ColorByRMSD
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| Type | Python Module |
|---|---|
| Download | colorbyrmsd.py |
| Author(s) | Shivender Shandilya, Jason Vertrees, Thomas Holder |
| License | BSD-2-Clause |
| This code has been put under version control in the project Pymol-script-repo | |
Introduction
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.
Usage
colorbyrmsd mobile, target [, doAlign [, doPretty [, guide [, method ]]]]
Arguments
- mobile = string: atom selection for mobile atoms
- target = string: atom selection for target atoms
- doAlign = 0 or 1: Superpose selections before calculating distances {default: 1}
- doPretty = 0 or 1: Show nice representation and colors {default: 1}
- guide = 0 or 1: Only use C-alpha atoms {default: 1}
- method = align or super: Method to match atoms {default: super}
Examples
# example #1
colorbyrmsd 1cbs, 1hmt, doAlign=1, doPretty=1
# example #2
colorbyrmsd 1eaz, 1fao, doAlign=1, doPretty=1
1cbs and 1hmt aligned and colored by RMSD. Dark blue is good alignment, higher deviations are in orange/yellow/red. Residues not used for alignment are colored white.
1eaz and 1fao aligned and colored by RMSD. Dark blue is good alignment, higher deviations are in orange/yellow/red. Residues not used for alignment are colored white.
