Calculate RMSD

RMSD is the measure of the average distance between the atoms of superimposed RNAs.

files from another job e.g., 614e0a1b

target: filename of file to be used as the reference, if empty the first file dropped will be used
target selection: e.g., A:1-17+24-110+115-168
model selection: e.g., A:1-17+24-110+115-168
target ignore selection: e.g., A/57/O2\'
model ignore selection: e.g., A/57/O2\'

The RMSD csv output file can be found here rmsds.csv

The raw output files for each step of the pipeline can be found here and downloaded as a ZIP file here.


rna_calc_rmsd.py - calculate RMSDs of structures to the target.

Demo files rp21.zip.

If you still have problem with various number of atoms, check out this issue: get_rnapuzzle_ready see Tools

fn                        rmsd_all
21_Adamiak_1_rpr.pdb      13.3
21_ChenHighLig_1_rpr.pdb  12.85
21_Das_1_rpr.pdb          12.88


It's also possible to compare all vs all structures to get a matrix (in numpy format) of RMSD values:
# 21_3dRNA_1_rpr.pdb 21_Adamiak_1_rpr.pdb 21_ChenHighLig_1_rpr.pdb 21_Das_1_rpr.pdb 

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