"label height" not accepting non-integer

[j.r.lewandowski@…]

The following bug report has been submitted:
Platform:        Windows-10-10.0.22000
ChimeraX Version: 1.3 (2021-12-08 23:08:33 UTC)
Description
Hi, I think it might be a bug but do tell me if this is an expected behaviour. When I try to Set label hight in A, I get "Height must be a number" when I use a number including a decimal (e.g. 1.5). Only integers seem to be accepted. Feature or bug?
Thank you,
Józef

Log:
Startup Errors  
---  
error | Bundle 'ChimeraX-Registration' custom initialization failed  
warning | Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\core\toolshed\info.py", line 360, in initialize  
api._api_caller.initialize(api, session, self)  
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\core\toolshed\\__init__.py", line 1276, in initialize  
return cls._get_func(api, "initialize")(session, bi)  
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\registration\\__init__.py", line 41, in initialize  
nag(session)  
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\registration\nag.py", line 37, in nag  
if not check_registration(logger=session.logger):  
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\registration\nag.py", line 56, in check_registration  
param = _get_registration(logger)  
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\registration\nag.py", line 131, in _get_registration  
for line in f:  
File "C:\Program Files\ChimeraX 1.3\bin\lib\codecs.py", line 322, in decode  
(result, consumed) = self._buffer_decode(data, self.errors, final)  
UnicodeDecodeError: 'utf-8' codec can't decode byte 0xf3 in position 155:
invalid continuation byte  
  
UCSF ChimeraX version: 1.3 (2021-12-08)  
© 2016-2021 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open D:\\\MD\\\Avon\\\PksJ_DH-ACP4\\\R55E_W78Y\\\lastframe.pdb

Chain information for lastframe.pdb #1  
---  
Chain | Description  
? | No description available  
  

> show :su2,asp,glu,hid

> style ball

Changed 6197 atom styles  

> set bgColor white

> graphics silhouettes true

> lighting full

> lighting simple

> select /?:363@H133

1 atom, 1 residue, 1 model selected  

> select add /?:57@NE2

2 atoms, 2 residues, 1 model selected  

> distance sel

Distance between /? SU2 363 H133 and HID 57 NE2: 3.1Å  

> hbonds

352 hydrogen bonds found  

> close session

> open D:/MD/Avon/PksJ_DH-ACP4/lastframe.pdb

Chain information for lastframe.pdb #1  
---  
Chain | Description  
? | No description available  
  

> show :su2,asp,glu,hid

> style ball

Changed 6209 atom styles  

> select /?:363@H133

1 atom, 1 residue, 1 model selected  

> select add /?:57@NE2

2 atoms, 2 residues, 1 model selected  

> distance sel

Distance between /? SU2 363 H133 and HID 57 NE2: 4.9Å  

> select /?:363@H81

1 atom, 1 residue, 1 model selected  

> select add /?:229@OD2

2 atoms, 2 residues, 1 model selected  

> distance sel

Distance between /? SU2 363 H81 and ASP 229 OD2: 5.1Å  

> close session

> open C:\Users\jrlew\Desktop\ACP3 format fasta

No such file/path: C:\Users\jrlew\Desktop\ACP3  

> open D:/MD/Avon/PksJ_DH-ACP3a/correct-charge/lastframe.pdb

Chain information for lastframe.pdb #1  
---  
Chain | Description  
? | No description available  
  

> show :su2,asp,glu,hid

> name ACP3a :1-99

> sequence chain #1

Alignment identifier is 1/  

> name DH :100-419

> name list

ACP3a :1-99  
DH :100-419  

> surface

> surface ACP3a

> surface

> color ACP3a red target s

> close session

> cd D:\MD\Avon\PksJ_DH-ACP3a\correct-charge

Current working directory is: D:\MD\Avon\PksJ_DH-ACP3a\correct-charge  

> open cMD.cxc

> cd D:\MD\Avon\PksJ_DH-ACP3a\correct-charge

Current working directory is: D:\MD\Avon\PksJ_DH-ACP3a\correct-charge  

> set bgColor white

> graphics silhouettes true

> open ref_stripped.pdb

Chain information for ref_stripped.pdb #1  
---  
Chain | Description  
A | No description available  
B | No description available  
  

> color /a grey target c

> view :375,119,127

> surface /a

> color /a grey transparency 50 target s

> material dull

> lighting multiShadow 64

> open prod_cMD100ns_stripped.nc

Replaced existing frames of ref_stripped.pdb #1 with 2500 new frames  

> ~show

> show :su2,asp,glu :375

> style ball

Changed 6427 atom styles  
executed cMD.cxc  

> close session

> open cMD.cxc

> cd D:\MD\Avon\PksJ_DH-ACP3a\correct-charge

Current working directory is: D:\MD\Avon\PksJ_DH-ACP3a\correct-charge  

> set bgColor white

> graphics silhouettes true

> open ref_stripped.pdb

Chain information for ref_stripped.pdb #1  
---  
Chain | Description  
A | No description available  
B | No description available  
  

> color /a grey target c

> view :375,119,127

> material dull

> lighting multiShadow 64

> open prod_cMD100ns_stripped.nc

Replaced existing frames of ref_stripped.pdb #1 with 2500 new frames  

> ~show

> show :su2,asp,glu :375

> style ball

Changed 6427 atom styles  
executed cMD.cxc  

> show :hid

> close session

> open cMD.cxc

> cd D:\MD\Avon\PksJ_DH-ACP3a\correct-charge

Current working directory is: D:\MD\Avon\PksJ_DH-ACP3a\correct-charge  

> set bgColor white

> graphics silhouettes true

> open ref_stripped.pdb

Chain information for ref_stripped.pdb #1  
---  
Chain | Description  
A | No description available  
B | No description available  
  

> color /a grey target c

> view :375,119,127

> material dull

> lighting multiShadow 64

> open prod_cMD100ns_stripped.nc

Replaced existing frames of ref_stripped.pdb #1 with 2500 new frames  

> ~show

> show :su2 :375,59,119,120,121,328,156

> style ball

Changed 6427 atom styles  

> style :59,119,120,121 sphere

Changed 60 atom styles  
executed cMD.cxc  

> select /B:121@CA

1 atom, 1 residue, 1 model selected  

> select add /B:120@CA

2 atoms, 2 residues, 1 model selected  

> select up

31 atoms, 30 bonds, 2 residues, 1 model selected  

> select add /B:119@CG

32 atoms, 30 bonds, 3 residues, 1 model selected  

> select up

45 atoms, 44 bonds, 3 residues, 1 model selected  

> hide sel atoms

> close session

> open cMD.cxc

> cd D:\MD\Avon\PksJ_DH-ACP3a\correct-charge

Current working directory is: D:\MD\Avon\PksJ_DH-ACP3a\correct-charge  

> set bgColor white

> graphics silhouettes true

> open ref_stripped.pdb

Chain information for ref_stripped.pdb #1  
---  
Chain | Description  
A | No description available  
B | No description available  
  

> color /a grey target c

> view :375,119,127

> material dull

> lighting multiShadow 64

> open prod_cMD100ns_stripped.nc

Replaced existing frames of ref_stripped.pdb #1 with 2500 new frames  

> ~show

> show :su2 :375,59,218,219,220,328,156

> style ball

Changed 6427 atom styles  

> style :59,218,219,220 sphere

Changed 57 atom styles  
executed cMD.cxc  

> close session

> open cMD.cxc

> cd D:\MD\Avon\PksJ_DH-ACP3a\correct-charge

Current working directory is: D:\MD\Avon\PksJ_DH-ACP3a\correct-charge  

> set bgColor white

> graphics silhouettes true

> open ref_stripped.pdb

Chain information for ref_stripped.pdb #1  
---  
Chain | Description  
A | No description available  
B | No description available  
  

> color /a grey target c

> view :375,119,127

> material dull

> lighting multiShadow 64

> open prod_cMD100ns_stripped.nc

Replaced existing frames of ref_stripped.pdb #1 with 2500 new frames  

> ~show

> show :su2 :375,59,218,219,220,226,328,156

> style ball

Changed 6427 atom styles  

> style :59,218,219,220,226 sphere

Changed 69 atom styles  
executed cMD.cxc  

> select /A:47@H133

1 atom, 1 residue, 1 model selected  

> select add /B:156@NE2

2 atoms, 2 residues, 1 model selected  

> distance sel

Distance between /A SU2 47 H133 and /B HID 156 NE2: 3.9Å  

> select /A:47@H81

1 atom, 1 residue, 1 model selected  

> select add /B:328@OD1

2 atoms, 2 residues, 1 model selected  

> distance sel

Distance between /A SU2 47 H81 and /B ASP 328 OD1: 1.8Å  

> select /A:59@OE1

1 atom, 1 residue, 1 model selected  

> label sel text E59

> label height 2

[Repeated 1 time(s)]Height must be a number  
[Repeated 2 time(s)]

> label height 1




OpenGL version: 3.3.0 NVIDIA 472.88
OpenGL renderer: Quadro RTX 5000 with Max-Q Design/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
Manufacturer: Dell Inc.
Model: Precision 7550
OS: Microsoft Windows 11 Enterprise (Build 22000)
Memory: 137,053,155,328
MaxProcessMemory: 137,438,953,344
CPU: 16 Intel(R) Xeon(R) W-10885M CPU @ 2.40GHz
OSLanguage: en-US
Locale: ('en_GB', 'cp1252')
PyQt5 5.15.2, Qt 5.15.2
Installed Packages:
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    appdirs: 1.4.4
    Babel: 2.9.1
    backcall: 0.2.0
    blockdiag: 2.0.1
    certifi: 2021.10.8
    cftime: 1.5.1.1
    charset-normalizer: 2.0.9
    ChimeraX-AddCharge: 1.2.2
    ChimeraX-AddH: 2.1.11
    ChimeraX-AlignmentAlgorithms: 2.0
    ChimeraX-AlignmentHdrs: 3.2
    ChimeraX-AlignmentMatrices: 2.0
    ChimeraX-Alignments: 2.2.3
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.0.1
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.0
    ChimeraX-Atomic: 1.31
    ChimeraX-AtomicLibrary: 4.2
    ChimeraX-AtomSearch: 2.0
    ChimeraX-AtomSearchLibrary: 1.0
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    ChimeraX-BasicActions: 1.1
    ChimeraX-BILD: 1.0
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    ChimeraX-ChemGroup: 2.0
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    ChimeraX-ColorActions: 1.0
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    ChimeraX-ColorKey: 1.5
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    ChimeraX-ConnectStructure: 2.0
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    ChimeraX-Core: 1.3
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    ChimeraX-CrystalContacts: 1.0
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    ChimeraX-DistMonitor: 1.1.5
    ChimeraX-DistUI: 1.0
    ChimeraX-Dssp: 2.0
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    ChimeraX-FunctionKey: 1.0
    ChimeraX-Geometry: 1.1
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.1
    ChimeraX-Hbonds: 2.1.2
    ChimeraX-Help: 1.2
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    ChimeraX-SideView: 1.0
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[Eric Pettersen]

Reported by Jozef Lewandowski

[Tom Goddard]

The label height option accepts a floating point value in ChimeraX 1.3, and I tested (on Mac) and it is working. So I don't understand this problem. The log in this bug report also does not show you trying "label height 1.5". Instead it shows "label height 2" giving this error. That makes no sense. Can you try again and tell me how you get this "Height must be a number" error?

In fact it makes even less sense, if I try "label height 1.2a" the error message I get in ChimeraX 1.3 is "Invalid "height" argument: Expected 'fixed' or a number". So I wonder have you redefined the label command?

> label height 2

[Repeated 1 time(s)]Height must be a number  
[Repeated 2 time(s)]

[Tom Goddard]

Begin forwarded message:

From: "Lewandowski, Jozef"

Hi Tom,

1. The log shows 2 because changed it to 2 (which worked) and only then decided to file the bug. The error came up when I tried 1.5.
2. I tracked that it happens for me only when I use the gui dialogue box (on Win I have not tried Mac). When I use command in the command line everything is OK.

Thanks,
Józef

[Tom Goddard]

Begin forwarded message:

From: "Lewandowski, Jozef"

P.S. I did not mess with label command (unless it is due to one of the plugins I installed).

Best,
Józef

[Tom Goddard]

I see now. The error is from the label height GUI, menu entry Actions / Set Label Height. I didn't know that existed since it was added by another developer. That bug was fixed 3 months ago. The fix is in the ChimeraX daily builds.

Duplicate of #5835