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

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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

<6wa1.png>_______________________________________________
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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/