Hi Tom, fantastic, it is exactly what I needed. FYI, I browsed yesterday the doc page you sent but couldn't figure it out. Thank you very much. Vincent Le 11/12/2023 à 22:51, Tom Goddard a écrit :
Hi Vincent,
I see. You want to color the A chains in 20 structures using one sequence of colors, and the B chains in the same 20 structures another sequence of colors. The rainbow command won't do that. If you tell it to color each structure a different color it always colors the entire structure. If you tell it to color each chain a different color it varies the chain colors within a single structure, not across multiple structures.
To do what you want you'd have to open two copies of your 20 structures #1.1-20 and #2.1-20 and keep only chain A in #1 (delete #1/B) and only chain B in #2 (delete #1/A) and then use rainbow on #1 and #2 separately
rainbow #1 structures palette blue:cyan rainbow #2 structures palette red_yellow
Example (image below)
open 6wa1 delete #1/B rainbow #1 structures palette blue:cyan
open 6wa1 delete #2/A rainbow #2 structures palette red:yellow
Here's the rainbow documentation
https://www.cgl.ucsf.edu/chimerax/docs/user/commands/color.html#sequential
Tom
double_rainbow.png
On Dec 11, 2023, at 1:09 PM, vincent Chaptal via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hi Tom,
I'm using ChimeraX1.5. I was waiting for 1.7 to upgrade, am I too old already?
I'm attaching a picture of 6aw1, where I want to color the 2 chains with a different palette.
rainbow #1 structures palette blue:cyan -> chain A on the right is colored 1.1 blue to 1.20 cyan, with the whole chain of 1 color. It is visible on the alpha-helix where all colors of the palette are visible. rainbow #1.1-20/B palette red:yellow -> chain B gets colored from N-ter red to C-ter yellow. The alpha helix is not colored as if using the first command.
Basically, I would like to use "rainbow #1 structures palette" twice with 2 different chain IDs.
Thanks Vincent
Le 11/12/2023 à 20:05, Tom Goddard a écrit :
Hi Vincent,
Your steps work correctly for me coloring just the chain you specified. Maybe you are using a very old ChimeraX. If you are using current ChimeraX you could use Help / Report a Bug... and maybe attach your structure since for my test case PDB 6WA1 it works correctly.
Tom
On Dec 11, 2023, at 1:03 AM, vincent Chaptal via ChimeraX-users<chimerax-users@cgl.ucsf.edu>wrote:
Hi,
on a pdb ensemble, when I use: rainbow #1 structures palette blue:cyan
it colors the whole chain 1.1 blue and varies the color to cyan all the way to chain 1.20 (which is what I want).
However, if I want to color a specific chain differently using: rainbow #1.1-10/O palette red:yellow
it colors the rainbow from N-ter to C-ter for all the chains.
How can I apply the first type of coloring (structures) to a specific chain?
Thank you. Vincent
-- Vincent Chaptal, PhD Director of GdR APPICOM Drug Resistance and Membrane Proteins Lab
MMSB -UMR5086 7 passage du Vercors 69007 LYON FRANCE +33 4 37 65 29 01 http://www.appicom.cnrs.fr http://mmsb.cnrs.fr/en/
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-- Vincent Chaptal, PhD Director of GdR APPICOM Drug Resistance and Membrane Proteins Lab
MMSB -UMR5086 7 passage du Vercors 69007 LYON FRANCE +33 4 37 65 29 01 http://www.appicom.cnrs.fr http://mmsb.cnrs.fr/en/
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-- Vincent Chaptal, PhD Director of GdR APPICOM Drug Resistance and Membrane Proteins Lab MMSB -UMR5086 7 passage du Vercors 69007 LYON FRANCE +33 4 37 65 29 01 http://www.appicom.cnrs.fr http://mmsb.cnrs.fr/en/
