[PyMOL] color ramp for colorbyrmsd

[Laura F. <lau...@gm...>]

Hi Pymolers


I would like some help regarding a spectrum bar.


I have generated an homology model of a structure and I wanted to compare
to the template, to achieve this I have used the colorbyrmsd script

https://pymolwiki.org/index.php/ColorByRMSD


It works great but I would like to generate a color bar with the colouring
scale used in the colorbyrmsd script. I am familiar with the spectrumbar.py
but I would like also to add the number scale which is not shown in the
colorbyrmsd script according to Pymolwiki

https://pymolwiki.org/index.php/ColorByRMSD

“This script allows you to color two structures by Root Mean Square
Deviation (RMSD). The distances between aligned C-alpha atom pairs are
stored as B-factors of these residues, which are colored by a color
spectrum, with blue specifying the minimum pairwise RMSD and red indicating
the maximum. Unaligned residues are colored gray.”

It does not specify the distance between the Ca atoms and I would need a
scale for my PhD thesis.


I have found the ramp the “ramp_new script”

https://pymolwiki.org/index.php/Ramp_New#Ramp_.2B_Distance_Measure


Would it be possible to implement the script of the colorbyrmsd and add a
ramp and specify which color correspond to which distance?


Thanks a lot


Laura