Dear Chimera developers, I have a quick question about coloring. I have a filament map with multiple monomers, how can I color each monomer density with different color? I have a built model, should I do it based on the atom number or should I segment the filament? Best, Yangqi Sent from Mail for Windows 10
Hi Yangqi, The choice is really yours, but my guess would be that since you already have an atomic model, you can just color the atomic model atoms how you like, select all those atoms, and then use Color Zone (or “scolor” command “zone” option) to color the nearby map surface to match the atoms. Details: <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/colorzone/colorzone.html> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/scolor.html#zone> You can also split the map by those colored zones, as mentioned in the Color Zone page. (If you used Segment Map then it might not divide up the map exactly the same as your monomers, and it would pick its own coloring, although you could then select and recolor each segment surface.) Best, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco On Nov 20, 2018, at 9:56 PM, BuddySphinx <yangqi.gu@yale.edu> wrote:
Dear Chimera developers, I have a quick question about coloring. I have a filament map with multiple monomers, how can I color each monomer density with different color? I have a built model, should I do it based on the atom number or should I segment the filament? Best, Yangqi
Hi Elaine, I tried what you suggested and using the command scolor #0 zone: *.c, now my c chain density becomes gradient color. Is there anyway showing a single color, let's say I want it red without gradient. Also, how do I change multiple chains color at the same time? Best, Yangqi On Wed, Nov 21, 2018 at 12:17 PM Elaine Meng <meng@cgl.ucsf.edu> wrote:
Hi Yangqi, The choice is really yours, but my guess would be that since you already have an atomic model, you can just color the atomic model atoms how you like, select all those atoms, and then use Color Zone (or “scolor” command “zone” option) to color the nearby map surface to match the atoms. Details:
< http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/colorzone/colorzon...
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/scolor.html#zone>
You can also split the map by those colored zones, as mentioned in the Color Zone page.
(If you used Segment Map then it might not divide up the map exactly the same as your monomers, and it would pick its own coloring, although you could then select and recolor each segment surface.) Best, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Nov 20, 2018, at 9:56 PM, BuddySphinx <yangqi.gu@yale.edu> wrote:
Dear Chimera developers, I have a quick question about coloring. I have a filament map with
multiple monomers, how can I color each monomer density with different color? I have a built model, should I do it based on the atom number or should I segment the filament?
Best, Yangqi
-- Yangqi Gu Graduate Student Malvankar Lab Yale University, West Campus
Hi Yangqi, “scolor” with “zone” option does not use gradients, it just colors the surface to match the specified atoms. Each patch of surface near some atom becomes the same color as the atom. So first color the atoms the way you want. Your command looks wrong, so maybe it tried to use gradient coloring instead. Try something like scolor #0 zone :.C range 5 where 5 is the distance cutoff, use what you want …or you can specify more than one chain, e.g. scolor #0 zone :.C-H range 8 scolor #0 zone :.C:.F range 8 Best, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Dec 12, 2018, at 2:04 PM, Yangqi Gu <yangqi.gu@yale.edu> wrote:
Hi Elaine, I tried what you suggested and using the command scolor #0 zone: *.c, now my c chain density becomes gradient color. Is there anyway showing a single color, let's say I want it red without gradient. Also, how do I change multiple chains color at the same time? Best, Yangqi
On Wed, Nov 21, 2018 at 12:17 PM Elaine Meng <meng@cgl.ucsf.edu> wrote: Hi Yangqi, The choice is really yours, but my guess would be that since you already have an atomic model, you can just color the atomic model atoms how you like, select all those atoms, and then use Color Zone (or “scolor” command “zone” option) to color the nearby map surface to match the atoms. Details:
<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/colorzone/colorzone.html> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/scolor.html#zone>
You can also split the map by those colored zones, as mentioned in the Color Zone page.
(If you used Segment Map then it might not divide up the map exactly the same as your monomers, and it would pick its own coloring, although you could then select and recolor each segment surface.) Best, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Nov 20, 2018, at 9:56 PM, BuddySphinx <yangqi.gu@yale.edu> wrote:
Dear Chimera developers, I have a quick question about coloring. I have a filament map with multiple monomers, how can I color each monomer density with different color? I have a built model, should I do it based on the atom number or should I segment the filament? Best, Yangqi
--
Yangqi Gu Graduate Student Malvankar Lab Yale University, West Campus _______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
Hi Elaine, I tried what you suggested. And it looks like this, still gradient. I used the command scolor #0 zone :.C range 5 Best, Yangqi Sent from Mail for Windows 10 From: Elaine Meng Sent: Wednesday, December 12, 2018 5:26 PM To: Yangqi Gu Cc: chimera-users Subject: Re: [Chimera-users] Color subunits for map density Hi Yangqi, “scolor” with “zone” option does not use gradients, it just colors the surface to match the specified atoms. Each patch of surface near some atom becomes the same color as the atom. So first color the atoms the way you want. Your command looks wrong, so maybe it tried to use gradient coloring instead. Try something like scolor #0 zone :.C range 5 where 5 is the distance cutoff, use what you want …or you can specify more than one chain, e.g. scolor #0 zone :.C-H range 8 scolor #0 zone :.C:.F range 8 Best, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Dec 12, 2018, at 2:04 PM, Yangqi Gu <yangqi.gu@yale.edu> wrote:
Hi Elaine, I tried what you suggested and using the command scolor #0 zone: *.c, now my c chain density becomes gradient color. Is there anyway showing a single color, let's say I want it red without gradient. Also, how do I change multiple chains color at the same time? Best, Yangqi
On Wed, Nov 21, 2018 at 12:17 PM Elaine Meng <meng@cgl.ucsf.edu> wrote: Hi Yangqi, The choice is really yours, but my guess would be that since you already have an atomic model, you can just color the atomic model atoms how you like, select all those atoms, and then use Color Zone (or “scolor” command “zone” option) to color the nearby map surface to match the atoms. Details:
<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/colorzone/colorzone.html> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/scolor.html#zone>
You can also split the map by those colored zones, as mentioned in the Color Zone page.
(If you used Segment Map then it might not divide up the map exactly the same as your monomers, and it would pick its own coloring, although you could then select and recolor each segment surface.) Best, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Nov 20, 2018, at 9:56 PM, BuddySphinx <yangqi.gu@yale.edu> wrote:
Dear Chimera developers, I have a quick question about coloring. I have a filament map with multiple monomers, how can I color each monomer density with different color? I have a built model, should I do it based on the atom number or should I segment the filament? Best, Yangqi
--
Yangqi Gu Graduate Student Malvankar Lab Yale University, West Campus _______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
Hi Yangqi, That is not a gradient. That is red patches near red-colored atoms (presumably oxygens) and blue patches near blue-colored atoms (presumably nitrogens). Maybe you don’t know what colors your atoms are if you are only displaying ribbons. Hide the surface for now, hide ribbons, show atoms, and color the atoms how you want first, e.g.: volume #0 hide ~ribbon display color sky blue :.C volume #0 show scolor #0 zone :.C range 5 (or whatever distance cutoff you want) Best, Elaine
On Dec 12, 2018, at 2:30 PM, BuddySphinx <yangqi.gu@yale.edu> wrote:
Hi Elaine, I tried what you suggested. And it looks like this, still gradient. <EBB3F6C0EAB24B58B48C5F7760E97009.png> I used the command scolor #0 zone :.C range 5 Best, Yangqi
Sent from Mail for Windows 10
From: Elaine Meng Sent: Wednesday, December 12, 2018 5:26 PM To: Yangqi Gu Cc: chimera-users Subject: Re: [Chimera-users] Color subunits for map density
Hi Yangqi, “scolor” with “zone” option does not use gradients, it just colors the surface to match the specified atoms. Each patch of surface near some atom becomes the same color as the atom. So first color the atoms the way you want.
Your command looks wrong, so maybe it tried to use gradient coloring instead. Try something like
scolor #0 zone :.C range 5
where 5 is the distance cutoff, use what you want …or you can specify more than one chain, e.g.
scolor #0 zone :.C-H range 8 scolor #0 zone :.C:.F range 8
Best, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Dec 12, 2018, at 2:04 PM, Yangqi Gu <yangqi.gu@yale.edu> wrote:
Hi Elaine, I tried what you suggested and using the command scolor #0 zone: *.c, now my c chain density becomes gradient color. Is there anyway showing a single color, let's say I want it red without gradient. Also, how do I change multiple chains color at the same time? Best, Yangqi
On Wed, Nov 21, 2018 at 12:17 PM Elaine Meng <meng@cgl.ucsf.edu> wrote: Hi Yangqi, The choice is really yours, but my guess would be that since you already have an atomic model, you can just color the atomic model atoms how you like, select all those atoms, and then use Color Zone (or “scolor” command “zone” option) to color the nearby map surface to match the atoms. Details:
<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/colorzone/colorzone.html> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/scolor.html#zone>
You can also split the map by those colored zones, as mentioned in the Color Zone page.
(If you used Segment Map then it might not divide up the map exactly the same as your monomers, and it would pick its own coloring, although you could then select and recolor each segment surface.) Best, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Nov 20, 2018, at 9:56 PM, BuddySphinx <yangqi.gu@yale.edu> wrote:
Dear Chimera developers, I have a quick question about coloring. I have a filament map with multiple monomers, how can I color each monomer density with different color? I have a built model, should I do it based on the atom number or should I segment the filament? Best, Yangqi
--
Yangqi Gu Graduate Student Malvankar Lab Yale University, West Campus _______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
<EBB3F6C0EAB24B58B48C5F7760E97009.png>_______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
I see. Thank you very much! Best, Yangqi Sent from Mail for Windows 10 From: Elaine Meng Sent: Wednesday, December 12, 2018 5:41 PM To: BuddySphinx Cc: chimera-users Subject: Re: [Chimera-users] Color subunits for map density Hi Yangqi, That is not a gradient. That is red patches near red-colored atoms (presumably oxygens) and blue patches near blue-colored atoms (presumably nitrogens). Maybe you don’t know what colors your atoms are if you are only displaying ribbons. Hide the surface for now, hide ribbons, show atoms, and color the atoms how you want first, e.g.: volume #0 hide ~ribbon display color sky blue :.C volume #0 show scolor #0 zone :.C range 5 (or whatever distance cutoff you want) Best, Elaine
On Dec 12, 2018, at 2:30 PM, BuddySphinx <yangqi.gu@yale.edu> wrote:
Hi Elaine, I tried what you suggested. And it looks like this, still gradient. <EBB3F6C0EAB24B58B48C5F7760E97009.png> I used the command scolor #0 zone :.C range 5 Best, Yangqi
Sent from Mail for Windows 10
From: Elaine Meng Sent: Wednesday, December 12, 2018 5:26 PM To: Yangqi Gu Cc: chimera-users Subject: Re: [Chimera-users] Color subunits for map density
Hi Yangqi, “scolor” with “zone” option does not use gradients, it just colors the surface to match the specified atoms. Each patch of surface near some atom becomes the same color as the atom. So first color the atoms the way you want.
Your command looks wrong, so maybe it tried to use gradient coloring instead. Try something like
scolor #0 zone :.C range 5
where 5 is the distance cutoff, use what you want …or you can specify more than one chain, e.g.
scolor #0 zone :.C-H range 8 scolor #0 zone :.C:.F range 8
Best, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Dec 12, 2018, at 2:04 PM, Yangqi Gu <yangqi.gu@yale.edu> wrote:
Hi Elaine, I tried what you suggested and using the command scolor #0 zone: *.c, now my c chain density becomes gradient color. Is there anyway showing a single color, let's say I want it red without gradient. Also, how do I change multiple chains color at the same time? Best, Yangqi
On Wed, Nov 21, 2018 at 12:17 PM Elaine Meng <meng@cgl.ucsf.edu> wrote: Hi Yangqi, The choice is really yours, but my guess would be that since you already have an atomic model, you can just color the atomic model atoms how you like, select all those atoms, and then use Color Zone (or “scolor” command “zone” option) to color the nearby map surface to match the atoms. Details:
<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/colorzone/colorzone.html> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/scolor.html#zone>
You can also split the map by those colored zones, as mentioned in the Color Zone page.
(If you used Segment Map then it might not divide up the map exactly the same as your monomers, and it would pick its own coloring, although you could then select and recolor each segment surface.) Best, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Nov 20, 2018, at 9:56 PM, BuddySphinx <yangqi.gu@yale.edu> wrote:
Dear Chimera developers, I have a quick question about coloring. I have a filament map with multiple monomers, how can I color each monomer density with different color? I have a built model, should I do it based on the atom number or should I segment the filament? Best, Yangqi
--
Yangqi Gu Graduate Student Malvankar Lab Yale University, West Campus _______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
<EBB3F6C0EAB24B58B48C5F7760E97009.png>_______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
participants (3)
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BuddySphinx -
Elaine Meng -
Yangqi Gu