Use different distances for several marker sets
Dear community, I'm wondering if there is any way for me to color a volume density with different distances from several marker sets. Thank you for your help! Best, Shiqing
Hi Shiqing, Although you can use "color zone" with more than one marker set at a time, you cannot use different distances. It will always use the same zone distance for all of the specified atoms/markers. <https://rbvi.ucsf.edu/chimerax/docs/user/tools/colorzone.html> <https://rbvi.ucsf.edu/chimerax/docs/user/commands/color.html#zone> I tried opening the same map twice and coloring one copy by zone from one set of atoms/markers, and coloring the other copy by zone from the other set of atoms/markers with a different distance, and then making one of the map surfaces partly transparent. It did show both colorings somewhat, but not very well, as you can see in the attached image. Best, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Aug 4, 2022, at 12:11 PM, SHIQING LIAO via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Dear community,
I'm wondering if there is any way for me to color a volume density with different distances from several marker sets. Thank you for your help!
Best, Shiqing
Hi Shiqing, You can color from different marker sets using the color zone ocmmand with the "farColor keep" option. For example, coloring surface of map #1 using marker sets #2 and #3 color zone #1 near #2 distance 30 color zone #1 near #3 distance 50 farColor keep The second command colors near markers #3 with a different distance but keeps the previous colors that are beyond distance 50 from markers #3. So for parts of the surface that are within the distance specified of the first command and also within the distance in the second command will get the colors from the second command. Tom
On Aug 4, 2022, at 12:54 PM, Elaine Meng via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hi Shiqing, Although you can use "color zone" with more than one marker set at a time, you cannot use different distances. It will always use the same zone distance for all of the specified atoms/markers.
<https://rbvi.ucsf.edu/chimerax/docs/user/tools/colorzone.html <https://rbvi.ucsf.edu/chimerax/docs/user/tools/colorzone.html>> <https://rbvi.ucsf.edu/chimerax/docs/user/commands/color.html#zone <https://rbvi.ucsf.edu/chimerax/docs/user/commands/color.html#zone>>
I tried opening the same map twice and coloring one copy by zone from one set of atoms/markers, and coloring the other copy by zone from the other set of atoms/markers with a different distance, and then making one of the map surfaces partly transparent. It did show both colorings somewhat, but not very well, as you can see in the attached image. Best, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
<2zones.png>
On Aug 4, 2022, at 12:11 PM, SHIQING LIAO via ChimeraX-users <chimerax-users@cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu>> wrote:
Dear community,
I'm wondering if there is any way for me to color a volume density with different distances from several marker sets. Thank you for your help!
Best, Shiqing
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participants (3)
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Elaine Meng -
SHIQING LIAO -
Tom Goddard