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#16192 closed defect (fixed)

Ca RMSD header wrong

Reported by:	vdalves@…	Owned by:	Eric Pettersen
Priority:	normal	Milestone:
Component:	Sequence	Version:
Keywords:		Cc:	Tom Goddard
Blocked By:		Blocking:
Notify when closed:		Platform:	all
Project:	ChimeraX

Description

The following bug report has been submitted:
Platform:        Linux-6.8.0-47-generic-x86_64-with-glibc2.39
ChimeraX Version: 1.9.dev202410240539 (2024-10-24 05:39:21 UTC)
Description
Hello
I was following your Youtube tutorial about coloring by C-alpha RMSD.
I cannot make sense of the units that appear on the histogram from Render/Select By Attribute.
I as expecting Angstrom, but 3.09762 as minimum is strange (see Screenshot attached). Also because on the tutorial the minimum value is around 0.17.
Thank you

Log:
Startup Messages  
---  
note | available bundle cache has not been initialized yet  
  
UCSF ChimeraX version: 1.9.dev202410240539 (2024-10-24)  
© 2016-2024 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open 4bql format mmcif fromDatabase pdb

4bql title:  
Crystal structure of archaeal actin [more info...]  
  
Chain information for 4bql #1  
---  
Chain | Description | UniProt  
A B C D | ACTIN/ACTIN FAMILY PROTEIN | A3MWN5_PYRCJ 1-432  
  
Non-standard residues in 4bql #1  
---  
ADP — adenosine-5'-diphosphate  
MG — magnesium ion  
  
4bql mmCIF Assemblies  
---  
1| author_and_software_defined_assembly  
2| software_defined_assembly  
  

> preset "overall look" "publication 1 (silhouettes)"

Using preset: Overall Look / Publication 1 (Silhouettes)  
Preset expands to these ChimeraX commands:

    
    
    set bg white
    graphics silhouettes t
    lighting depthCue f

  

> delete /B,C,D

> open 1j6z

1j6z title:  
Uncomplexed actin [more info...]  
  
Chain information for 1j6z #2  
---  
Chain | Description | UniProt  
A | ACTIN ALPHA 1 | ACTS_RABIT 2-375  
  
Non-standard residues in 1j6z #2  
---  
ADP — adenosine-5'-diphosphate  
CA — calcium ion  
RHO — tetramethylrhodamine-5-maleimide (TMR)  
  
5 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.  

> matchmaker #2 to #1 showAlignment true

Computing secondary structure  
[Repeated 1 time(s)]  Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker 4bql, chain A (#1) with 1j6z, chain A (#2), sequence alignment
score = 412.6  
Alignment identifier is 1  
Showing conservation header ("seq_conservation" residue attribute) for
alignment 1  
Hiding conservation header for alignment 1  
Chains used in RMSD evaluation for alignment 1: 4bql #1/A, 1j6z #2/A  
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 1  
RMSD between 177 pruned atom pairs is 1.198 angstroms; (across all 349 pairs:
4.965)  
  

> hide atoms

> ui tool show "Render/Select by Attribute"

QTextCursor::setPosition: Position '73' out of range  

[Repeated 1 time(s)]

QTextCursor::setPosition: Position '2' out of range  

QTextCursor::setPosition: Position '3' out of range  

QTextCursor::setPosition: Position '4' out of range  

QTextCursor::setPosition: Position '5' out of range  

QTextCursor::setPosition: Position '6' out of range  

QTextCursor::setPosition: Position '7' out of range  

QTextCursor::setPosition: Position '8' out of range  

QTextCursor::setPosition: Position '9' out of range  

QTextCursor::setPosition: Position '10' out of range  

QTextCursor::setPosition: Position '11' out of range  

QTextCursor::setPosition: Position '12' out of range  

QTextCursor::setPosition: Position '13' out of range  

QTextCursor::setPosition: Position '14' out of range  

QTextCursor::setPosition: Position '15' out of range  

QTextCursor::setPosition: Position '16' out of range  

QTextCursor::setPosition: Position '17' out of range  

QTextCursor::setPosition: Position '18' out of range  

QTextCursor::setPosition: Position '19' out of range  

QTextCursor::setPosition: Position '20' out of range  

QTextCursor::setPosition: Position '21' out of range  

QTextCursor::setPosition: Position '22' out of range  

QTextCursor::setPosition: Position '23' out of range  

QTextCursor::setPosition: Position '24' out of range  

QTextCursor::setPosition: Position '25' out of range  

QTextCursor::setPosition: Position '26' out of range  

QTextCursor::setPosition: Position '27' out of range  

QTextCursor::setPosition: Position '28' out of range  

QTextCursor::setPosition: Position '29' out of range  

QTextCursor::setPosition: Position '30' out of range  

QTextCursor::setPosition: Position '31' out of range  

QTextCursor::setPosition: Position '32' out of range  

QTextCursor::setPosition: Position '33' out of range  

QTextCursor::setPosition: Position '34' out of range  

QTextCursor::setPosition: Position '35' out of range  

QTextCursor::setPosition: Position '36' out of range  

QTextCursor::setPosition: Position '37' out of range  

QTextCursor::setPosition: Position '38' out of range  

QTextCursor::setPosition: Position '39' out of range  

QTextCursor::setPosition: Position '40' out of range  

QTextCursor::setPosition: Position '41' out of range  

QTextCursor::setPosition: Position '42' out of range  

QTextCursor::setPosition: Position '43' out of range  

QTextCursor::setPosition: Position '44' out of range  

QTextCursor::setPosition: Position '45' out of range  

[Repeated 1 time(s)]

QTextCursor::setPosition: Position '46' out of range  

QTextCursor::setPosition: Position '47' out of range  

QTextCursor::setPosition: Position '48' out of range  

QTextCursor::setPosition: Position '49' out of range  

QTextCursor::setPosition: Position '50' out of range  

QTextCursor::setPosition: Position '51' out of range  

QTextCursor::setPosition: Position '52' out of range  

QTextCursor::setPosition: Position '53' out of range  

QTextCursor::setPosition: Position '54' out of range  

QTextCursor::setPosition: Position '55' out of range  

QTextCursor::setPosition: Position '56' out of range  

QTextCursor::setPosition: Position '57' out of range  

QTextCursor::setPosition: Position '58' out of range  

QTextCursor::setPosition: Position '59' out of range  

QTextCursor::setPosition: Position '60' out of range  

QTextCursor::setPosition: Position '61' out of range  

QTextCursor::setPosition: Position '62' out of range  

QTextCursor::setPosition: Position '63' out of range  

QTextCursor::setPosition: Position '64' out of range  

QTextCursor::setPosition: Position '65' out of range  

QTextCursor::setPosition: Position '66' out of range  

QTextCursor::setPosition: Position '67' out of range  

QTextCursor::setPosition: Position '68' out of range  

QTextCursor::setPosition: Position '69' out of range  

QTextCursor::setPosition: Position '70' out of range  

QTextCursor::setPosition: Position '71' out of range  

QTextCursor::setPosition: Position '72' out of range  

QTextCursor::setPosition: Position '73' out of range  

QTextCursor::setPosition: Position '74' out of range  

QTextCursor::setPosition: Position '75' out of range  

QTextCursor::setPosition: Position '76' out of range  

QTextCursor::setPosition: Position '77' out of range  

QTextCursor::setPosition: Position '78' out of range  

QTextCursor::setPosition: Position '79' out of range  

QTextCursor::setPosition: Position '80' out of range  

QTextCursor::setPosition: Position '81' out of range  

QTextCursor::setPosition: Position '80' out of range  

QTextCursor::setPosition: Position '79' out of range  

QTextCursor::setPosition: Position '78' out of range  

QTextCursor::setPosition: Position '77' out of range  

QTextCursor::setPosition: Position '78' out of range  

QTextCursor::setPosition: Position '79' out of range  

QTextCursor::setPosition: Position '80' out of range  

QTextCursor::setPosition: Position '81' out of range  

QTextCursor::setPosition: Position '82' out of range  

QTextCursor::setPosition: Position '83' out of range  

QTextCursor::setPosition: Position '84' out of range  

QTextCursor::setPosition: Position '85' out of range  

QTextCursor::setPosition: Position '86' out of range  

QTextCursor::setPosition: Position '87' out of range  

QTextCursor::setPosition: Position '88' out of range  

QTextCursor::setPosition: Position '89' out of range  

QTextCursor::setPosition: Position '90' out of range  

QTextCursor::setPosition: Position '91' out of range  

QTextCursor::setPosition: Position '92' out of range  

QTextCursor::setPosition: Position '93' out of range  

QTextCursor::setPosition: Position '94' out of range  

QTextCursor::setPosition: Position '95' out of range  

QTextCursor::setPosition: Position '96' out of range  

QTextCursor::setPosition: Position '97' out of range  

QTextCursor::setPosition: Position '98' out of range  

QTextCursor::setPosition: Position '99' out of range  

QTextCursor::setPosition: Position '100' out of range  

QTextCursor::setPosition: Position '101' out of range  

QTextCursor::setPosition: Position '102' out of range  

QTextCursor::setPosition: Position '103' out of range  

QTextCursor::setPosition: Position '104' out of range  

QTextCursor::setPosition: Position '105' out of range  

QTextCursor::setPosition: Position '106' out of range  

QTextCursor::setPosition: Position '107' out of range  

QTextCursor::setPosition: Position '108' out of range  

QTextCursor::setPosition: Position '109' out of range  

QTextCursor::setPosition: Position '110' out of range  

QTextCursor::setPosition: Position '111' out of range  

QTextCursor::setPosition: Position '112' out of range  

QTextCursor::setPosition: Position '113' out of range  

QTextCursor::setPosition: Position '114' out of range  

QTextCursor::setPosition: Position '115' out of range  

QTextCursor::setPosition: Position '116' out of range  

QTextCursor::setPosition: Position '117' out of range  

QTextCursor::setPosition: Position '118' out of range  

QTextCursor::setPosition: Position '119' out of range  

QTextCursor::setPosition: Position '120' out of range  

QTextCursor::setPosition: Position '121' out of range  

QTextCursor::setPosition: Position '122' out of range  

QTextCursor::setPosition: Position '123' out of range  

QTextCursor::setPosition: Position '124' out of range  

QTextCursor::setPosition: Position '125' out of range  

QTextCursor::setPosition: Position '126' out of range  

QTextCursor::setPosition: Position '127' out of range  

QTextCursor::setPosition: Position '128' out of range  

QTextCursor::setPosition: Position '129' out of range  

QTextCursor::setPosition: Position '130' out of range  

QTextCursor::setPosition: Position '131' out of range  

QTextCursor::setPosition: Position '132' out of range  

QTextCursor::setPosition: Position '133' out of range  

QTextCursor::setPosition: Position '134' out of range  

QTextCursor::setPosition: Position '135' out of range  

QTextCursor::setPosition: Position '136' out of range  

QTextCursor::setPosition: Position '137' out of range  

QTextCursor::setPosition: Position '138' out of range  

QTextCursor::setPosition: Position '139' out of range  

QTextCursor::setPosition: Position '140' out of range  

QTextCursor::setPosition: Position '141' out of range  

QTextCursor::setPosition: Position '142' out of range  

QTextCursor::setPosition: Position '143' out of range  

QTextCursor::setPosition: Position '144' out of range  

QTextCursor::setPosition: Position '145' out of range  

QTextCursor::setPosition: Position '146' out of range  

QTextCursor::setPosition: Position '147' out of range  

QTextCursor::setPosition: Position '148' out of range  

QTextCursor::setPosition: Position '149' out of range  

QTextCursor::setPosition: Position '150' out of range  

QTextCursor::setPosition: Position '151' out of range  

QTextCursor::setPosition: Position '152' out of range  

QTextCursor::setPosition: Position '153' out of range  

QTextCursor::setPosition: Position '154' out of range  

QTextCursor::setPosition: Position '155' out of range  

QTextCursor::setPosition: Position '156' out of range  

QTextCursor::setPosition: Position '157' out of range  

QTextCursor::setPosition: Position '158' out of range  

QTextCursor::setPosition: Position '159' out of range  

QTextCursor::setPosition: Position '160' out of range  

QTextCursor::setPosition: Position '161' out of range  

QTextCursor::setPosition: Position '162' out of range  

QTextCursor::setPosition: Position '163' out of range  

QTextCursor::setPosition: Position '164' out of range  

QTextCursor::setPosition: Position '163' out of range  

QTextCursor::setPosition: Position '164' out of range  

QTextCursor::setPosition: Position '165' out of range  

QTextCursor::setPosition: Position '166' out of range  

QTextCursor::setPosition: Position '167' out of range  

QTextCursor::setPosition: Position '168' out of range  

QTextCursor::setPosition: Position '169' out of range  

QTextCursor::setPosition: Position '170' out of range  

QTextCursor::setPosition: Position '171' out of range  

QTextCursor::setPosition: Position '172' out of range  

QTextCursor::setPosition: Position '173' out of range  

QTextCursor::setPosition: Position '174' out of range  

QTextCursor::setPosition: Position '175' out of range  

QTextCursor::setPosition: Position '176' out of range  

QTextCursor::setPosition: Position '177' out of range  

QTextCursor::setPosition: Position '178' out of range  

QTextCursor::setPosition: Position '179' out of range  

QTextCursor::setPosition: Position '180' out of range  

QTextCursor::setPosition: Position '181' out of range  

QTextCursor::setPosition: Position '182' out of range  

QTextCursor::setPosition: Position '181' out of range  

QTextCursor::setPosition: Position '182' out of range  

QTextCursor::setPosition: Position '183' out of range  

QTextCursor::setPosition: Position '184' out of range  

QTextCursor::setPosition: Position '185' out of range  

QTextCursor::setPosition: Position '186' out of range  

QTextCursor::setPosition: Position '187' out of range  

QTextCursor::setPosition: Position '188' out of range  

QTextCursor::setPosition: Position '189' out of range  

QTextCursor::setPosition: Position '190' out of range  

QTextCursor::setPosition: Position '191' out of range  

QTextCursor::setPosition: Position '192' out of range  

QTextCursor::setPosition: Position '193' out of range  

QTextCursor::setPosition: Position '194' out of range  

QTextCursor::setPosition: Position '193' out of range  

QTextCursor::setPosition: Position '192' out of range  

QTextCursor::setPosition: Position '191' out of range  

QTextCursor::setPosition: Position '192' out of range  

QTextCursor::setPosition: Position '193' out of range  

QTextCursor::setPosition: Position '194' out of range  

QTextCursor::setPosition: Position '195' out of range  

QTextCursor::setPosition: Position '196' out of range  

QTextCursor::setPosition: Position '197' out of range  

QTextCursor::setPosition: Position '198' out of range  

QTextCursor::setPosition: Position '199' out of range  

QTextCursor::setPosition: Position '200' out of range  

QTextCursor::setPosition: Position '201' out of range  

QTextCursor::setPosition: Position '202' out of range  

QTextCursor::setPosition: Position '203' out of range  

QTextCursor::setPosition: Position '204' out of range  

QTextCursor::setPosition: Position '205' out of range  

QTextCursor::setPosition: Position '206' out of range  

QTextCursor::setPosition: Position '207' out of range  

QTextCursor::setPosition: Position '208' out of range  

QTextCursor::setPosition: Position '209' out of range  

QTextCursor::setPosition: Position '210' out of range  

QTextCursor::setPosition: Position '211' out of range  

QTextCursor::setPosition: Position '212' out of range  

QTextCursor::setPosition: Position '213' out of range  

QTextCursor::setPosition: Position '214' out of range  

QTextCursor::setPosition: Position '215' out of range  

QTextCursor::setPosition: Position '216' out of range  

QTextCursor::setPosition: Position '217' out of range  

QTextCursor::setPosition: Position '218' out of range  

QTextCursor::setPosition: Position '219' out of range  

QTextCursor::setPosition: Position '220' out of range  

QTextCursor::setPosition: Position '221' out of range  

QTextCursor::setPosition: Position '222' out of range  

QTextCursor::setPosition: Position '223' out of range  

QTextCursor::setPosition: Position '224' out of range  

QTextCursor::setPosition: Position '225' out of range  

QTextCursor::setPosition: Position '226' out of range  

QTextCursor::setPosition: Position '225' out of range  

QTextCursor::setPosition: Position '224' out of range  

QTextCursor::setPosition: Position '225' out of range  

QTextCursor::setPosition: Position '226' out of range  

QTextCursor::setPosition: Position '227' out of range  

QTextCursor::setPosition: Position '228' out of range  

QTextCursor::setPosition: Position '227' out of range  

QTextCursor::setPosition: Position '226' out of range  

QTextCursor::setPosition: Position '225' out of range  

QTextCursor::setPosition: Position '226' out of range  

QTextCursor::setPosition: Position '227' out of range  

QTextCursor::setPosition: Position '228' out of range  

QTextCursor::setPosition: Position '229' out of range  

[Repeated 1 time(s)]

QTextCursor::setPosition: Position '230' out of range  

QTextCursor::setPosition: Position '231' out of range  

QTextCursor::setPosition: Position '232' out of range  

QTextCursor::setPosition: Position '233' out of range  

QTextCursor::setPosition: Position '234' out of range  

QTextCursor::setPosition: Position '235' out of range  

QTextCursor::setPosition: Position '236' out of range  

QTextCursor::setPosition: Position '237' out of range  

QTextCursor::setPosition: Position '238' out of range  

QTextCursor::setPosition: Position '239' out of range  

QTextCursor::setPosition: Position '240' out of range  

QTextCursor::setPosition: Position '241' out of range  

QTextCursor::setPosition: Position '242' out of range  

QTextCursor::setPosition: Position '243' out of range  

QTextCursor::setPosition: Position '244' out of range  

QTextCursor::setPosition: Position '245' out of range  

QTextCursor::setPosition: Position '246' out of range  

QTextCursor::setPosition: Position '247' out of range  

QTextCursor::setPosition: Position '248' out of range  

QTextCursor::setPosition: Position '249' out of range  

QTextCursor::setPosition: Position '250' out of range  

QTextCursor::setPosition: Position '251' out of range  

QTextCursor::setPosition: Position '252' out of range  

QTextCursor::setPosition: Position '253' out of range  

QTextCursor::setPosition: Position '254' out of range  

QTextCursor::setPosition: Position '255' out of range  

QTextCursor::setPosition: Position '256' out of range  

QTextCursor::setPosition: Position '257' out of range  

QTextCursor::setPosition: Position '258' out of range  

QTextCursor::setPosition: Position '259' out of range  

QTextCursor::setPosition: Position '260' out of range  

QTextCursor::setPosition: Position '261' out of range  

QTextCursor::setPosition: Position '262' out of range  

QTextCursor::setPosition: Position '263' out of range  

QTextCursor::setPosition: Position '264' out of range  

QTextCursor::setPosition: Position '265' out of range  

QTextCursor::setPosition: Position '266' out of range  

QTextCursor::setPosition: Position '267' out of range  

QTextCursor::setPosition: Position '268' out of range  

QTextCursor::setPosition: Position '269' out of range  

QTextCursor::setPosition: Position '268' out of range  

QTextCursor::setPosition: Position '267' out of range  

QTextCursor::setPosition: Position '268' out of range  

QTextCursor::setPosition: Position '269' out of range  

QTextCursor::setPosition: Position '270' out of range  

QTextCursor::setPosition: Position '271' out of range  

QTextCursor::setPosition: Position '272' out of range  

QTextCursor::setPosition: Position '273' out of range  

QTextCursor::setPosition: Position '274' out of range  

QTextCursor::setPosition: Position '275' out of range  

QTextCursor::setPosition: Position '276' out of range  

QTextCursor::setPosition: Position '277' out of range  

QTextCursor::setPosition: Position '278' out of range  

QTextCursor::setPosition: Position '279' out of range  

QTextCursor::setPosition: Position '280' out of range  

QTextCursor::setPosition: Position '281' out of range  

QTextCursor::setPosition: Position '282' out of range  

QTextCursor::setPosition: Position '283' out of range  

QTextCursor::setPosition: Position '284' out of range  

QTextCursor::setPosition: Position '283' out of range  

QTextCursor::setPosition: Position '282' out of range  

QTextCursor::setPosition: Position '281' out of range  

QTextCursor::setPosition: Position '280' out of range  

QTextCursor::setPosition: Position '281' out of range  

QTextCursor::setPosition: Position '280' out of range  

QTextCursor::setPosition: Position '279' out of range  

QTextCursor::setPosition: Position '280' out of range  

QTextCursor::setPosition: Position '281' out of range  

QTextCursor::setPosition: Position '282' out of range  

QTextCursor::setPosition: Position '283' out of range  

QTextCursor::setPosition: Position '284' out of range  

QTextCursor::setPosition: Position '285' out of range  

QTextCursor::setPosition: Position '286' out of range  

QTextCursor::setPosition: Position '287' out of range  

QTextCursor::setPosition: Position '288' out of range  

QTextCursor::setPosition: Position '289' out of range  

QTextCursor::setPosition: Position '290' out of range  

QTextCursor::setPosition: Position '291' out of range  

QTextCursor::setPosition: Position '292' out of range  

QTextCursor::setPosition: Position '293' out of range  

QTextCursor::setPosition: Position '294' out of range  

QTextCursor::setPosition: Position '295' out of range  

QTextCursor::setPosition: Position '296' out of range  

QTextCursor::setPosition: Position '297' out of range  

QTextCursor::setPosition: Position '298' out of range  

QTextCursor::setPosition: Position '299' out of range  

QTextCursor::setPosition: Position '300' out of range  

QTextCursor::setPosition: Position '301' out of range  

QTextCursor::setPosition: Position '302' out of range  

QTextCursor::setPosition: Position '301' out of range  

QTextCursor::setPosition: Position '300' out of range  

QTextCursor::setPosition: Position '299' out of range  

QTextCursor::setPosition: Position '298' out of range  

QTextCursor::setPosition: Position '299' out of range  

QTextCursor::setPosition: Position '300' out of range  

QTextCursor::setPosition: Position '301' out of range  

QTextCursor::setPosition: Position '302' out of range  

QTextCursor::setPosition: Position '303' out of range  




OpenGL version: 3.3.0 NVIDIA 535.183.01
OpenGL renderer: NVIDIA GeForce GTX 970/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation

Python: 3.11.4
Locale: en_US.UTF-8
Qt version: PyQt6 6.7.1, Qt 6.7.1
Qt runtime version: 6.7.3
Qt platform: xcb

XDG_SESSION_TYPE=x11
DESKTOP_SESSION=cinnamon
XDG_SESSION_DESKTOP=cinnamon
XDG_CURRENT_DESKTOP=X-Cinnamon
DISPLAY=:0
Manufacturer: Micro-Star International Co., Ltd.
Model: MS-7D54
OS: Linux Mint 22
Architecture: 64bit ELF
Virtual Machine: none
CPU: 16 AMD Ryzen 7 5800X 8-Core Processor
Cache Size: 512 KB
Memory:
	               total        used        free      shared  buff/cache   available
	Mem:            31Gi       8.9Gi       1.0Gi       127Mi        21Gi        22Gi
	Swap:          2.0Gi       512Ki       2.0Gi

Graphics:
	2d:00.0 VGA compatible controller [0300]: NVIDIA Corporation GM204 [GeForce GTX 970] [10de:13c2] (rev a1)	
	Subsystem: ASUSTeK Computer Inc. GM204 [GeForce GTX 970] [1043:853f]	
	Kernel driver in use: nvidia

Installed Packages:
    alabaster: 1.0.0
    appdirs: 1.4.4
    asttokens: 2.4.1
    babel: 2.16.0
    beautifulsoup4: 4.12.3
    blockdiag: 3.0.0
    blosc2: 2.7.1
    build: 1.2.1
    certifi: 2024.8.30
    cftime: 1.6.4.post1
    charset-normalizer: 3.4.0
    ChimeraX-AddCharge: 1.5.17
    ChimeraX-AddH: 2.2.6
    ChimeraX-AlignmentAlgorithms: 2.0.2
    ChimeraX-AlignmentHdrs: 3.5
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 2.15.1
    ChimeraX-AlphaFold: 1.0.1
    ChimeraX-AltlocExplorer: 1.1.2
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.1
    ChimeraX-Atomic: 1.58.7
    ChimeraX-AtomicLibrary: 14.1.8
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.4
    ChimeraX-BasicActions: 1.1.2
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 2.4.7
    ChimeraX-BondRot: 2.0.4
    ChimeraX-BugReporter: 1.0.1
    ChimeraX-BuildStructure: 2.13
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.3.4
    ChimeraX-ButtonPanel: 1.0.1
    ChimeraX-CageBuilder: 1.0.1
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.4
    ChimeraX-ChangeChains: 1.1
    ChimeraX-CheckWaters: 1.4
    ChimeraX-ChemGroup: 2.0.1
    ChimeraX-Clashes: 2.3
    ChimeraX-ColorActions: 1.0.5
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.6
    ChimeraX-CommandLine: 1.2.5
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.9.dev202410240539
    ChimeraX-CoreFormats: 1.2
    ChimeraX-coulombic: 1.4.4
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0.1
    ChimeraX-DataFormats: 1.2.3
    ChimeraX-Dicom: 1.2.5
    ChimeraX-DiffPlot: 1.0
    ChimeraX-DistMonitor: 1.4.2
    ChimeraX-DockPrep: 1.1.3
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ESMFold: 1.0
    ChimeraX-FileHistory: 1.0.1
    ChimeraX-FunctionKey: 1.0.1
    ChimeraX-Geometry: 1.3
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.4.1
    ChimeraX-Hbonds: 2.5
    ChimeraX-Help: 1.3
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.2
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.3
    ChimeraX-ItemsInspection: 1.0.1
    ChimeraX-IUPAC: 1.0
    ChimeraX-KVFinder: 1.2
    ChimeraX-Label: 1.1.11
    ChimeraX-LinuxSupport: 1.0.1
    ChimeraX-ListInfo: 1.2.2
    ChimeraX-Log: 1.2
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.9.1
    ChimeraX-Map: 1.3
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0.1
    ChimeraX-MapFilter: 2.0.1
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.1.1
    ChimeraX-Markers: 1.0.1
    ChimeraX-Mask: 1.0.2
    ChimeraX-MatchMaker: 2.1.6
    ChimeraX-MCopy: 1.0
    ChimeraX-MDcrds: 2.7.1
    ChimeraX-MedicalToolbar: 1.1
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1.1
    ChimeraX-mmCIF: 2.14.2
    ChimeraX-MMTF: 2.2
    ChimeraX-ModelArchive: 1.0
    ChimeraX-Modeller: 1.5.17
    ChimeraX-ModelPanel: 1.5
    ChimeraX-ModelSeries: 1.0.1
    ChimeraX-Mol2: 2.0.3
    ChimeraX-Mole: 1.0
    ChimeraX-Morph: 1.0.2
    ChimeraX-MouseModes: 1.2
    ChimeraX-Movie: 1.0
    ChimeraX-MutationScores: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nifti: 1.2
    ChimeraX-NMRSTAR: 1.0.2
    ChimeraX-NRRD: 1.2
    ChimeraX-Nucleotides: 2.0.3
    ChimeraX-OpenCommand: 1.14
    ChimeraX-OrthoPick: 1.0.1
    ChimeraX-PDB: 2.7.6
    ChimeraX-PDBBio: 1.0.1
    ChimeraX-PDBLibrary: 1.0.4
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0.1
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.1.2
    ChimeraX-PubChem: 2.2
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1.2
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenderByAttr: 1.6
    ChimeraX-RenumberResidues: 1.1
    ChimeraX-ResidueFit: 1.0.1
    ChimeraX-RestServer: 1.3.1
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 4.0
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.5.1
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0.2
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0.1
    ChimeraX-Segmentations: 3.2.1
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.14
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0.1
    ChimeraX-Shortcuts: 1.2.0
    ChimeraX-ShowSequences: 1.0.3
    ChimeraX-SideView: 1.0.1
    ChimeraX-SimilarStructures: 1.0.1
    ChimeraX-Smiles: 2.1.2
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.18.1
    ChimeraX-STL: 1.0.1
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.2.1
    ChimeraX-Struts: 1.0.1
    ChimeraX-Surface: 1.0.1
    ChimeraX-SwapAA: 2.0.1
    ChimeraX-SwapRes: 2.5
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-TaskManager: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.2.3
    ChimeraX-ToolshedUtils: 1.2.4
    ChimeraX-Topography: 1.0
    ChimeraX-ToQuest: 1.0
    ChimeraX-Tug: 1.0.1
    ChimeraX-UI: 1.41
    ChimeraX-uniprot: 2.3.1
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDockX: 1.4.4
    ChimeraX-VIPERdb: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0.1
    ChimeraX-vrml: 1.0
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0.2
    ChimeraX-WebServices: 1.1.4
    ChimeraX-Zone: 1.0.1
    colorama: 0.4.6
    comm: 0.2.2
    contourpy: 1.3.0
    cxservices: 1.2.3
    cycler: 0.12.1
    Cython: 3.0.10
    debugpy: 1.8.7
    decorator: 5.1.1
    distro: 1.9.0
    docutils: 0.21.2
    executing: 2.1.0
    filelock: 3.15.4
    fonttools: 4.54.1
    funcparserlib: 2.0.0a0
    glfw: 2.7.0
    grako: 3.16.5
    h5py: 3.12.1
    html2text: 2024.2.26
    idna: 3.10
    ihm: 1.3
    imagecodecs: 2024.6.1
    imagesize: 1.4.1
    ipykernel: 6.29.5
    ipython: 8.26.0
    ipywidgets: 8.1.5
    jedi: 0.19.1
    Jinja2: 3.1.4
    jupyter_client: 8.6.2
    jupyter_core: 5.7.2
    jupyterlab_widgets: 3.0.13
    kiwisolver: 1.4.7
    line_profiler: 4.1.3
    lxml: 5.2.2
    lz4: 4.3.3
    MarkupSafe: 3.0.2
    matplotlib: 3.9.2
    matplotlib-inline: 0.1.7
    msgpack: 1.0.8
    ndindex: 1.9.2
    nest-asyncio: 1.6.0
    netCDF4: 1.6.5
    networkx: 3.3
    nibabel: 5.2.0
    nptyping: 2.5.0
    numexpr: 2.10.1
    numpy: 1.26.4
    openvr: 1.26.701
    packaging: 23.2
    ParmEd: 4.2.2
    parso: 0.8.4
    pep517: 0.13.1
    pexpect: 4.9.0
    pillow: 10.4.0
    pip: 24.2
    pkginfo: 1.11.1
    platformdirs: 4.3.6
    prompt_toolkit: 3.0.48
    psutil: 6.0.0
    ptyprocess: 0.7.0
    pure_eval: 0.2.3
    py-cpuinfo: 9.0.0
    pycollada: 0.8
    pydicom: 2.4.4
    Pygments: 2.18.0
    pynmrstar: 3.3.4
    pynrrd: 1.0.0
    PyOpenGL: 3.1.7
    PyOpenGL-accelerate: 3.1.7
    pyopenxr: 1.0.3401
    pyparsing: 3.2.0
    pyproject_hooks: 1.2.0
    PyQt6-commercial: 6.7.1
    PyQt6-Qt6: 6.7.3
    PyQt6-WebEngine-commercial: 6.7.0
    PyQt6-WebEngine-Qt6: 6.7.3
    PyQt6-WebEngineSubwheel-Qt6: 6.7.3
    PyQt6_sip: 13.8.0
    python-dateutil: 2.9.0.post0
    pytz: 2024.2
    pyzmq: 26.2.0
    qtconsole: 5.5.2
    QtPy: 2.4.1
    qtshim: 1.0
    RandomWords: 0.4.0
    requests: 2.32.3
    scipy: 1.14.0
    setuptools: 72.1.0
    sfftk-rw: 0.8.1
    six: 1.16.0
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    soupsieve: 2.6
    Sphinx: 8.0.2
    sphinx-autodoc-typehints: 2.2.3
    sphinxcontrib-applehelp: 2.0.0
    sphinxcontrib-blockdiag: 3.0.0
    sphinxcontrib-devhelp: 2.0.0
    sphinxcontrib-htmlhelp: 2.1.0
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 2.0.0
    sphinxcontrib-serializinghtml: 2.0.0
    stack-data: 0.6.3
    superqt: 0.6.3
    tables: 3.10.1
    tcia_utils: 1.5.1
    tifffile: 2024.7.24
    tinyarray: 1.2.4
    tornado: 6.4.1
    traitlets: 5.14.3
    typing_extensions: 4.12.2
    tzdata: 2024.2
    urllib3: 2.2.3
    wcwidth: 0.2.13
    webcolors: 24.6.0
    wheel: 0.43.0
    wheel-filename: 1.4.1
    widgetsnbextension: 4.0.13
File attachment: Screenshot from 2024-10-25 16-54-12.png

Screenshot from 2024-10-25 16-54-12.png

Change History (3)

comment:1 by Eric Pettersen, 12 months ago

Cc:	Tom Goddard added
Component:	Unassigned → Sequence
Owner:	set to Eric Pettersen
Platform:	→ all
Project:	→ ChimeraX
Status:	new → accepted
Summary:	ChimeraX bug report submission → Ca RMSD header wrong

Hi Victor,

Thanks for reporting this problem. I can reproduce it and will work to fix it as soon as possible.

--Eric

Eric Pettersen
UCSF Computer Graphics Lab

comment:2 by Eric Pettersen, 12 months ago

It's not the header -- the sequence alignment reported by MatchMaker is wrong (though the structural superposition is still correct).

comment:3 by Eric Pettersen, 12 months ago

Resolution:	→ fixed
Status:	accepted → closed

The actual problem was that there was a typo in the attribute name of a getattr() that prevented the RMSD header from updating when the superposition was actually carried out. Fix available in next daily build.

Fix: https://github.com/RBVI/ChimeraX/commit/0e9e91f0f7d32416b76e6b13ecbca304417fc271

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