id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 2572 Atom matching occurring in input order rather than name order andrei@… Conrad Huang "{{{ The following bug report has been submitted: Platform: Darwin-19.0.0-x86_64-i386-64bit ChimeraX Version: 0.91 (2019-11-09) Description There is a problem with the alignment of the small molecules. It seems that the command ""align #1 to #2"" selects the two atom groups based on the order they appear in the input files and does not take into account the atom names. This leads to incorrect alignment of the two GLU residues in the attached file. If the two atom groups are explicitly given (""align #1@c,ca,cb,cg,cd,o,oe1,oe2,n to #2@c,ca,cb,cg,cd,o,oe1,oe2,n"") than it works correctly. Log: UCSF ChimeraX version: 0.91 (2019-11-09) © 2016-2019 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open /Users/andrei/tmp/test/glu_superimpose/glu-184-D-10077_residue_shift.cif Summary of feedback from opening /Users/andrei/tmp/test/glu_superimpose/glu-184-D-10077_residue_shift.cif --- warnings | Unknown polymer entity '1' near line 88 Missing or incomplete entity_poly_seq table. Inferred polymer connectivity. > open /Users/andrei/tmp/test/glu_superimpose/glu-189-A-9918_residue_shift.cif Summary of feedback from opening /Users/andrei/tmp/test/glu_superimpose/glu-189-A-9918_residue_shift.cif --- warnings | Unknown polymer entity '1' near line 24 Missing or incomplete entity_poly_seq table. Inferred polymer connectivity. > align #8@c* toAtoms #5@c* No atoms paired for alignment > align #1@c* toAtoms #2@c* RMSD between 5 atom pairs is 1.943 angstroms > align #1 toAtoms #2 RMSD between 9 atom pairs is 2.595 angstroms > align #1 toAtoms #2 RMSD between 9 atom pairs is 2.595 angstroms > align #1 toAtoms #2 RMSD between 9 atom pairs is 2.595 angstroms > align #1@ca,cb,cd toAtoms #2@ca,cb,cd RMSD between 3 atom pairs is 0.020 angstroms > align #1 toAtoms #2 RMSD between 9 atom pairs is 2.595 angstroms > label #1 > label #1@ca > ~label #1 > label #1@ca > label #1@ca > label #1@cb > select #1@cb 1 atom, 1 model selected > label #1@cb > align #1@c* toAtoms #2@c* RMSD between 5 atom pairs is 1.943 angstroms > align #1@c,ca,cb,cg,cd toAtoms #2@c,ca,cb,cg,cd RMSD between 5 atom pairs is 0.075 angstroms > align #1@c,ca,cb,cg,cd toAtoms #2@c,ca,cb,cg,cd RMSD between 5 atom pairs is 0.075 angstroms > align #1@c,ca,cb,cg,cd,o toAtoms #2@c,ca,cb,cg,cd,o RMSD between 6 atom pairs is 0.494 angstroms > align #1@c,ca,cb,cg,cd,o,oe1,oe2 toAtoms #2@c,ca,cb,cg,cd,o,oe1,oe2 RMSD between 8 atom pairs is 1.177 angstroms > select 18 atoms, 16 bonds, 3 models selected > select #2@c,ca,cb,cg,cd,o,oe1,oe2 8 atoms, 7 bonds, 1 model selected > align #1@c,ca,cb,cg,cd,o,oe1,oe2,n toAtoms #2@c,ca,cb,cg,cd,o,oe1,oe2,n RMSD between 9 atom pairs is 1.120 angstroms > align #1 toAtoms #2 RMSD between 9 atom pairs is 2.595 angstroms > align #1 toAtoms #2 RMSD between 9 atom pairs is 2.595 angstroms > align #1@n,c,ca,cb,cg,cd,o,oe1,oe2 toAtoms #2@c,ca,cb,cg,cd,o,oe1,oe2,n RMSD between 9 atom pairs is 2.730 angstroms > close session > open /Users/andrei/tmp/test/glu_superimpose/glu-184-D-10077_residue_shift.cif Summary of feedback from opening /Users/andrei/tmp/test/glu_superimpose/glu-184-D-10077_residue_shift.cif --- warnings | Unknown polymer entity '1' near line 26 Missing or incomplete entity_poly_seq table. Inferred polymer connectivity. > open /Users/andrei/tmp/test/glu_superimpose/glu-189-A-9918_residue_shift.cif Summary of feedback from opening /Users/andrei/tmp/test/glu_superimpose/glu-189-A-9918_residue_shift.cif --- warnings | Unknown polymer entity '1' near line 24 Missing or incomplete entity_poly_seq table. Inferred polymer connectivity. > align #1@n,c,ca,cb,cg,cd,o,oe1,oe2 toAtoms #2@c,ca,cb,cg,cd,o,oe1,oe2,n RMSD between 9 atom pairs is 2.730 angstroms > align #1 toAtoms #2 RMSD between 9 atom pairs is 2.595 angstroms > align #1@c,ca,cb,cg,cd,o,oe1,oe2,n toAtoms #2@c,ca,cb,cg,cd,o,oe1,oe2,n RMSD between 9 atom pairs is 1.120 angstroms > matchmaker #1@c,ca,cb,cg,cd,o,oe1,oe2,n to #2@c,ca,cb,cg,cd,o,oe1,oe2,n Reference and/or match model contains no nucleic or amino acid chains. Use the command-line 'match' command to superimpose small molecules/ligands. > matchmaker #1 to #2 Reference and/or match model contains no nucleic or amino acid chains. Use the command-line 'match' command to superimpose small molecules/ligands. > matchmaker #1@c,ca,cb,cg,cd,o,oe1,oe2,n to #2@c,ca,cb,cg,cd,o,oe1,oe2,n Reference and/or match model contains no nucleic or amino acid chains. Use the command-line 'match' command to superimpose small molecules/ligands. > align #1@c,ca,cb,cg,cd,o,oe1,oe2,n toAtoms #2@c,ca,cb,cg,cd,o,oe1,oe2,n RMSD between 9 atom pairs is 1.120 angstroms > align #1@c,ca,cb,cg,cd,o,oe1,oe2,n toAtoms #2@c,ca,cb,cg,cd,o,oe1,oe2,n RMSD between 9 atom pairs is 1.120 angstroms OpenGL version: 4.1 ATI-3.0.68 OpenGL renderer: AMD Radeon Pro 560 OpenGL Engine OpenGL vendor: ATI Technologies Inc. File attachment: glu.zip }}} [attachment:""glu.zip""] " defect closed normal Command Line fixed Eric Pettersen all ChimeraX