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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.
Documentation
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
https://rna-tools.readthedocs.io/en/latest/tools.html#root-mean-square-deviation-rmsd
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 0.0,13.299,12.851,12.882 13.299,0.0,3.77,5.161 12.851,3.77,0.0,4.566 12.882,5.161,4.566,0.0https://rna-tools.readthedocs.io/en/latest/tools.html#rna-calc-rmsd-all-vs-all
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