QChASM
unique.py
I am getting unexpected behavior with unique.py it characterizes the following four files as not unique using the default RMSD cutoff.
If we set 01_opt as the reference structure, it is outputting RMSDs of
04_opt (RMSD = 0.135) 05_opt (RMSD = 0.022) 06_opt (RMSD = 0.149)
when I open these files in ChimeraX and use the align function align #2 toAtoms #1 I get much larger RMSDs
04_opt (RMSD = 1.887) 05_opt (RMSD = 1.896) 06_opt (RMSD = 2.189)
Maybe I just need to decrease the RMSD tolerance in unique.py. Bringing this to your attention because I did not expect unique.py to describe these structures as not unique and I was surprised by the difference in RMSD assigned by unique.py vs align in chimeraX.
04_no_cat_int_cis_01_opt.txt 04_no_cat_int_cis_04_opt.txt 04_no_cat_int_cis_05_opt.txt 04_no_cat_int_cis_06_opt.txt
Another example of where the results of unique.py are surprising. Using RMSD threshold 0.01 we, unique.py assigns
there are 3 structures similar to 04_opt: grey in screenshot below 07_opt (RMSD = 0.008) red in screenshot below 09_opt (RMSD = 0.000) 13_opt (RMSD = 0.000) there are 2 structures similar to 05_opt: black in screenshot below
grey-vs-red is assigned identical, despite a 90 degree rotation about the C-C(aryl) bond grey-vs-black is assigned inequivalent, even though there is only a small nudge to the amide bond.
04_no_cat_int_cis_04_opt.txt 04_no_cat_int_cis_07_opt.txt 04_no_cat_int_cis_05_opt.txt
It looks like there's a bug in the code we use to reorder atoms to account for symmetry. After shifting these structures' centroids to the origin, everything except the Cl atom is disregarded. If you ignore the other atoms, the Cl atoms look like they're in a similar spot.
I'll have to look more into this.
I think it's fixed. Among these structures using the default threshold, I'm getting that 01 is unique, 04 and 05 are similar to each other, and 06 and 07 are similar to each other.