Using an atomic model and map, when I colour a different zone, I "lose" the colour from the previous zone I coloured. Is this a bug? This is in Windows 11. Thanks in advance.
Hi Mark, This is intentional in that it will always recolor the whole surface according to the current settings. If you wanted multiple different colors at the same time you would color all the atoms accordingly, different sets in different colors, and then "color zone" the surface in one step to make the surface match. Especially if one adjusts the zone distance, you would want the regions that no longer meet the criteria to no longer be colored, so the whole surface needs to be re-evaluated... at least, that is how I understand it. I hope this makes sense, 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 Oct 7, 2024, at 9:18 AM, Mark Rosenberg via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Using an atomic model and map, when I colour a different zone, I "lose" the colour from the previous zone I coloured. Is this a bug? This is in Windows 11. Thanks in advance.
Hi Elaine Yes, that worked. I colored each set separately and then applied to the surface as you kindly suggested. Thank you. Mark ________________________________ From: Elaine Meng <meng@cgl.ucsf.edu> Sent: Monday, October 7, 2024 5:37 PM To: Mark Rosenberg <http://mark.rosenberg@manchester.ac.uk> Cc: chimerax-users@cgl.ucsf.edu <chimerax-users@cgl.ucsf.edu> Subject: Re: [chimerax-users] Color Zone Hi Mark, This is intentional in that it will always recolor the whole surface according to the current settings. If you wanted multiple different colors at the same time you would color all the atoms accordingly, different sets in different colors, and then "color zone" the surface in one step to make the surface match. Especially if one adjusts the zone distance, you would want the regions that no longer meet the criteria to no longer be colored, so the whole surface needs to be re-evaluated... at least, that is how I understand it. I hope this makes sense, 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 Oct 7, 2024, at 9:18 AM, Mark Rosenberg via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Using an atomic model and map, when I colour a different zone, I "lose" the colour from the previous zone I coloured. Is this a bug? This is in Windows 11. Thanks in advance.
Hi Mark, The color zone command can be used multiple times where it keeps the previous colors that are beyond the distance range specified with the most recent command. You use the color zone option "farColor keep" to do this. open 8of8 open 16850 from emdb color zone #2 near /A-F distance 10 color zone #2 near /K distance 10 far keep This is described in the color zone documentation https://www.cgl.ucsf.edu/chimerax/docs/user/commands/color.html#zone If you change the map contour level after coloring, only the coloring done by the most recent color zone command will be applied to the new surface. Tom 
On Oct 7, 2024, at 9:47 AM, Mark Rosenberg via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hi Elaine
Yes, that worked. I colored each set separately and then applied to the surface as you kindly suggested.
Thank you.
Mark From: Elaine Meng <meng@cgl.ucsf.edu> Sent: Monday, October 7, 2024 5:37 PM To: Mark Rosenberg <mark.rosenberg@manchester.ac.uk> Cc: chimerax-users@cgl.ucsf.edu <chimerax-users@cgl.ucsf.edu> Subject: Re: [chimerax-users] Color Zone
Hi Mark, This is intentional in that it will always recolor the whole surface according to the current settings. If you wanted multiple different colors at the same time you would color all the atoms accordingly, different sets in different colors, and then "color zone" the surface in one step to make the surface match. Especially if one adjusts the zone distance, you would want the regions that no longer meet the criteria to no longer be colored, so the whole surface needs to be re-evaluated... at least, that is how I understand it. I hope this makes sense, 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 Oct 7, 2024, at 9:18 AM, Mark Rosenberg via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Using an atomic model and map, when I colour a different zone, I "lose" the colour from the previous zone I coloured. Is this a bug? This is in Windows 11. Thanks in advance.
_______________________________________________ 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/
Hi Tom Thanks Tom. Very helpful. BW Mark ________________________________ From: Tom Goddard <goddard@sonic.net> Sent: Monday, October 7, 2024 8:02 PM To: Mark Rosenberg <http://mark.rosenberg@manchester.ac.uk> Cc: chimerax-users <chimerax-users@cgl.ucsf.edu> Subject: Re: [chimerax-users] Color Zone Hi Mark, The color zone command can be used multiple times where it keeps the previous colors that are beyond the distance range specified with the most recent command. You use the color zone option "farColor keep" to do this. open 8of8 open ZjQcmQRYFpfptBannerStart This Message Is From a New External Sender You have not previously corresponded with this sender. Please exercise caution when opening links or attachments included in this message. ZjQcmQRYFpfptBannerEnd Hi Mark, The color zone command can be used multiple times where it keeps the previous colors that are beyond the distance range specified with the most recent command. You use the color zone option "farColor keep" to do this. open 8of8 open 16850 from emdb color zone #2 near /A-F distance 10 color zone #2 near /K distance 10 far keep This is described in the color zone documentation https://www.cgl.ucsf.edu/chimerax/docs/user/commands/color.html#zone [cgl.ucsf.edu]<https://urldefense.com/v3/__https://www.cgl.ucsf.edu/chimerax/docs/user/comm...> If you change the map contour level after coloring, only the coloring done by the most recent color zone command will be applied to the new surface. Tom [8of8.png] On Oct 7, 2024, at 9:47 AM, Mark Rosenberg via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote: Hi Elaine Yes, that worked. I colored each set separately and then applied to the surface as you kindly suggested. Thank you. Mark ________________________________ From: Elaine Meng <meng@cgl.ucsf.edu> Sent: Monday, October 7, 2024 5:37 PM To: Mark Rosenberg <http://mark.rosenberg@manchester.ac.uk> Cc: chimerax-users@cgl.ucsf.edu <chimerax-users@cgl.ucsf.edu> Subject: Re: [chimerax-users] Color Zone Hi Mark, This is intentional in that it will always recolor the whole surface according to the current settings. If you wanted multiple different colors at the same time you would color all the atoms accordingly, different sets in different colors, and then "color zone" the surface in one step to make the surface match. Especially if one adjusts the zone distance, you would want the regions that no longer meet the criteria to no longer be colored, so the whole surface needs to be re-evaluated... at least, that is how I understand it. I hope this makes sense, 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 Oct 7, 2024, at 9:18 AM, Mark Rosenberg via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Using an atomic model and map, when I colour a different zone, I "lose" the colour from the previous zone I coloured. Is this a bug? This is in Windows 11. Thanks in advance.
_______________________________________________ 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/ [mail.cgl.ucsf.edu]<https://urldefense.com/v3/__https://mail.cgl.ucsf.edu/mailman/archives/list/...>
participants (3)
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Elaine Meng -
Mark Rosenberg -
Tom Goddard