Bogus "incompatible matrix" error

[Elaine Meng]

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:

<http://rbvi.ucsf.edu/chimerax/docs/user/commands/matchmaker.html#restrict>


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.

[Eric Pettersen]

The temporary "domain sequences" that matchmaker was creating to do partial-chain matching weren't having their "polymer type" set correctly, so the matrix-compatibility check didn't work right.