kerning

[jack.stevenson@…]

The following bug report has been submitted:
Platform:        macOS-10.16-x86_64-i386-64bit
ChimeraX Version: 1.3 (2021-12-08 23:08:33 UTC)
Description
In all text boxes,  kerning is weird after some letters.  In particular,  I notice problems after capital C and D: Cw,  Cy,  Cz, Cx, and Cv are kerned noticeably too wide.  I see this at least in the command line,  in this feedback text box and in the model panel.  Haven't checked every letter. Thanks!

Log:
Startup Messages  
---  
note | available bundle cache has not been initialized yet  
  
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 30xz

Fetching url http://files.rcsb.org/download/30xz.cif failed: HTTP Error 404:
Not Found  

> open 3oxz

Summary of feedback from opening 3oxz fetched from pdb  
---  
notes | Fetching compressed mmCIF 3oxz from
http://files.rcsb.org/download/3oxz.cif  
Fetching CCD 0LI from http://ligand-expo.rcsb.org/reports/0/0LI/0LI.cif  
  
3oxz title:  
Crystal structure of ABL kinase domain bound with a DFG-out inhibitor AP24534
[more info...]  
  
Chain information for 3oxz #1  
---  
Chain | Description | UniProt  
A | Tyrosine-protein kinase ABL1 | ABL1_MOUSE  
  
Non-standard residues in 3oxz #1  
---  
0LI —
3-(imidazo[1,2-b]pyridazin-3-ylethynyl)-4-methyl-N-{4-[(4-methylpiperazin-1-yl)methyl]-3-(trifluoromethyl)phenyl}benzamide
(Ponatinib)  
  

> open 3cs9

Summary of feedback from opening 3cs9 fetched from pdb  
---  
notes | Fetching compressed mmCIF 3cs9 from
http://files.rcsb.org/download/3cs9.cif  
Fetching CCD NIL from http://ligand-expo.rcsb.org/reports/N/NIL/NIL.cif  
  
3cs9 title:  
Human ABL kinase in complex with nilotinib [more info...]  
  
Chain information for 3cs9 #2  
---  
Chain | Description | UniProt  
A B C D | Proto-oncogene tyrosine-protein kinase ABL1 | ABL1_HUMAN  
  
Non-standard residues in 3cs9 #2  
---  
NIL — Nilotinib
(4-methyl-N-[3-(4-methyl-1H-imidazol-1-yl)-5-(trifluoromethyl)phenyl]-3-[(4-pyridin-3-ylpyrimidin-2-yl)amino]benzamide)  
  
3cs9 mmCIF Assemblies  
---  
1| author_and_software_defined_assembly  
2| author_and_software_defined_assembly  
3| author_and_software_defined_assembly  
4| author_and_software_defined_assembly  
  

> ui tool show Matchmaker

> matchmaker #!2 to #1

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 3oxz, chain A (#1) with 3cs9, chain B (#2), sequence alignment
score = 1373.8  
RMSD between 242 pruned atom pairs is 0.591 angstroms; (across all 244 pairs:
0.623)  
  

> select #1

2280 atoms, 2249 bonds, 3 pseudobonds, 358 residues, 2 models selected  

> ~select #1

Nothing selected  

> log metadata #1

Metadata for 3oxz #1  
---  
Title | Crystal structure of ABL kinase domain bound with a DFG-out inhibitor
AP24534  
Citation | Zhou, T., Commodore, L., Huang, W.S., Wang, Y., Thomas, M., Keats,
J., Xu, Q., Rivera, V.M., Shakespeare, W.C., Clackson, T., Dalgarno, D.C.,
Zhu, X. (2011). Structural Mechanism of the Pan-BCR-ABL Inhibitor Ponatinib
(AP24534): Lessons for Overcoming Kinase Inhibitor Resistance. Chem.Biol.Drug
Des., 77, 1-11. PMID: 21118377. DOI: 10.1111/j.1747-0285.2010.01054.x  
Non-standard residue | 0LI —
3-(imidazo[1,2-b]pyridazin-3-ylethynyl)-4-methyl-N-{4-[(4-methylpiperazin-1-yl)methyl]-3-(trifluoromethyl)phenyl}benzamide
(Ponatinib)  
Gene source | Mus musculus (mouse)  
Experimental method | X-ray diffraction  
Resolution | 2.2Å  
  
> log chains #1

Chain information for 3oxz #1  
---  
Chain | Description | UniProt  
A | Tyrosine-protein kinase ABL1 | ABL1_MOUSE  
  

> show #!1 target m

> view #1 clip false

> help help:user/tools/modelpanel.html

> hide #!1 target m

> show #!1 target m

> log metadata #1

Metadata for 3oxz #1  
---  
Title | Crystal structure of ABL kinase domain bound with a DFG-out inhibitor
AP24534  
Citation | Zhou, T., Commodore, L., Huang, W.S., Wang, Y., Thomas, M., Keats,
J., Xu, Q., Rivera, V.M., Shakespeare, W.C., Clackson, T., Dalgarno, D.C.,
Zhu, X. (2011). Structural Mechanism of the Pan-BCR-ABL Inhibitor Ponatinib
(AP24534): Lessons for Overcoming Kinase Inhibitor Resistance. Chem.Biol.Drug
Des., 77, 1-11. PMID: 21118377. DOI: 10.1111/j.1747-0285.2010.01054.x  
Non-standard residue | 0LI —
3-(imidazo[1,2-b]pyridazin-3-ylethynyl)-4-methyl-N-{4-[(4-methylpiperazin-1-yl)methyl]-3-(trifluoromethyl)phenyl}benzamide
(Ponatinib)  
Gene source | Mus musculus (mouse)  
Experimental method | X-ray diffraction  
Resolution | 2.2Å  
  
> log chains #1

Chain information for 3oxz #1  
---  
Chain | Description | UniProt  
A | Tyrosine-protein kinase ABL1 | ABL1_MOUSE  
  

> log metadata #1

Metadata for 3oxz #1  
---  
Title | Crystal structure of ABL kinase domain bound with a DFG-out inhibitor
AP24534  
Citation | Zhou, T., Commodore, L., Huang, W.S., Wang, Y., Thomas, M., Keats,
J., Xu, Q., Rivera, V.M., Shakespeare, W.C., Clackson, T., Dalgarno, D.C.,
Zhu, X. (2011). Structural Mechanism of the Pan-BCR-ABL Inhibitor Ponatinib
(AP24534): Lessons for Overcoming Kinase Inhibitor Resistance. Chem.Biol.Drug
Des., 77, 1-11. PMID: 21118377. DOI: 10.1111/j.1747-0285.2010.01054.x  
Non-standard residue | 0LI —
3-(imidazo[1,2-b]pyridazin-3-ylethynyl)-4-methyl-N-{4-[(4-methylpiperazin-1-yl)methyl]-3-(trifluoromethyl)phenyl}benzamide
(Ponatinib)  
Gene source | Mus musculus (mouse)  
Experimental method | X-ray diffraction  
Resolution | 2.2Å  
  
> log chains #1

Chain information for 3oxz #1  
---  
Chain | Description | UniProt  
A | Tyrosine-protein kinase ABL1 | ABL1_MOUSE  
  

> ui tool show "Selection Inspector"

> log metadata #1

Metadata for 3oxz #1  
---  
Title | Crystal structure of ABL kinase domain bound with a DFG-out inhibitor
AP24534  
Citation | Zhou, T., Commodore, L., Huang, W.S., Wang, Y., Thomas, M., Keats,
J., Xu, Q., Rivera, V.M., Shakespeare, W.C., Clackson, T., Dalgarno, D.C.,
Zhu, X. (2011). Structural Mechanism of the Pan-BCR-ABL Inhibitor Ponatinib
(AP24534): Lessons for Overcoming Kinase Inhibitor Resistance. Chem.Biol.Drug
Des., 77, 1-11. PMID: 21118377. DOI: 10.1111/j.1747-0285.2010.01054.x  
Non-standard residue | 0LI —
3-(imidazo[1,2-b]pyridazin-3-ylethynyl)-4-methyl-N-{4-[(4-methylpiperazin-1-yl)methyl]-3-(trifluoromethyl)phenyl}benzamide
(Ponatinib)  
Gene source | Mus musculus (mouse)  
Experimental method | X-ray diffraction  
Resolution | 2.2Å  
  
> log chains #1

Chain information for 3oxz #1  
---  
Chain | Description | UniProt  
A | Tyrosine-protein kinase ABL1 | ABL1_MOUSE  
  

> help help:user

> rename #1 Abl ponatinib

Expected a keyword  

> rename #1 "Abl ponatinib"

> rename #2 "Abl nilotinib"

> sym #2

Abl nilotinib mmCIF Assemblies  
---  
1| author_and_software_defined_assembly| 1 copy of chain A  
2| author_and_software_defined_assembly| 1 copy of chain B  
3| author_and_software_defined_assembly| 1 copy of chain C  
4| author_and_software_defined_assembly| 1 copy of chain D  
  

> log metadata #2

Metadata for Abl nilotinib #2  
---  
Title | Human ABL kinase in complex with nilotinib  
Citations | Weisberg, E., Manley, P.W., Breitenstein, W., Brueggen, J., Cowan-
Jacob, S.W., Ray, A., Huntly, B., Fabbro, D., Fendrich, G., Hall-Meyers, E.,
Kung, A.L., Mestan, J., Daley, G.Q., Callahan, L., Catley, L., Cavazza, C.,
Azam, M., Neuberg, D., Wright, R.D., Gilliland, D.G., Griffin, J.D. (2005).
Characterization of AMN107, a selective inhibitor of native and mutant Bcr-
Abl. Cancer Cell, 7, 129-141. PMID: 15710326. DOI: 10.1016/j.ccr.2005.01.007  
Vajpai, N., Strauss, A., Fendrich, G., Cowan-Jacob, S.W., Manley, P.W.,
Grzesiek, S., Jahnke, W. (?). Solution conformations and dynamics of ABL
kinase inhibitor complexes determined by NMR substantiate the different
binding modes of imatinib/nilotinib and dasatinib. To be Published  
Non-standard residue | NIL — Nilotinib
(4-methyl-N-[3-(4-methyl-1H-imidazol-1-yl)-5-(trifluoromethyl)phenyl]-3-[(4-pyridin-3-ylpyrimidin-2-yl)amino]benzamide)  
Gene source | Homo sapiens (human)  
Experimental method | X-ray diffraction  
Resolution | 2.20Å  
  
> log chains #2

Chain information for Abl nilotinib #2  
---  
Chain | Description | UniProt  
A B C D | Proto-oncogene tyrosine-protein kinase ABL1 | ABL1_HUMAN  
  

> rename #2 "Abl nilotinib 3cs9"

> rename #1 "Abl ponatinib 3oxz"

> open 2gqg

Summary of feedback from opening 2gqg fetched from pdb  
---  
warning | Atom P has no neighbors to form bonds with according to residue
template for PTR /A:393  
notes | Fetching compressed mmCIF 2gqg from
http://files.rcsb.org/download/2gqg.cif  
Fetching CCD 1N1 from http://ligand-expo.rcsb.org/reports/1/1N1/1N1.cif  
Fetching CCD GOL from http://ligand-expo.rcsb.org/reports/G/GOL/GOL.cif  
Fetching CCD PTR from http://ligand-expo.rcsb.org/reports/P/PTR/PTR.cif  
  
2gqg title:  
X-ray Crystal Structure of Dasatinib (BMS-354825) Bound to Activated ABL
Kinase Domain [more info...]  
  
Chain information for 2gqg #3  
---  
Chain | Description | UniProt  
A B | Proto-oncogene tyrosine-protein kinase ABL1 | ABL1_HUMAN  
  
Non-standard residues in 2gqg #3  
---  
1N1 —
N-(2-chloro-6-methylphenyl)-2-({6-[4-(2-hydroxyethyl)piperazin-1-yl]-2-methylpyrimidin-4-yl}amino)-1,3-thiazole-5-carboxamide
(Dasatinib)  
GOL — glycerol (glycerin; propane-1,2,3-triol)  
  
2gqg mmCIF Assemblies  
---  
1| author_defined_assembly  
2| author_defined_assembly  
  

> rename #3 "Abl dasatinib 2gqg"

> open 1iep

Summary of feedback from opening 1iep fetched from pdb  
---  
notes | Fetching compressed mmCIF 1iep from
http://files.rcsb.org/download/1iep.cif  
Fetching CCD CL from http://ligand-expo.rcsb.org/reports/C/CL/CL.cif  
Fetching CCD STI from http://ligand-expo.rcsb.org/reports/S/STI/STI.cif  
  
1iep title:  
Crystal structure of the C-abl kinase domain In complex with sti-571. [more
info...]  
  
Chain information for 1iep #4  
---  
Chain | Description | UniProt  
A B | proto-oncogene tyrosine-protein kinase abl | ABL1_MOUSE  
  
Non-standard residues in 1iep #4  
---  
CL — chloride ion  
STI — 4-(4-methyl-piperazin-1-ylmethyl)-N-[4-methyl-3-(4-pyridin-3-yl-
pyrimidin-2-ylamino)-phenyl]-benzamide (sti-571;imatinib)  
  
1iep mmCIF Assemblies  
---  
1| author_defined_assembly  
2| author_defined_assembly  
  

> rename #4 "Abl imatinib 1iep"

> open 3ue4

Summary of feedback from opening 3ue4 fetched from pdb  
---  
warning | Unable to fetch template for 'DB8': might have incorrect bonds  
note | Fetching compressed mmCIF 3ue4 from
http://files.rcsb.org/download/3ue4.cif  
  
3ue4 title:  
Structural and spectroscopic analysis of the kinase inhibitor bosutinib
binding to the Abl tyrosine kinase domain [more info...]  
  
Chain information for 3ue4 #5  
---  
Chain | Description | UniProt  
A B | Tyrosine-protein kinase ABL1 | ABL1_HUMAN  
  
Non-standard residues in 3ue4 #5  
---  
DB8 —
4-[(2,4-dichloro-5-methoxyphenyl)amino]-6-methoxy-7-[3-(4-methylpiperazin-1-yl)propoxy]quinoline-3-carbonitrile
(Bosutinib)  
  
3ue4 mmCIF Assemblies  
---  
1| author_and_software_defined_assembly  
2| author_and_software_defined_assembly  
  

> rename #5 "Abl bosutinib 3ue4"

> open 1opl

Summary of feedback from opening 1opl fetched from pdb  
---  
notes | Fetching compressed mmCIF 1opl from
http://files.rcsb.org/download/1opl.cif  
Fetching CCD MYR from http://ligand-expo.rcsb.org/reports/M/MYR/MYR.cif  
Fetching CCD P16 from http://ligand-expo.rcsb.org/reports/P/P16/P16.cif  
  
1opl title:  
Structural basis for the auto-inhibition of c-Abl tyrosine kinase [more
info...]  
  
Chain information for 1opl #6  
---  
Chain | Description | UniProt  
A B | proto-oncogene tyrosine-protein kinase | ABL1_HUMAN  
  
Non-standard residues in 1opl #6  
---  
MYR — myristic acid  
P16 —
6-(2,6-dichlorophenyl)-2-{[3-(hydroxymethyl)phenyl]amino}-8-methylpyrido[2,3-D]pyrimidin-7(8H)-one
(PD166326)  
  
1opl mmCIF Assemblies  
---  
1| author_defined_assembly  
2| author_and_software_defined_assembly  
3| software_defined_assembly  
  

> rename #6 "Abl myristic acid 1opl"

> open 5mo4

Summary of feedback from opening 5mo4 fetched from pdb  
---  
notes | Fetching compressed mmCIF 5mo4 from
http://files.rcsb.org/download/5mo4.cif  
Fetching CCD AY7 from http://ligand-expo.rcsb.org/reports/A/AY7/AY7.cif  
  
5mo4 title:  
ABL1 kinase (T334I_D382N) in complex with asciminib and nilotinib [more
info...]  
  
Chain information for 5mo4 #7  
---  
Chain | Description | UniProt  
A | Tyrosine-protein kinase ABL1 | ABL1_HUMAN  
  
Non-standard residues in 5mo4 #7  
---  
AY7 — asciminib  
NIL — Nilotinib
(4-methyl-N-[3-(4-methyl-1H-imidazol-1-yl)-5-(trifluoromethyl)phenyl]-3-[(4-pyridin-3-ylpyrimidin-2-yl)amino]benzamide)  
  

> rename #7 "Abl asciminib nilotonib 5mo4"

> ui tool show Matchmaker

> matchmaker #3-4#!2,5-7 to #1

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 Abl ponatinib 3oxz, chain A (#1) with Abl dasatinib 2gqg, chain B
(#3), sequence alignment score = 1361.8  
RMSD between 233 pruned atom pairs is 0.585 angstroms; (across all 256 pairs:
2.409)  
  
Matchmaker Abl ponatinib 3oxz, chain A (#1) with Abl imatinib 1iep, chain A
(#4), sequence alignment score = 1423.3  
RMSD between 248 pruned atom pairs is 0.529 angstroms; (across all 255 pairs:
0.929)  
  
Matchmaker Abl ponatinib 3oxz, chain A (#1) with Abl nilotinib 3cs9, chain B
(#2), sequence alignment score = 1373.8  
RMSD between 242 pruned atom pairs is 0.591 angstroms; (across all 244 pairs:
0.623)  
  
Matchmaker Abl ponatinib 3oxz, chain A (#1) with Abl bosutinib 3ue4, chain B
(#5), sequence alignment score = 1388.5  
RMSD between 238 pruned atom pairs is 0.619 angstroms; (across all 252 pairs:
2.418)  
  
Matchmaker Abl ponatinib 3oxz, chain A (#1) with Abl myristic acid 1opl, chain
A (#6), sequence alignment score = 1404.8  
RMSD between 230 pruned atom pairs is 0.619 angstroms; (across all 268 pairs:
4.522)  
  
Matchmaker Abl ponatinib 3oxz, chain A (#1) with Abl asciminib nilotonib 5mo4,
chain A (#7), sequence alignment score = 1398.8  
RMSD between 227 pruned atom pairs is 0.742 angstroms; (across all 260 pairs:
3.986)  
  

> open 5u8l

Summary of feedback from opening 5u8l fetched from pdb  
---  
notes | Fetching compressed mmCIF 5u8l from
http://files.rcsb.org/download/5u8l.cif  
Fetching CCD O44 from http://ligand-expo.rcsb.org/reports/O/O44/O44.cif  
Fetching CCD SO4 from http://ligand-expo.rcsb.org/reports/S/SO4/SO4.cif  
  
5u8l title:  
Crystal structure of EGFR kinase domain in complex with a sulfonyl fluoride
probe XO44 [more info...]  
  
Chain information for 5u8l #8  
---  
Chain | Description | UniProt  
A | Epidermal growth factor receptor | EGFR_HUMAN  
  
Non-standard residues in 5u8l #8  
---  
GOL — glycerol (glycerin; propane-1,2,3-triol)  
O44 —
4-[(4-{4-[(3-cyclopropyl-1H-pyrazol-5-yl)amino]-6-[(prop-2-yn-1-yl)carbamoyl]pyrimidin-2-yl}piperazin-1-yl)methyl]benzene-1-sulfonyl
fluoride  
SO4 — sulfate ion  
  

> rename #8 "EGFR XO44 5u8l"

> open 1fin

Summary of feedback from opening 1fin fetched from pdb  
---  
notes | Fetching compressed mmCIF 1fin from
http://files.rcsb.org/download/1fin.cif  
Fetching CCD ATP from http://ligand-expo.rcsb.org/reports/A/ATP/ATP.cif  
  
1fin title:  
Cyclin A-cyclin-dependent kinase 2 complex [more info...]  
  
Chain information for 1fin #9  
---  
Chain | Description | UniProt  
A C | cyclin-dependent kinase 2 | CDK2_HUMAN  
B D | cyclin A | CCNA2_HUMAN  
  
Non-standard residues in 1fin #9  
---  
ATP — adenosine-5'-triphosphate  
  
1fin mmCIF Assemblies  
---  
1| author_and_software_defined_assembly  
2| author_and_software_defined_assembly  
  

> rename #9 "CDK2 CycA ATP active 1fin"




OpenGL version: 4.1 INTEL-18.5.8
OpenGL renderer: Intel(R) Iris(TM) Plus Graphics 640
OpenGL vendor: Intel Inc.Hardware:

    Hardware Overview:

      Model Name: MacBook Pro
      Model Identifier: MacBookPro14,1
      Processor Name: Dual-Core Intel Core i5
      Processor Speed: 2.3 GHz
      Number of Processors: 1
      Total Number of Cores: 2
      L2 Cache (per Core): 256 KB
      L3 Cache: 4 MB
      Hyper-Threading Technology: Enabled
      Memory: 8 GB
      System Firmware Version: 429.140.8.0.0
      OS Loader Version: 540.100.7~23
      SMC Version (system): 2.43f11

Software:

    System Software Overview:

      System Version: macOS 12.3.1 (21E258)
      Kernel Version: Darwin 21.4.0
      Time since boot: 2:46

Graphics/Displays:

    Intel Iris Plus Graphics 640:

      Chipset Model: Intel Iris Plus Graphics 640
      Type: GPU
      Bus: Built-In
      VRAM (Dynamic, Max): 1536 MB
      Vendor: Intel
      Device ID: 0x5926
      Revision ID: 0x0006
      Metal Family: Supported, Metal GPUFamily macOS 2
      Displays:
        Color LCD:
          Display Type: Built-In Retina LCD
          Resolution: 2560 x 1600 Retina
          Framebuffer Depth: 24-Bit Color (ARGB8888)
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: No
          Connection Type: Internal

Locale: (None, 'UTF-8')
PyQt5 5.15.2, Qt 5.15.2
Installed Packages:
    alabaster: 0.7.12
    appdirs: 1.4.4
    appnope: 0.1.2
    Babel: 2.9.1
    backcall: 0.2.0
    blockdiag: 2.0.1
    certifi: 2021.5.30
    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
    ChimeraX-AxesPlanes: 2.0
    ChimeraX-BasicActions: 1.1
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 2.0
    ChimeraX-BondRot: 2.0
    ChimeraX-BugReporter: 1.0
    ChimeraX-BuildStructure: 2.6.1
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.1
    ChimeraX-ButtonPanel: 1.0
    ChimeraX-CageBuilder: 1.0
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.2
    ChimeraX-ChemGroup: 2.0
    ChimeraX-Clashes: 2.2.2
    ChimeraX-ColorActions: 1.0
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5
    ChimeraX-CommandLine: 1.1.5
    ChimeraX-ConnectStructure: 2.0
    ChimeraX-Contacts: 1.0
    ChimeraX-Core: 1.3
    ChimeraX-CoreFormats: 1.1
    ChimeraX-coulombic: 1.3.2
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0
    ChimeraX-DataFormats: 1.2.2
    ChimeraX-Dicom: 1.0
    ChimeraX-DistMonitor: 1.1.5
    ChimeraX-DistUI: 1.0
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ExperimentalCommands: 1.0
    ChimeraX-FileHistory: 1.0
    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
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.2
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.1
    ChimeraX-ItemsInspection: 1.0
    ChimeraX-Label: 1.1
    ChimeraX-ListInfo: 1.1.1
    ChimeraX-Log: 1.1.4
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.8.1
    ChimeraX-Map: 1.1
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0
    ChimeraX-MapFilter: 2.0
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.1
    ChimeraX-Markers: 1.0
    ChimeraX-Mask: 1.0
    ChimeraX-MatchMaker: 2.0.4
    ChimeraX-MDcrds: 2.6
    ChimeraX-MedicalToolbar: 1.0.1
    ChimeraX-Meeting: 1.0
    ChimeraX-MLP: 1.1
    ChimeraX-mmCIF: 2.4
    ChimeraX-MMTF: 2.1
    ChimeraX-Modeller: 1.2.6
    ChimeraX-ModelPanel: 1.2.1
    ChimeraX-ModelSeries: 1.0
    ChimeraX-Mol2: 2.0
    ChimeraX-Morph: 1.0
    ChimeraX-MouseModes: 1.1
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nucleotides: 2.0.2
    ChimeraX-OpenCommand: 1.7
    ChimeraX-PDB: 2.6.5
    ChimeraX-PDBBio: 1.0
    ChimeraX-PDBLibrary: 1.0.2
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.0.1
    ChimeraX-PubChem: 2.1
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1
    ChimeraX-RemoteControl: 1.0
    ChimeraX-ResidueFit: 1.0
    ChimeraX-RestServer: 1.1
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 2.0.1
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.5
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.4.6
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0
    ChimeraX-Shortcuts: 1.1
    ChimeraX-ShowAttr: 1.0
    ChimeraX-ShowSequences: 1.0
    ChimeraX-SideView: 1.0
    ChimeraX-Smiles: 2.1
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.6.1
    ChimeraX-STL: 1.0
    ChimeraX-Storm: 1.0
    ChimeraX-Struts: 1.0
    ChimeraX-Surface: 1.0
    ChimeraX-SwapAA: 2.0
    ChimeraX-SwapRes: 2.1
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.1
    ChimeraX-ToolshedUtils: 1.2
    ChimeraX-Tug: 1.0
    ChimeraX-UI: 1.13.7
    ChimeraX-uniprot: 2.2
    ChimeraX-UnitCell: 1.0
    ChimeraX-ViewDockX: 1.0.1
    ChimeraX-VIPERdb: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0
    ChimeraX-WebServices: 1.0
    ChimeraX-Zone: 1.0
    colorama: 0.4.4
    cxservices: 1.1
    cycler: 0.11.0
    Cython: 0.29.24
    decorator: 5.1.0
    docutils: 0.17.1
    filelock: 3.0.12
    funcparserlib: 0.3.6
    grako: 3.16.5
    h5py: 3.6.0
    html2text: 2020.1.16
    idna: 3.3
    ihm: 0.21
    imagecodecs: 2021.4.28
    imagesize: 1.3.0
    ipykernel: 5.5.5
    ipython: 7.23.1
    ipython-genutils: 0.2.0
    jedi: 0.18.0
    Jinja2: 3.0.1
    jupyter-client: 6.1.12
    jupyter-core: 4.9.1
    kiwisolver: 1.3.2
    lxml: 4.6.3
    lz4: 3.1.3
    MarkupSafe: 2.0.1
    matplotlib: 3.4.3
    matplotlib-inline: 0.1.3
    msgpack: 1.0.2
    netCDF4: 1.5.7
    networkx: 2.6.3
    numexpr: 2.8.0
    numpy: 1.21.2
    openvr: 1.16.801
    packaging: 21.0
    ParmEd: 3.2.0
    parso: 0.8.3
    pexpect: 4.8.0
    pickleshare: 0.7.5
    Pillow: 8.3.2
    pip: 21.2.4
    pkginfo: 1.7.1
    prompt-toolkit: 3.0.23
    psutil: 5.8.0
    ptyprocess: 0.7.0
    pycollada: 0.7.1
    pydicom: 2.1.2
    Pygments: 2.10.0
    PyOpenGL: 3.1.5
    PyOpenGL-accelerate: 3.1.5
    pyparsing: 3.0.6
    PyQt5-commercial: 5.15.2
    PyQt5-sip: 12.8.1
    PyQtWebEngine-commercial: 5.15.2
    python-dateutil: 2.8.2
    pytz: 2021.3
    pyzmq: 22.3.0
    qtconsole: 5.1.1
    QtPy: 1.11.3
    RandomWords: 0.3.0
    requests: 2.26.0
    scipy: 1.7.1
    setuptools: 57.5.0
    sfftk-rw: 0.7.1
    six: 1.16.0
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    Sphinx: 4.2.0
    sphinx-autodoc-typehints: 1.12.0
    sphinxcontrib-applehelp: 1.0.2
    sphinxcontrib-blockdiag: 2.0.0
    sphinxcontrib-devhelp: 1.0.2
    sphinxcontrib-htmlhelp: 2.0.0
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 1.0.3
    sphinxcontrib-serializinghtml: 1.1.5
    suds-jurko: 0.6
    tifffile: 2021.4.8
    tinyarray: 1.2.3
    tornado: 6.1
    traitlets: 5.1.1
    urllib3: 1.26.7
    wcwidth: 0.2.5
    webcolors: 1.11.1
    wheel: 0.37.0
    wheel-filename: 1.3.0
File attachment: Screen Shot 2022-06-07 at 13.27.04.png

Screen Shot 2022-06-07 at 13.27.04.png​

[jack.stevenson@…]

Added by email2trac

[pett]

Hi Jack,
	This kerning issue does not occur on my Mac:



Could you try the ChimeraX 1.4 release candidate?  That uses an entirely new version of the Qt windowing toolkit, which might solve this issue without us needing to do anything specific.

--Eric

	Eric Pettersen
	UCSF Computer Graphics Lab

[pett]

Added by email2trac

[Jack.Stevenson@…]

Hi, Eric. On rc2022-06-03 this issue is resolved for me too!
Jack

[pett]

Excellent!

--Eric