <chimerax-users@cgl.ucsf.edu<mailto:chimerax-users@cgl.ucsf.edu>> wrote: Hi, I’m having issues with coloring a surface by volume. When I compare the two volumes I don’t get the larger volume completely colored and even when I set ‘Color outside volume’ to match the same color as the 0 value which in this case is the blue it still renders grey. Can you help me with which step I’m messing up? Thanks. Bryan Hansen Computational Biologist / Electron Microscopist NIH/NIAID/RTB/RML/EMU Rocky Mountain Laboratories 903 S. 4th St Hamilton, MT 59840 406.363.9202 *********************************************************** The information in this e-mail and any of its attachments is confidential and may contain sensitive information.It should not be used by anyone who is not the original intended recipient. If you have received this e-mail in error, please inform the sender and delete it from your mailbox or any other storage devices. National Institute of Allergy and Infectious Diseases shall not accept liability for any statements made that are sender's own and not expressly made on behalf of the NIAID by one of its representatives. *********************************************************** <image7.png>_______________________________________________ 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/ CAUTION: This email originated from outside of the organization. Do not click links or open attachments unless you recognize the sender and are confident the content is safe.
Hi Bryan, I forgot to push the outside color fix to Github yesterday so it didn't get into the Jan 24 builds. Sorry about that. It will be in the Jan 25 builds. Tom
On Jan 24, 2025, at 7:08 AM, Hansen, Bryan (NIH/NIAID) [E] via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Great! Thanks so much. I’ll grab that daily build and try again.
Bryan
*********************************************************** The information in this e-mail and any of its attachments is confidential and may contain sensitive information.It should not be used by anyone who is not the original intended recipient. If you have received this e-mail in error, please inform the sender and delete it from your mailbox or any other storage devices. National Institute of Allergy and Infectious Diseases shall not accept liability for any statements made that are sender's own and not expressly made on behalf of the NIAID by one of its representatives. ***********************************************************
From: Tom Goddard <goddard@sonic.net> Sent: Thursday, January 23, 2025 5:24 PM To: Hansen, Bryan (NIH/NIAID) [E] <hansenbry@niaid.nih.gov> Cc: chimerax-users@cgl.ucsf.edu Subject: [EXTERNAL] Re: [chimerax-users] Surface Color
Hi Bryan,
Thanks for reporting the problem. I see the "Color outside volume" option of the Surface Color panel does nothing. Apparently I forgot to implement it when I ported it from Chimera to ChimeraX. I have now implemented it in the ChimeraX daily builds dated January 24, 2025 and newer. I also added an "outsideColor" option to the "color sample", "color gradient", and "color electrostatic" commands. The default outsideColor is gray (#808080).
Tom
On Jan 23, 2025, at 2:55 PM, Hansen, Bryan (NIH/NIAID) [E] via ChimeraX-users <chimerax-users@cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu>> wrote:
Hi,
I’m having issues with coloring a surface by volume. When I compare the two volumes I don’t get the larger volume completely colored and even when I set ‘Color outside volume’ to match the same color as the 0 value which in this case is the blue it still renders grey. Can you help me with which step I’m messing up? Thanks.
Bryan Hansen Computational Biologist / Electron Microscopist NIH/NIAID/RTB/RML/EMU Rocky Mountain Laboratories 903 S. 4th St Hamilton, MT 59840 406.363.9202
*********************************************************** The information in this e-mail and any of its attachments is confidential and may contain sensitive information.It should not be used by anyone who is not the original intended recipient. If you have received this e-mail in error, please inform the sender and delete it from your mailbox or any other storage devices. National Institute of Allergy and Infectious Diseases shall not accept liability for any statements made that are sender's own and not expressly made on behalf of the NIAID by one of its representatives. ***********************************************************
<image7.png>_______________________________________________ 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/
CAUTION: This email originated from outside of the organization. Do not click links or open attachments unless you recognize the sender and are confident the content is safe.
_______________________________________________ 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/
participants (2)
-
Hansen, Bryan (NIH/NIAID) [E] -
Tom Goddard