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unique.py #25

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joegair opened this issue Feb 2, 2025 · 3 comments
Open

unique.py #25

joegair opened this issue Feb 2, 2025 · 3 comments

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@joegair
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joegair commented Feb 2, 2025

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

@joegair
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joegair commented Feb 2, 2025

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

Image

@ajs99778
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ajs99778 commented Feb 3, 2025

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.

@ajs99778
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ajs99778 commented Feb 3, 2025

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.

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