[Chimera-users] Using ChimeraX in no-gui mode

Elaine Meng meng at cgl.ucsf.edu
Tue Apr 16 09:26:53 PDT 2019

In Chimera start Color Key (menu: Tools… Utilities… Color Key) and change number of colors to 5 and make them the same as what is in the Rainbow tool (Menu: Tools.. Depiction… Rainbow).  E.g. you can click on the color square in Rainbow and  drag over to release on the color square in Color Key to make them the same.  

I see that currently there is a minor bug in the Rainbow tool that the green is the darker CSS “green" and not standard bright green (CSS name “lime green”).  So you should change the green square to lime green, for example by clicking its border to open the Color Editor and entering “lime green” for the Color name.  I will make a bug report for this issue.


> On Apr 16, 2019, at 1:27 AM, James Starlight <jmsstarlight at gmail.com> wrote:
> Thank you so much Elaine!
> I have some problems both with --nogui and --offscreen options with
> the python error message. I will now copy it to the ChimeraX mailing
> list.
> Just one question: assuming that in ChimeraX I color the structure
> according to B-factors using
> color byattribute bfactor palette rainbow range 2,100
> what gradient colouring I should use in Chimera to obtain the "bar
> plot" with the
> rangecolor bfactor
> ?
> Thank youin advance!
> пн, 15 апр. 2019 г. в 23:31, Elaine Meng <meng at cgl.ucsf.edu>:
>> Hi James,
>> ChimeraX does not have the ability to make a color key yet. if you are using the “composite” approach you mentioned before,
>> <http://plato.cgl.ucsf.edu/pipermail/chimera-users/2019-March/015590.html>
>> ...you could make the color key image in Chimera and composite it with the molecule images from ChimeraX.
>> Elaine
>>> On Apr 15, 2019, at 9:51 AM, James Starlight <jmsstarlight at gmail.com> wrote:
>>> P.S. just forgot also to ask - how it would be possible to place bar
>>> diagram to range b-factors colouring gradient in the manner of the
>>> "key" option in the previous version of chimera?
>>> пн
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