id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 1687 "Bogus ""incompatible matrix"" error" Elaine Meng Eric Pettersen "{{{ The following bug report has been submitted: Platform: Darwin-17.7.0-x86_64-i386-64bit ChimeraX Version: 0.9 (2019-02-05) Description matchmaker error about chain not compatible with BLOSUM when specific residues are specified open 2fw0 open 2gbp ...this works to superimpose my protein chains: align #1/A:10-20@ca to #2/A:10-20@ca ...but these two both give the error matchmaker #1/A:10-20@ca to #2/A:10-20@ca matchmaker #1/A:10-20 #2/A:10-20 ... even though they should supposedly work to restrict the sequence alignment to those parts according to the docs: Log: > open /Users/meng/Desktop/startup.cxc > alias nucrib car style nucleic x oval width 1.6 thick 1.6 > alias cylinders car style protein modeh tube rad 2 sides 24 > alias licorice car style protein modeh default arrows f x oval width 1 thick 1 > alias rib1 car style modeh def arrows t wid 2 thick 0.4; car style (nucleic|strand) x rect > alias reset view orient; view initial executed startup.cxc UCSF ChimeraX version: 0.9 (2019-02-05) © 2016-2019 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open 2fw0 2fw0 title: Apo Open Form of Glucose/Galactose Binding Protein [more info...] Chain information for 2fw0 #1 --- Chain | Description A | D-galactose-binding periplasmic protein Non-standard residues in 2fw0 #1 --- CA — calcium ion CIT — citric acid MLA — malonic acid (dicarboxylic acid C3; propanediolic acid; methanedicarboxylic acid) NA — sodium ion > open 2gbp 2gbp title: Sugar and signal-transducer binding sites of the escherichia coli galactose chemoreceptor protein [more info...] Chain information for 2gbp #2 --- Chain | Description A | D-galactose/D-glucose binding protein Non-standard residues in 2gbp #2 --- BGC — β-D-glucose CA — calcium ion > align #1/A:10-20@ca toAtoms #2/A:10-20@ca RMSD between 11 atom pairs is 0.318 angstroms > view > matchmaker #1/A:10-20@ca to #2/A:10-20@ca No chains in reference structure 2gbp #2 compatible with BLOSUM-62 similarity matrix > matchmaker #1/A:10-20 to #2/A:10-20 No chains in reference structure 2gbp #2 compatible with BLOSUM-62 similarity matrix OpenGL version: 4.1 INTEL-10.36.22 OpenGL renderer: Intel Iris Pro OpenGL Engine OpenGL vendor: Intel Inc. }}} " defect closed normal Sequence fixed all ChimeraX