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Opened 2 years ago
Closed 2 years ago
#9110 closed defect (limitation)
Hiding/showing model changes lighting
| Reported by: | Owned by: | Tom Goddard | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Depiction | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: macOS-10.16-x86_64-i386-64bit
ChimeraX Version: 1.6.1 (2023-05-09 17:57:07 UTC)
Description
I am trying to produce parallel images of the same view of the same model of a protein and ligand with and without showing a second ligand from a different model that I have aligned. In practice, I have a model (#1) in which I show the protein surface and the first ligand, and a second model (#7) in which I have just the second ligand shown.
Unexpectedly, hiding and unhiding this second model seems to change the lighting appearance of the first model! When I unhide the model with the second ligand, shadows appear on distant parts of the protein surface that are definitely not cast by the ligand. This behavior happens on every lighting preset except simple, and unless I'm missing something I think it is undesired.
It doesn't seem like I can attach multiple files, so I am attaching a Chimera session that is set up to demonstrate this behavior. Please try hiding and unhiding #7 to see the effect on the lighting.
Log:
UCSF ChimeraX version: 1.6.1 (2023-05-09)
© 2016-2023 Regents of the University of California. All rights reserved.
> open "/Users/jackstevenson/Desktop/2023-06-01 bug report session ponatinib
> and asciminib.cxs"
Log from Thu Jun 1 17:11:29 2023UCSF ChimeraX version: 1.6.1 (2023-05-09)
© 2016-2023 Regents of the University of California. All rights reserved.
> open "/Users/jackstevenson/Library/CloudStorage/Box-Box/Shokat/Bcr-Abl
> project/Bcr-Abl figures/PonatiLink illustration.cxs"
Log from Wed May 31 14:50:19 2023UCSF ChimeraX version: 1.5 (2022-11-24)
© 2016-2022 Regents of the University of California. All rights reserved.
> open "/Users/jackstevenson/Desktop/PonatiLink illustration.cxs"
Log from Thu May 25 17:47:11 2023UCSF ChimeraX version: 1.5 (2022-11-24)
© 2016-2022 Regents of the University of California. All rights reserved.
> open "/Users/jackstevenson/Desktop/PonatiLink illustration.cxs"
Log from Thu May 25 17:06:04 2023UCSF ChimeraX version: 1.5 (2022-11-24)
© 2016-2022 Regents of the University of California. All rights reserved.
> open "/Users/jackstevenson/Library/CloudStorage/Box-
> Box/Shokat/structures/PonatiLink illustration 2023-05.cxs"
Log from Fri Feb 17 18:35:47 2023UCSF ChimeraX version: 1.4 (2022-06-03)
© 2016-2022 Regents of the University of California. All rights reserved.
> open "/Users/stevenson/Library/CloudStorage/Box-Box/Shokat/structures/kinase
> comparison.cxs"
Log from Thu Jun 9 17:22:25 2022UCSF ChimeraX version: 1.3 (2021-12-08)
© 2016-2021 Regents of the University of California. All rights reserved.
> open "/Users/stevenson/Library/CloudStorage/Box-Box/Shokat/structures/kinase
> comparison.cxs"
Log from Thu Jun 9 14:14:26 2022UCSF ChimeraX version: 1.3 (2021-12-08)
© 2016-2021 Regents of the University of California. All rights reserved.
> open "/Users/stevenson/Library/CloudStorage/Box-Box/Shokat/structures/kinase
> comparison.cxs"
Log from Tue Jun 7 19:50:43 2022UCSF ChimeraX version: 1.3 (2021-12-08)
© 2016-2021 Regents of the University of California. All rights reserved.
> open "/Users/stevenson/Library/CloudStorage/Box-Box/Shokat/structures/kinase
> comparison.cxs"
Log from Tue Jun 7 19:46:25 2022UCSF ChimeraX version: 1.3 (2021-12-08)
© 2016-2021 Regents of the University of California. All rights reserved.
> open "/Users/stevenson/Library/CloudStorage/Box-Box/Shokat/structures/kinase
> comparison.cxs"
Log from Tue Jun 7 19:28:57 2022 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"
> open 1yoj
Summary of feedback from opening 1yoj fetched from pdb
---
note | Fetching compressed mmCIF 1yoj from
http://files.rcsb.org/download/1yoj.cif
1yoj title:
Crystal structure of Src kinase domain [more info...]
Chain information for 1yoj #10
---
Chain | Description | UniProt
A B | proto-oncogene tyrosine-protein kinase SRC | SRC_HUMAN
1yoj mmCIF Assemblies
---
1| author_defined_assembly
2| author_defined_assembly
> rename #10 "Src 1yoj"
> open 7kjs
Summary of feedback from opening 7kjs fetched from pdb
---
notes | Fetching compressed mmCIF 7kjs from
http://files.rcsb.org/download/7kjs.cif
Fetching CCD WG1 from http://ligand-expo.rcsb.org/reports/W/WG1/WG1.cif
7kjs title:
Crystal structure of CDK2/cyclin E in complex with PF-06873600 [more info...]
Chain information for 7kjs #11
---
Chain | Description | UniProt
A | Cyclin-dependent kinase 2 | CDK2_HUMAN
B | G1/S-specific cyclin-E1 | CCNE1_HUMAN
Non-standard residues in 7kjs #11
---
WG1 —
6-(difluoromethyl)-8-[(1R,2R)-2-hydroxy-2-methylcyclopentyl]-2-{[1-(methylsulfonyl)piperidin-4-yl]amino}pyrido[2,3-d]pyrimidin-7(8H)-one
> rename #11 "CDK2 CycE1 PF-06873600 7kjs"
> log metadata #11
Metadata for CDK2 CycE1 PF-06873600 7kjs #11
---
Title | Crystal structure of CDK2/cyclin E in complex with PF-06873600
Citation | Freeman-Cook, K.D., Hoffman, R.L., Behenna, D.C., Boras, B.,
Carelli, J., Diehl, W., Ferre, R.A., He, Y.A., Hui, A., Huang, B., Huser, N.,
Jones, R., Kephart, S.E., Lapek, J., McTigue, M., Miller, N., Murray, B.W.,
Nagata, A., Nguyen, L., Niessen, S., Ninkovic, S., O'Doherty, I., Ornelas,
M.A., Solowiej, J., Sutton, S.C., Tran, K., Tseng, E., Visswanathan, R., Xu,
M., Zehnder, L., Zhang, Q., Zhang, C., Dann, S. (2021). Discovery of
PF-06873600, a CDK2/4/6 Inhibitor for the Treatment of Cancer. J.Med.Chem.,
64, 9056-9077. PMID: 34110834. DOI: 10.1021/acs.jmedchem.1c00159
Non-standard residue | WG1 —
6-(difluoromethyl)-8-[(1R,2R)-2-hydroxy-2-methylcyclopentyl]-2-{[1-(methylsulfonyl)piperidin-4-yl]amino}pyrido[2,3-d]pyrimidin-7(8H)-one
Gene source | Homo sapiens (human)
Experimental method | X-ray diffraction
Resolution | 2.187Å
> log chains #11
Chain information for CDK2 CycE1 PF-06873600 7kjs #11
---
Chain | Description | UniProt
A | Cyclin-dependent kinase 2 | CDK2_HUMAN
B | G1/S-specific cyclin-E1 | CCNE1_HUMAN
> log metadata #11
Metadata for CDK2 CycE1 PF-06873600 7kjs #11
---
Title | Crystal structure of CDK2/cyclin E in complex with PF-06873600
Citation | Freeman-Cook, K.D., Hoffman, R.L., Behenna, D.C., Boras, B.,
Carelli, J., Diehl, W., Ferre, R.A., He, Y.A., Hui, A., Huang, B., Huser, N.,
Jones, R., Kephart, S.E., Lapek, J., McTigue, M., Miller, N., Murray, B.W.,
Nagata, A., Nguyen, L., Niessen, S., Ninkovic, S., O'Doherty, I., Ornelas,
M.A., Solowiej, J., Sutton, S.C., Tran, K., Tseng, E., Visswanathan, R., Xu,
M., Zehnder, L., Zhang, Q., Zhang, C., Dann, S. (2021). Discovery of
PF-06873600, a CDK2/4/6 Inhibitor for the Treatment of Cancer. J.Med.Chem.,
64, 9056-9077. PMID: 34110834. DOI: 10.1021/acs.jmedchem.1c00159
Non-standard residue | WG1 —
6-(difluoromethyl)-8-[(1R,2R)-2-hydroxy-2-methylcyclopentyl]-2-{[1-(methylsulfonyl)piperidin-4-yl]amino}pyrido[2,3-d]pyrimidin-7(8H)-one
Gene source | Homo sapiens (human)
Experimental method | X-ray diffraction
Resolution | 2.187Å
> log chains #11
Chain information for CDK2 CycE1 PF-06873600 7kjs #11
---
Chain | Description | UniProt
A | Cyclin-dependent kinase 2 | CDK2_HUMAN
B | G1/S-specific cyclin-E1 | CCNE1_HUMAN
> rename #10 #12
No name or id option specified for renaming
> rename #10 id #12
> rename #9 id #10
> rename #12 id #9
> open 6p8g
Summary of feedback from opening 6p8g fetched from pdb
---
note | Fetching compressed mmCIF 6p8g from
http://files.rcsb.org/download/6p8g.cif
6p8g title:
Crystal structure of CDK4 in complex with CyclinD1 and P27 [more info...]
Chain information for 6p8g #12
---
Chain | Description | UniProt
A | G1/S-specific cyclin-D1 | CCND1_HUMAN
B | Cyclin-dependent kinase 4 | CDK4_HUMAN
C | Cyclin-dependent kinase inhibitor 1B | CDN1B_HUMAN
> ui tool show Matchmaker
> matchmaker #10#!9,11-12 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 CDK2 CycA ATP active 1fin,
chain C (#10), sequence alignment score = 382
RMSD between 148 pruned atom pairs is 1.099 angstroms; (across all 243 pairs:
7.338)
Matchmaker Abl ponatinib 3oxz, chain A (#1) with Src 1yoj, chain A (#9),
sequence alignment score = 716.1
RMSD between 205 pruned atom pairs is 0.859 angstroms; (across all 230 pairs:
2.958)
Matchmaker Abl ponatinib 3oxz, chain A (#1) with CDK2 CycE1 PF-06873600 7kjs,
chain A (#11), sequence alignment score = 379
RMSD between 149 pruned atom pairs is 1.037 angstroms; (across all 243 pairs:
7.614)
Matchmaker Abl ponatinib 3oxz, chain A (#1) with 6p8g, chain B (#12), sequence
alignment score = 277.3
RMSD between 112 pruned atom pairs is 1.082 angstroms; (across all 219 pairs:
6.618)
> ui tool show Matchmaker
> matchmaker #8#!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 EGFR XO44 5u8l, chain A (#8),
sequence alignment score = 625.5
RMSD between 200 pruned atom pairs is 0.845 angstroms; (across all 255 pairs:
4.178)
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)
> hide #!2 models
> hide #3 models
> hide #4 models
> hide #!5 models
> hide #!6 models
> hide #!7 models
> hide #8 models
> hide #!9 models
> hide #10 models
> hide #!11 models
> cofr frontCenter
> cofr centerOfView
> ui tool show "Side View"
> save "/Users/stevenson/Library/CloudStorage/Box-Box/Shokat/structures/kinase
> comparison.cxs"
> hide #!1 models
> select #12/C:73
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #12/C:74
9 atoms, 8 bonds, 1 residue, 1 model selected
> ui tool show "Show Sequence Viewer"
> sequence chain #12/A
Alignment identifier is 12/A
> open 6p8f
Summary of feedback from opening 6p8f fetched from pdb
---
note | Fetching compressed mmCIF 6p8f from
http://files.rcsb.org/download/6p8f.cif
6p8f title:
Crystal structure of CDK4 in complex with CyclinD1 and P27 [more info...]
Chain information for 6p8f #13
---
Chain | Description | UniProt
A | G1/S-specific cyclin-D1 | CCND1_HUMAN
B | Cyclin-dependent kinase 4 | CDK4_HUMAN
C | Cyclin-dependent kinase inhibitor 1B | CDN1B_HUMAN
> ui tool show Matchmaker
> matchmaker #8,10#!9,11-13 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 EGFR XO44 5u8l, chain A (#8),
sequence alignment score = 625.5
RMSD between 200 pruned atom pairs is 0.845 angstroms; (across all 255 pairs:
4.178)
Matchmaker Abl ponatinib 3oxz, chain A (#1) with CDK2 CycA ATP active 1fin,
chain C (#10), sequence alignment score = 382
RMSD between 148 pruned atom pairs is 1.099 angstroms; (across all 243 pairs:
7.338)
Matchmaker Abl ponatinib 3oxz, chain A (#1) with Src 1yoj, chain A (#9),
sequence alignment score = 716.1
RMSD between 205 pruned atom pairs is 0.859 angstroms; (across all 230 pairs:
2.958)
Matchmaker Abl ponatinib 3oxz, chain A (#1) with CDK2 CycE1 PF-06873600 7kjs,
chain A (#11), sequence alignment score = 379
RMSD between 149 pruned atom pairs is 1.037 angstroms; (across all 243 pairs:
7.614)
Matchmaker Abl ponatinib 3oxz, chain A (#1) with 6p8g, chain B (#12), sequence
alignment score = 277.3
RMSD between 112 pruned atom pairs is 1.082 angstroms; (across all 219 pairs:
6.618)
Matchmaker Abl ponatinib 3oxz, chain A (#1) with 6p8f, chain B (#13), sequence
alignment score = 315.1
RMSD between 115 pruned atom pairs is 1.122 angstroms; (across all 222 pairs:
6.634)
> select clear
> ui tool show "Show Sequence Viewer"
> sequence chain #13/C
Alignment identifier is 13/C
> ui tool show "Show Sequence Viewer"
> sequence chain #12/C
Alignment identifier is 12/C
> rename #12 "CDK4 CycD1 p27 phosphomimetic 6p8g"
> rename #12 "K4-D1-p27 phosphomimetic 6p8g"
> rename #13 "K4-D1-phosphop27 6p8f"
> rename #12 "K4-D1-phosphomimetic p27 6p8g"
> rename #13 "K4-D1-phospho p27 6p8f"
> save "/Users/stevenson/Library/CloudStorage/Box-Box/Shokat/structures/kinase
> comparison.cxs"
[Repeated 1 time(s)]
——— End of log from Tue Jun 7 19:28:57 2022 ———
opened ChimeraX session
> open 6p8e
6p8e title:
Crystal structure of CDK4 in complex with CyclinD1 and P27 [more info...]
Chain information for 6p8e #14
---
Chain | Description | UniProt
A | G1/S-specific cyclin-D1 | CCND1_HUMAN
B | Cyclin-dependent kinase 4 | CDK4_HUMAN
C | Cyclin-dependent kinase inhibitor 1B | CDN1B_HUMAN
Non-standard residues in 6p8e #14
---
MG — magnesium ion
> rename #14 "K4-D1-unphos p27 6p8e"
> open 6p8h
6p8h title:
Crystal structure of CDK4 in complex with CyclinD1 and P21 [more info...]
Chain information for 6p8h #15
---
Chain | Description | UniProt
A | G1/S-specific cyclin-D1 | CCND1_HUMAN
B | Cyclin-dependent kinase 4 | CDK4_HUMAN
C | Cyclin-dependent kinase inhibitor 1 | CDN1A_HUMAN
> open 5l2i
5l2i title:
The X-ray co-crystal structure of human CDK6 and Palbociclib. [more info...]
Chain information for 5l2i #16
---
Chain | Description | UniProt
A | Cyclin-dependent kinase 6 | CDK6_HUMAN
Non-standard residues in 5l2i #16
---
LQQ —
6-acetyl-8-cyclopentyl-5-methyl-2-[(5-piperazin-1-ylpyridin-2-yl)amino]pyrido[2,3-D]pyrimidin-7(8H)-one
(Palbociclib)
> open 5l2t
5l2t title:
The X-ray co-crystal structure of human CDK6 and Ribociclib. [more info...]
Chain information for 5l2t #17
---
Chain | Description | UniProt
A | Cyclin-dependent kinase 6 | CDK6_HUMAN
Non-standard residues in 5l2t #17
---
6ZZ —
7-cyclopentyl-N,N-dimethyl-2-{[5-(piperazin-1-yl)pyridin-2-yl]amino}-7H-pyrrolo[2,3-d]pyrimidine-6-carboxamide
(Ribociclib)
> open 2w96
2w96 title:
Crystal Structure of CDK4 in complex with a D-type cyclin [more info...]
Chain information for 2w96 #18
---
Chain | Description | UniProt
A | G1/S-specific cyclin-D1 | CCND1_HUMAN
B | cell division protein kinase 4 | CDK4_HUMAN
Non-standard residues in 2w96 #18
---
GOL — glycerol (glycerin; propane-1,2,3-triol)
> open 1blx
1blx title:
P19INK4D/CDK6 complex [more info...]
Chain information for 1blx #19
---
Chain | Description | UniProt
A | cyclin-dependent kinase 6 | CDK6_HUMAN
B | P19INK4D | CDN2D_MOUSE
Non-standard residues in 1blx #19
---
CA — calcium ion
> open 2bkk
2bkk title:
Crystal structure of Aminoglycoside Phosphotransferase APH(3')-IIIa in complex
with the inhibitor AR_3a [more info...]
Chain information for 2bkk #20
---
Chain | Description | UniProt
A C | aminoglycoside 3'-phosphotransferase | KKA3_ENTFA
B D | designed ankyrin repeat inhibitor Ar_3A |
Non-standard residues in 2bkk #20
---
ADP — adenosine-5'-diphosphate
MG — magnesium ion
2bkk mmCIF Assemblies
---
1| author_and_software_defined_assembly
2| author_and_software_defined_assembly
> rename #15 "K4-D1-p21 6p8h"
> rename #16 "CDK6 palbociclib 5l2i"
> rename #17 "CDK6 ribociclib 5l2t"
> rename #18 CDK4 CycD1 2w96
Expected a keyword
> rename #18 "CDK4 CycD1 2w96"
> rename #19 "CDK6 p19 1blx"
> rename #20 "APH(3')-IIIa N87T 2nd-site suppressor 2bkk"
> save "/Users/stevenson/Library/CloudStorage/Box-Box/Shokat/structures/kinase
> comparison.cxs"
——— End of log from Tue Jun 7 19:46:25 2022 ———
opened ChimeraX session
> ui tool show Matchmaker
> matchmaker #3-4,8,10#!1-2,5-7,11-20 to #9
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 Src 1yoj, chain A (#9) with Abl dasatinib 2gqg, chain A (#3),
sequence alignment score = 736.3
RMSD between 208 pruned atom pairs is 0.830 angstroms; (across all 223 pairs:
1.571)
Matchmaker Src 1yoj, chain A (#9) with Abl imatinib 1iep, chain A (#4),
sequence alignment score = 730.9
RMSD between 201 pruned atom pairs is 0.961 angstroms; (across all 221 pairs:
1.545)
Matchmaker Src 1yoj, chain A (#9) with EGFR XO44 5u8l, chain A (#8), sequence
alignment score = 537.7
RMSD between 189 pruned atom pairs is 1.004 angstroms; (across all 227 pairs:
2.140)
Matchmaker Src 1yoj, chain A (#9) with CDK2 CycA ATP active 1fin, chain C
(#10), sequence alignment score = 399
RMSD between 147 pruned atom pairs is 1.001 angstroms; (across all 223 pairs:
5.863)
Matchmaker Src 1yoj, chain A (#9) with Abl ponatinib 3oxz, chain A (#1),
sequence alignment score = 716.1
RMSD between 205 pruned atom pairs is 0.859 angstroms; (across all 230 pairs:
2.958)
Matchmaker Src 1yoj, chain A (#9) with Abl nilotinib 3cs9, chain C (#2),
sequence alignment score = 744.4
RMSD between 188 pruned atom pairs is 0.942 angstroms; (across all 220 pairs:
1.551)
Matchmaker Src 1yoj, chain A (#9) with Abl bosutinib 3ue4, chain A (#5),
sequence alignment score = 738.3
RMSD between 209 pruned atom pairs is 0.862 angstroms; (across all 225 pairs:
1.703)
Matchmaker Src 1yoj, chain A (#9) with Abl myristic acid 1opl, chain B (#6),
sequence alignment score = 724.4
RMSD between 203 pruned atom pairs is 0.934 angstroms; (across all 222 pairs:
1.535)
Matchmaker Src 1yoj, chain A (#9) with Abl asciminib nilotonib 5mo4, chain A
(#7), sequence alignment score = 699.6
RMSD between 195 pruned atom pairs is 0.943 angstroms; (across all 224 pairs:
2.923)
Matchmaker Src 1yoj, chain A (#9) with CDK2 CycE1 PF-06873600 7kjs, chain A
(#11), sequence alignment score = 385.2
RMSD between 143 pruned atom pairs is 1.098 angstroms; (across all 222 pairs:
7.664)
Matchmaker Src 1yoj, chain A (#9) with K4-D1-phosphomimetic p27 6p8g, chain B
(#12), sequence alignment score = 251.6
RMSD between 109 pruned atom pairs is 1.050 angstroms; (across all 197 pairs:
7.899)
Matchmaker Src 1yoj, chain A (#9) with K4-D1-phospho p27 6p8f, chain B (#13),
sequence alignment score = 283.3
RMSD between 110 pruned atom pairs is 1.046 angstroms; (across all 197 pairs:
4.159)
Matchmaker Src 1yoj, chain A (#9) with K4-D1-unphos p27 6p8e, chain B (#14),
sequence alignment score = 290.2
RMSD between 108 pruned atom pairs is 0.984 angstroms; (across all 199 pairs:
6.593)
Matchmaker Src 1yoj, chain A (#9) with K4-D1-p21 6p8h, chain B (#15), sequence
alignment score = 275.6
RMSD between 98 pruned atom pairs is 1.007 angstroms; (across all 195 pairs:
7.033)
Matchmaker Src 1yoj, chain A (#9) with CDK6 palbociclib 5l2i, chain A (#16),
sequence alignment score = 331.1
RMSD between 119 pruned atom pairs is 1.084 angstroms; (across all 208 pairs:
4.914)
Matchmaker Src 1yoj, chain A (#9) with CDK6 ribociclib 5l2t, chain A (#17),
sequence alignment score = 331.1
RMSD between 121 pruned atom pairs is 1.084 angstroms; (across all 209 pairs:
4.908)
Matchmaker Src 1yoj, chain A (#9) with CDK4 CycD1 2w96, chain B (#18),
sequence alignment score = 269.1
RMSD between 97 pruned atom pairs is 1.005 angstroms; (across all 204 pairs:
3.447)
Matchmaker Src 1yoj, chain A (#9) with CDK6 p19 1blx, chain A (#19), sequence
alignment score = 334.3
RMSD between 117 pruned atom pairs is 1.056 angstroms; (across all 223 pairs:
6.177)
Matchmaker Src 1yoj, chain A (#9) with APH(3')-IIIa N87T 2nd-site suppressor
2bkk, chain C (#20), sequence alignment score = 64.4
RMSD between 7 pruned atom pairs is 1.482 angstroms; (across all 142 pairs:
21.872)
> hide #!12 models
> hide #!13 models
> hide #!14 models
> hide #!16 models
> hide #!15 models
> hide #!17 models
> hide #!18 models
> hide #!19 models
> hide #!20 models
> show #!7 models
> hide #!7 models
> show #!1 models
> save "/Users/stevenson/Library/CloudStorage/Box-Box/Shokat/structures/kinase
> comparison.cxs"
——— End of log from Tue Jun 7 19:50:43 2022 ———
opened ChimeraX session
> show #!7 models
> select #7
3762 atoms, 3551 bonds, 2 pseudobonds, 738 residues, 2 models selected
> ui tool show "Color Actions"
> color sel cornsilk
> color sel old lace
> color sel light yellow
> color sel white smoke
> color sel beige
> color sel wheat
> color sel seashell
> color sel cornsilk
> color sel byhetero
> ~select #7
Nothing selected
> select #1
2280 atoms, 2249 bonds, 3 pseudobonds, 358 residues, 2 models selected
> ~select #1
Nothing selected
> select #1
2280 atoms, 2249 bonds, 3 pseudobonds, 358 residues, 2 models selected
> ui tool show "Color Actions"
> color sel pale turquoise
> color sel dodger blue
> color sel dark turquoise
> color sel cornflower blue
> color sel byhetero
> select clear
> ui tool show Matchmaker
> matchmaker #3-4,8,10#!2,5-7,9,11-20 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 EGFR XO44 5u8l, chain A (#8),
sequence alignment score = 625.5
RMSD between 200 pruned atom pairs is 0.845 angstroms; (across all 255 pairs:
4.178)
Matchmaker Abl ponatinib 3oxz, chain A (#1) with CDK2 CycA ATP active 1fin,
chain C (#10), sequence alignment score = 382
RMSD between 148 pruned atom pairs is 1.099 angstroms; (across all 243 pairs:
7.338)
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)
Matchmaker Abl ponatinib 3oxz, chain A (#1) with Src 1yoj, chain A (#9),
sequence alignment score = 716.1
RMSD between 205 pruned atom pairs is 0.859 angstroms; (across all 230 pairs:
2.958)
Matchmaker Abl ponatinib 3oxz, chain A (#1) with CDK2 CycE1 PF-06873600 7kjs,
chain A (#11), sequence alignment score = 379
RMSD between 149 pruned atom pairs is 1.037 angstroms; (across all 243 pairs:
7.614)
Matchmaker Abl ponatinib 3oxz, chain A (#1) with K4-D1-phosphomimetic p27
6p8g, chain B (#12), sequence alignment score = 277.3
RMSD between 112 pruned atom pairs is 1.082 angstroms; (across all 219 pairs:
6.618)
Matchmaker Abl ponatinib 3oxz, chain A (#1) with K4-D1-phospho p27 6p8f, chain
B (#13), sequence alignment score = 315.1
RMSD between 115 pruned atom pairs is 1.122 angstroms; (across all 222 pairs:
6.634)
Matchmaker Abl ponatinib 3oxz, chain A (#1) with K4-D1-unphos p27 6p8e, chain
B (#14), sequence alignment score = 319.9
RMSD between 113 pruned atom pairs is 1.050 angstroms; (across all 216 pairs:
6.668)
Matchmaker Abl ponatinib 3oxz, chain A (#1) with K4-D1-p21 6p8h, chain B
(#15), sequence alignment score = 305.9
RMSD between 104 pruned atom pairs is 1.133 angstroms; (across all 214 pairs:
6.793)
Matchmaker Abl ponatinib 3oxz, chain A (#1) with CDK6 palbociclib 5l2i, chain
A (#16), sequence alignment score = 347.5
RMSD between 138 pruned atom pairs is 1.115 angstroms; (across all 222 pairs:
4.832)
Matchmaker Abl ponatinib 3oxz, chain A (#1) with CDK6 ribociclib 5l2t, chain A
(#17), sequence alignment score = 337.5
RMSD between 140 pruned atom pairs is 1.168 angstroms; (across all 219 pairs:
4.693)
Matchmaker Abl ponatinib 3oxz, chain A (#1) with CDK4 CycD1 2w96, chain B
(#18), sequence alignment score = 292.5
RMSD between 126 pruned atom pairs is 1.235 angstroms; (across all 230 pairs:
5.745)
Matchmaker Abl ponatinib 3oxz, chain A (#1) with CDK6 p19 1blx, chain A (#19),
sequence alignment score = 330.7
RMSD between 129 pruned atom pairs is 1.095 angstroms; (across all 246 pairs:
6.987)
Matchmaker Abl ponatinib 3oxz, chain A (#1) with APH(3')-IIIa N87T 2nd-site
suppressor 2bkk, chain B (#20), sequence alignment score = 65.7
RMSD between 6 pruned atom pairs is 1.423 angstroms; (across all 102 pairs:
18.433)
> save "/Users/stevenson/Library/CloudStorage/Box-Box/Shokat/structures/kinase
> comparison.cxs"
——— End of log from Thu Jun 9 14:14:26 2022 ———
opened ChimeraX session
> show #3 models
> hide #!1 models
> select #3
4887 atoms, 4699 bonds, 868 residues, 1 model selected
> ui tool show "Color Actions"
> color sel tomato
[Repeated 1 time(s)]
> color sel indian red
> ui tool show "Color Actions"
> color sel byhetero
> select clear
> hide #!7 models
> show #!1 models
> ui tool show "Side View"
> select #5
4588 atoms, 4551 bonds, 1 pseudobond, 692 residues, 2 models selected
> ui tool show "Color Actions"
> color sel slate blue
> show #!5 models
> color sel byhetero
> ~select #5
Nothing selected
> hide #!5 models
> select #4
4710 atoms, 4658 bonds, 728 residues, 1 model selected
> show #4 models
> ui tool show "Color Actions"
> color sel blanched almond
> color sel ghost white
> color sel mint cream
> color sel white smoke
> color sel linen
> color sel old lace
> color sel byhetero
> ~select #4
Nothing selected
> hide #4 models
> select #4
4710 atoms, 4658 bonds, 728 residues, 1 model selected
> show #4 models
> ui tool show "Color Actions"
> color sel light gray
> color sel gray
> color sel dark gray
> color sel byhetero
> ~select #4
Nothing selected
> hide #4 models
> show #!6 models
> select #6
6655 atoms, 6832 bonds, 1 pseudobond, 819 residues, 2 models selected
> ui tool show "Color Actions"
QMainWindowLayout::tabPosition called with out-of-bounds value '0'
> color sel lime green
> color sel forest green
> color sel sea green
> color sel olive drab
> color sel sea green
> color sel steel blue
> color sel light slate gray
> color sel byhetero
> hide #!6 models
> ~select #6
Nothing selected
> select #9
3848 atoms, 3701 bonds, 7 pseudobonds, 675 residues, 2 models selected
> color #1,3 medium blue
> show #!9 models
> hide #!9 models
> undo
[Repeated 2 time(s)]
> show #!6 models
> hide #!6 models
> show #!6 models
> hide #!6 models
> show #!9 models
> color (#!9 & sel) medium blue
> color (#!9 & sel) byhetero
[Repeated 1 time(s)]
> hide #!9 models
> ~select #9
Nothing selected
> save "/Users/stevenson/Library/CloudStorage/Box-Box/Shokat/structures/kinase
> comparison.cxs"
——— End of log from Thu Jun 9 17:22:25 2022 ———
opened ChimeraX session
> hide #3 models
> show #!7 models
> hide #!7 models
> select #1/A:315
7 atoms, 6 bonds, 1 residue, 1 model selected
> show sel target ab
> select clear
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> show #!2 models
> hide #!2 models
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
7 atoms, 6 bonds, 1 residue, 1 model selected
> show #!2 models
> hide #!2 models
> open 4wa9
Summary of feedback from opening 4wa9 fetched from pdb
---
notes | Fetching compressed mmCIF 4wa9 from
http://files.rcsb.org/download/4wa9.cif
Fetching CCD AXI from http://ligand-expo.rcsb.org/reports/A/AXI/AXI.cif
4wa9 title:
The crystal structure of human abl1 wild type kinase domain in complex with
axitinib [more info...]
Chain information for 4wa9 #21
---
Chain | Description | UniProt
A B | Tyrosine-protein kinase ABL1 | ABL1_HUMAN
Non-standard residues in 4wa9 #21
---
AXI — axitinib (N-methyl-2-(3-((E)-2-pyridin-2-yl-
vinyl)-1H-indazol-6-ylsulfanyl)-benzamide)
4wa9 mmCIF Assemblies
---
1| author_defined_assembly
2| author_defined_assembly
> rename #21 "Abl axitinib"
> open 4t2p
Fetching url http://files.rcsb.org/download/4t2p.cif failed: HTTP Error 404:
Not Found
> open 4twp
Summary of feedback from opening 4twp fetched from pdb
---
notes | Fetching compressed mmCIF 4twp from
http://files.rcsb.org/download/4twp.cif
Fetching CCD NI from http://ligand-expo.rcsb.org/reports/N/NI/NI.cif
Fetching CCD NA from http://ligand-expo.rcsb.org/reports/N/NA/NA.cif
4twp title:
The crystal structure of human abl1 T315I gatekeeper mutant kinase domain in
complex with axitinib [more info...]
Chain information for 4twp #22
---
Chain | Description | UniProt
A B | Tyrosine-protein kinase ABL1 | ABL1_HUMAN
Non-standard residues in 4twp #22
---
AXI — axitinib (N-methyl-2-(3-((E)-2-pyridin-2-yl-
vinyl)-1H-indazol-6-ylsulfanyl)-benzamide)
NA — sodium ion
NI — nickel (II) ion
4twp mmCIF Assemblies
---
1| author_defined_assembly
2| author_defined_assembly
> rename #22 "Abl T315I axitinib"
> ui tool show Matchmaker
> matchmaker #!21-22 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 axitinib, chain B (#21),
sequence alignment score = 1394.8
RMSD between 242 pruned atom pairs is 0.643 angstroms; (across all 260 pairs:
2.361)
Matchmaker Abl ponatinib 3oxz, chain A (#1) with Abl T315I axitinib, chain A
(#22), sequence alignment score = 1372.8
RMSD between 246 pruned atom pairs is 0.539 angstroms; (across all 255 pairs:
2.147)
> hide #!1 models
> select #22/B:246
10 atoms, 10 bonds, 1 residue, 1 model selected
> select up
43 atoms, 43 bonds, 5 residues, 1 model selected
> select up
2201 atoms, 2257 bonds, 271 residues, 1 model selected
> cartoon hide sel
> hide sel target a
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
28 atoms, 31 bonds, 1 residue, 1 model selected
> hide sel target a
> select #22/B:604@NA
1 atom, 1 residue, 1 model selected
> select add #22/B:602@NI
2 atoms, 2 residues, 1 model selected
> select add #22/B:603@NI
3 atoms, 3 residues, 1 model selected
> hide sel target a
> select clear
> select #22/A:315
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel target ab
> select clear
> show #!1 models
> hide #!22 models
> show #!22 models
> hide #!21 models
> hide #!1 models
> show #!21 models
> show #!1 models
> select #1/A:1@C22
1 atom, 1 residue, 1 model selected
> hide #!21 models
> hide #!22 models
> show #!22 models
> hide #!22 models
> show #!22 models
> show #!21 models
> hide #!1 models
> color #21 #b4b5cf transparency 0
> color #21 #97b9cf transparency 0
> color #21 #8cb6cf transparency 0
> color #21 #a399cf transparency 0
> show #!1 models
> hide #!21 models
> hide #!22 models
> select add #1
2280 atoms, 2249 bonds, 3 pseudobonds, 358 residues, 2 models selected
> select subtract #1
Nothing selected
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
7 atoms, 6 bonds, 1 residue, 1 model selected
> save "/Users/stevenson/Library/CloudStorage/Box-Box/Shokat/structures/kinase
> comparison.cxs"
——— End of log from Fri Feb 17 18:35:47 2023 ———
opened ChimeraX session
> select clear
> close #8,10#9,11-20
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!7 models
> hide #!1 models
> select #7@H2O
Nothing selected
> select #7@HOH
Nothing selected
> select #7@hoh
Nothing selected
> select #7/A@hoh
Nothing selected
> select #7/A
3762 atoms, 3551 bonds, 2 pseudobonds, 738 residues, 2 models selected
> select clear
> select @hoh
Nothing selected
> select clear
[Repeated 1 time(s)]
> select #7/A:768@O
1 atom, 1 residue, 1 model selected
> select #7@O
736 atoms, 736 residues, 1 model selected
> select #7@HOH
Nothing selected
> select #7@HOH
Nothing selected
> select #7/A:872@O
1 atom, 1 residue, 1 model selected
> select #7/A:400
8 atoms, 7 bonds, 1 residue, 1 model selected
> select clear
> select ::name="HOH"
1790 atoms, 1790 residues, 8 models selected
> select #7::name="HOH
Nothing selected
> select #7 ::name="HOH
Nothing selected
> select ::name="HOH
Nothing selected
> select #7::name="HOH
Nothing selected
> select ::name="HOH
Nothing selected
> select ::name="HOH"
1790 atoms, 1790 residues, 8 models selected
> select #7::name="HOH"
307 atoms, 307 residues, 1 model selected
> hide sel atoms
> select clear
> show #!1 models
> hide #!1 models
> show #!1 models
> select clear
> select #7/A:156
5 atoms, 4 bonds, 1 residue, 1 model selected
> select up
78 atoms, 78 bonds, 10 residues, 1 model selected
> select up
1667 atoms, 1712 bonds, 213 residues, 1 model selected
> select up
1672 atoms, 1716 bonds, 214 residues, 1 model selected
> select up
2494 atoms, 2554 bonds, 317 residues, 1 model selected
> select up
3762 atoms, 3551 bonds, 738 residues, 1 model selected
> select clear
> select #7/A:529
8 atoms, 7 bonds, 1 residue, 1 model selected
> select up
80 atoms, 79 bonds, 12 residues, 1 model selected
> select up
891 atoms, 920 bonds, 112 residues, 1 model selected
> select up
3762 atoms, 3551 bonds, 738 residues, 1 model selected
> select clear
> select #7/A:527
5 atoms, 4 bonds, 1 residue, 1 model selected
> select up
80 atoms, 79 bonds, 12 residues, 1 model selected
> select up
891 atoms, 920 bonds, 112 residues, 1 model selected
> hide sel cartoons
> hide sel atoms
> select #7/A:348
9 atoms, 8 bonds, 1 residue, 1 model selected
> select up
78 atoms, 78 bonds, 9 residues, 1 model selected
> select up
827 atoms, 842 bonds, 104 residues, 1 model selected
> hide sel cartoons
> hide sel atoms
> select clear
> select #7/A:236
5 atoms, 4 bonds, 1 residue, 1 model selected
> select up
170 atoms, 176 bonds, 21 residues, 1 model selected
> select up
1667 atoms, 1712 bonds, 213 residues, 1 model selected
> hide sel atoms
> hide sel cartoons
> select #1/A:294
5 atoms, 4 bonds, 1 residue, 1 model selected
> select up
71 atoms, 72 bonds, 9 residues, 1 model selected
> select #7/A:601@C25
1 atom, 1 residue, 1 model selected
> select up
39 atoms, 43 bonds, 1 residue, 1 model selected
> hide sel atoms
> select clear
> select #1/A:324
8 atoms, 7 bonds, 1 residue, 1 model selected
> select up
78 atoms, 78 bonds, 9 residues, 1 model selected
> select up
837 atoms, 852 bonds, 106 residues, 1 model selected
> select up
885 atoms, 900 bonds, 112 residues, 1 model selected
> select up
1780 atoms, 1825 bonds, 222 residues, 1 model selected
> hide sel atoms
> undo
> hide sel atoms
> select #1/A:254
4 atoms, 3 bonds, 1 residue, 1 model selected
> select up
25 atoms, 25 bonds, 3 residues, 1 model selected
> select up
372 atoms, 381 bonds, 46 residues, 1 model selected
> hide sel atoms
> select clear
> save "/Users/jackstevenson/Desktop/PonatiLink illustration.cxs"
> select clear
> select #1/A:289
7 atoms, 6 bonds, 1 residue, 1 model selected
> select up
96 atoms, 96 bonds, 12 residues, 1 model selected
> select up
837 atoms, 852 bonds, 106 residues, 1 model selected
> select up
885 atoms, 900 bonds, 112 residues, 1 model selected
> select up
1780 atoms, 1825 bonds, 222 residues, 1 model selected
> select up
2280 atoms, 2249 bonds, 358 residues, 1 model selected
> select clear
> select #1/A:1@C12
1 atom, 1 residue, 1 model selected
> select up
39 atoms, 43 bonds, 1 residue, 1 model selected
> name frozen ponatinib sel
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
31 atoms, 34 bonds, 1 residue, 1 model selected
> name frozen asciminib sel
> select #1/A:367
11 atoms, 10 bonds, 1 residue, 1 model selected
> select up
21 atoms, 20 bonds, 3 residues, 1 model selected
> select up
837 atoms, 852 bonds, 106 residues, 1 model selected
> select up
885 atoms, 900 bonds, 112 residues, 1 model selected
> select up
1780 atoms, 1825 bonds, 222 residues, 1 model selected
> select up
2280 atoms, 2249 bonds, 358 residues, 1 model selected
> select down
1780 atoms, 1825 bonds, 222 residues, 1 model selected
> select up
2280 atoms, 2249 bonds, 358 residues, 1 model selected
> select subtract ponatinib
2241 atoms, 2206 bonds, 357 residues, 1 model selected
> name frozen ABL_ponatinib sel
> select clear
> select ABL_ponatinib
2241 atoms, 2206 bonds, 3 pseudobonds, 357 residues, 2 models selected
> show sel surfaces
> lighting full
> lighting soft
> ui tool show "Surface Color"
> lighting flat
> lighting soft
> graphics silhouettes false
> graphics silhouettes true
> lighting full
> lighting soft
> set bgColor white
> select clear
> transparency #1,7 50
> select clear
> select #1/A:250@O
1 atom, 1 residue, 1 model selected
> select ABL_ponatinib
2241 atoms, 2206 bonds, 3 pseudobonds, 357 residues, 2 models selected
> select clear
> select ABL_ponatinib
2241 atoms, 2206 bonds, 3 pseudobonds, 357 residues, 2 models selected
> hide sel surfaces
> color (#!1 & sel) gray
> show sel surfaces
> transparency (#!1 & sel) 50
> select clear
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select ponatinib
39 atoms, 43 bonds, 1 residue, 1 model selected
> select clear
> select ABL_ponatinib
2241 atoms, 2206 bonds, 3 pseudobonds, 357 residues, 2 models selected
> color (#!1 & sel) light gray
> transparency (#!1 & sel) 40
> select clear
> color #1,7 dark gray
> transparency #1,7 50
> transparency #1,7 30
> transparency #1,7 40
> select ponatinib
39 atoms, 43 bonds, 1 residue, 1 model selected
> color sel blue
> color sel light sea green
> select clear
> select #1/A:299@CB
1 atom, 1 residue, 1 model selected
> select ponatinib
39 atoms, 43 bonds, 1 residue, 1 model selected
> color sel byhetero
> select clear
> select #7/A:602@C12
1 atom, 1 residue, 1 model selected
> select asciminig
Expected an objects specifier or a keyword
> select asciminib
31 atoms, 34 bonds, 1 residue, 1 model selected
> color sel light sea green
> color sel byhetero
> select clear
> select asciminib
31 atoms, 34 bonds, 1 residue, 1 model selected
> style sel sphere
Changed 31 atom styles
> style sel ball
Changed 31 atom styles
> style sel sphere
Changed 31 atom styles
> select ponatinib
39 atoms, 43 bonds, 1 residue, 1 model selected
> style sel sphere
Changed 39 atom styles
> select clear
> save "/Users/jackstevenson/Desktop/PonatiLink illustration.cxs"
> select ponatinib
39 atoms, 43 bonds, 1 residue, 1 model selected
> style sel stick
Changed 39 atom styles
> style sel ball
Changed 39 atom styles
> style sel stick
Changed 39 atom styles
> select clear
> select ponatinib
39 atoms, 43 bonds, 1 residue, 1 model selected
> style sel sphere
Changed 39 atom styles
> select clear
[Repeated 1 time(s)]
> select ABL_ponatinib
2241 atoms, 2206 bonds, 3 pseudobonds, 357 residues, 2 models selected
> transparency (#!1 & sel) 60
[Repeated 1 time(s)]
> transparency (#!1 & sel) 50
> transparency (#!1 & sel) 40
> transparency (#!1 & sel) 50
> select clear
> lighting full
> lighting soft
> lighting flat
> graphics silhouettes false
> lighting soft
> graphics silhouettes true
> graphics silhouettes false
> graphics silhouettes true
> graphics silhouettes false
> graphics silhouettes true
> graphics silhouettes false
> graphics silhouettes true
> lighting simple
> graphics silhouettes false
> lighting flat
> lighting soft
> select clear
> save "/Users/jackstevenson/Desktop/PonatiLink illustration.cxs"
> lighting shadows true intensity 0.5
> lighting flat
> lighting shadows true intensity 0.5
> lighting shadows false
> lighting shadows true
> lighting shadows false
> lighting shadows true
> lighting soft
> lighting shadows true intensity 0.5
> lighting shadows false
> lighting shadows true
> lighting shadows false
> lighting shadows true
> lighting shadows false
> lighting shadows true
> lighting shadows false
> lighting shadows true
> lighting gentle
> lighting soft
> lighting gentle
> select clear
> save "/Users/jackstevenson/Desktop/pona asc.png" width 936 height 739
> supersample 4 transparentBackground true
> undo
> redo
Could not map key to character for event NSEvent: type=AppDefined loc=(0,0)
time=0.0 flags=0 win=0x0 winNum=0 ctxt=0x0 subtype=32767 data1=0 data2=0
> save /Users/jackstevenson/Desktop/atest.png width 936 height 739 supersample
> 3
> select clear
[Repeated 1 time(s)]
> save "/Users/jackstevenson/Desktop/PonatiLink illustration.cxs"
——— End of log from Thu May 25 17:06:04 2023 ———
opened ChimeraX session
> select ABL_ponatinib
2241 atoms, 2206 bonds, 3 pseudobonds, 357 residues, 2 models selected
> hide sel cartoons
> select clear
> transparency #1,7 50
> transparency #1,7 30
> select clear
> save "/Users/jackstevenson/Desktop/pona asc.png" width 2000 height 1579
> supersample 3 transparentBackground true
> save /Users/jackstevenson/Desktop/bigger.png width 3000 height 2369
> supersample 3 transparentBackground true
> lighting flat
> lighting soft
> lighting full
> lighting flat
> lighting soft
> lighting gentle
> save "/Users/jackstevenson/Desktop/PonatiLink illustration.cxs"
——— End of log from Thu May 25 17:47:11 2023 ———
opened ChimeraX session
> select asciminib
31 atoms, 34 bonds, 1 residue, 1 model selected
> color sel forest green
> select clear
> select ponatinib
39 atoms, 43 bonds, 1 residue, 1 model selected
> ui tool show "Color Actions"
> color sel dark cyan
> select clear
> save "/Users/jackstevenson/Desktop/PonatiLink illustration.cxs"
——— End of log from Wed May 31 14:50:19 2023 ———
opened ChimeraX session
> view name illustration
> view
> view illustration
> view illustration 100
> view illustration 50
[Repeated 2 time(s)]
> save "/Users/jackstevenson/Desktop/PonatiLink illustration.cxs"
> sym #6
Abl myristic acid 1opl mmCIF Assemblies
---
1| author_defined_assembly| 1 copy of chain A
2| author_and_software_defined_assembly| 1 copy of chain B
3| software_defined_assembly| 2 copies of chain A
> log metadata #6
No models had metadata
> log chains #6
Chain information for Abl myristic acid 1opl #6
---
Chain | Description | UniProt
A B | proto-oncogene tyrosine-protein kinase | ABL1_HUMAN 1-531
> rename -h
Missing or invalid "models" argument: invalid models specifier
> rename
Missing or invalid "models" argument: empty atom specifier
> rename #6 Abl myristic acid PD166326
Expected a keyword
> rename #6 "Abl myristic acid PD166326"
> view illustration
> view illustration 10
> save "/Users/jackstevenson/Desktop/PonatiLink illustration.cxs"
> show #!6 models
> hide #!7 models
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
15 atoms, 14 bonds, 1 residue, 1 model selected
> show sel atoms
> select up
3672 atoms, 3769 bonds, 453 residues, 1 model selected
> select clear
> select #1/A:463@O
1 atom, 1 residue, 1 model selected
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
15 atoms, 14 bonds, 1 residue, 1 model selected
> name frozen myristate sel
> hide #!6 models
> show #!6 models
> select #6:!myristate
Expected an objects specifier or a keyword
> select #6
6655 atoms, 6832 bonds, 1 pseudobond, 819 residues, 2 models selected
> hide sel atoms
> hide sel cartoons
> select myristate
15 atoms, 14 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel sphere
Changed 15 atom styles
> select clear
> select #6/A:538@C1
1 atom, 1 residue, 1 model selected
> select myristate
15 atoms, 14 bonds, 1 residue, 1 model selected
> color sel lime
> ui tool show "Color Actions"
> color sel yellow green
> color sel saddle brown
> color sel chocolate
> color sel saddle brown
> color sel brown
> color sel tomato
> color sel fire brick
> color sel saddle brown
> select clear
> view illustratin
Expected an objects specifier or a view name or a keyword
> view illustration
> hide #!6 models
> show #!6 models
> hide #!6 models
> show #!6 models
> hide #!6 models
> show #!6 models
> select clear
> hide #!6 models
> select clear
> view illustration
> show #!6 models
> view illustration
> hide #!6 models
> show #!7 models
> show #!6 models
> hide #!6 models
> show #!6 models
> hide #!6 models
> hide #!7 models
> show #!7 models
> hide #!7 models
> show #!7 models
> hide #!7 models
> lighting flat
> show #!7 models
> hide #!7 models
> lighting soft
> lighting flat
> show #!7 models
> hide #!1 models
> show #!1 models
> lighting gentle
> hide #!7 models
> show #!7 models
> hide #!7 models
> lighting gentle
[Repeated 1 time(s)]
> show #!7 models
> hide #!7 models
> lighting soft
> lighting gentle
> show #!7 models
> hide #!7 models
> show #!7 models
> show #!6 models
> hide #!6 models
> hide #!7 models
> hide #!1 models
> show #!7 models
> show #!6 models
> hide #!6 models
> show #!1 models
> hide #!1 models
> lighting gentle
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!7 models
> show #!7 models
> hide #!7 models
> show #!7 models
> hide #!7 models
> save "/Users/jackstevenson/Desktop/2023-06-01 bug report session ponatinib
> only.cxs"
> show #!7 models
> save "/Users/jackstevenson/Desktop/2023-06-01 bug report session ponatinib
> and asciminib.cxs"
——— End of log from Thu Jun 1 17:11:29 2023 ———
opened ChimeraX session
> lighting gentle
> lighting soft
> hide #!7 models
> show #!7 models
> hide #!7 models
> show #!7 models
> lighting gentle
> hide #!7 models
> show #!7 models
> lighting full
> hide #!7 models
> show #!7 models
> hide #!7 models
> show #!7 models
> lighting soft
> hide #!7 models
> show #!7 models
> lighting simple
> hide #!7 models
> show #!7 models
> hide #!7 models
> show #!7 models
OpenGL version: 4.1 Metal - 83.1
OpenGL renderer: Apple M2 Pro
OpenGL vendor: Apple
Python: 3.9.11
Locale: UTF-8
Qt version: PyQt6 6.4.2, Qt 6.4.2
Qt runtime version: 6.4.3
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: Mac
Model Identifier: Mac14,9
Model Number: Z17G002HTLL/A
Chip: Unknown
Total Number of Cores: 10 (6 performance and 4 efficiency)
Memory: 32 GB
System Firmware Version: 8422.100.650
OS Loader Version: 8422.100.650
Software:
System Software Overview:
System Version: macOS 13.3.1 (22E261)
Kernel Version: Darwin 22.4.0
Time since boot: 1 day, 2 hours, 44 minutes
Graphics/Displays:
Apple M2 Pro:
Chipset Model: Apple M2 Pro
Type: GPU
Bus: Built-In
Total Number of Cores: 16
Vendor: Apple (0x106b)
Metal Support: Metal 3
Displays:
Color LCD:
Display Type: Built-in Liquid Retina XDR Display
Resolution: 3024 x 1964 Retina
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: No
Connection Type: Internal
Installed Packages:
alabaster: 0.7.13
appdirs: 1.4.4
appnope: 0.1.3
asttokens: 2.2.1
Babel: 2.12.1
backcall: 0.2.0
beautifulsoup4: 4.11.2
blockdiag: 3.0.0
build: 0.10.0
certifi: 2021.10.8
cftime: 1.6.2
charset-normalizer: 3.1.0
ChimeraX-AddCharge: 1.5.9.1
ChimeraX-AddH: 2.2.5
ChimeraX-AlignmentAlgorithms: 2.0.1
ChimeraX-AlignmentHdrs: 3.3.1
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.9.3
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.0.3
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.43.10
ChimeraX-AtomicLibrary: 10.0.6
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.3.2
ChimeraX-BasicActions: 1.1.2
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 2.1.2
ChimeraX-BondRot: 2.0.1
ChimeraX-BugReporter: 1.0.1
ChimeraX-BuildStructure: 2.8
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.2.2
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.3.2
ChimeraX-ChangeChains: 1.0.2
ChimeraX-CheckWaters: 1.3.1
ChimeraX-ChemGroup: 2.0.1
ChimeraX-Clashes: 2.2.4
ChimeraX-ColorActions: 1.0.3
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.3
ChimeraX-CommandLine: 1.2.5
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.6.1
ChimeraX-CoreFormats: 1.1
ChimeraX-coulombic: 1.4.2
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.3
ChimeraX-Dicom: 1.2
ChimeraX-DistMonitor: 1.4
ChimeraX-DockPrep: 1.1.1
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: 1.1.1
ChimeraX-Hbonds: 2.4
ChimeraX-Help: 1.2.1
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.1
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-Label: 1.1.7
ChimeraX-ListInfo: 1.1.1
ChimeraX-Log: 1.1.5
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.8.2
ChimeraX-Map: 1.1.4
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: 2.0.12
ChimeraX-MDcrds: 2.6
ChimeraX-MedicalToolbar: 1.0.2
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.12
ChimeraX-MMTF: 2.2
ChimeraX-Modeller: 1.5.9
ChimeraX-ModelPanel: 1.3.7
ChimeraX-ModelSeries: 1.0.1
ChimeraX-Mol2: 2.0
ChimeraX-Mole: 1.0
ChimeraX-Morph: 1.0.2
ChimeraX-MouseModes: 1.2
ChimeraX-Movie: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nifti: 1.0
ChimeraX-NRRD: 1.0
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.10.1
ChimeraX-PDB: 2.7.2
ChimeraX-PDBBio: 1.0
ChimeraX-PDBLibrary: 1.0.2
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0.1
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1
ChimeraX-PubChem: 2.1
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.1
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.1
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.1
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 3.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5.1
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0.1
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0.1
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.8.3
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.1.1
ChimeraX-ShowSequences: 1.0.1
ChimeraX-SideView: 1.0.1
ChimeraX-Smiles: 2.1
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.10.3
ChimeraX-STL: 1.0.1
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.1.2
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0.1
ChimeraX-SwapAA: 2.0.1
ChimeraX-SwapRes: 2.2.1
ChimeraX-TapeMeasure: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.1.2
ChimeraX-ToolshedUtils: 1.2.1
ChimeraX-Topography: 1.0
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.28.4
ChimeraX-uniprot: 2.2.2
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.2
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0.1
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0.2
ChimeraX-WebServices: 1.1.1
ChimeraX-Zone: 1.0.1
colorama: 0.4.6
comm: 0.1.3
contourpy: 1.0.7
cxservices: 1.2.2
cycler: 0.11.0
Cython: 0.29.33
debugpy: 1.6.7
decorator: 5.1.1
docutils: 0.19
executing: 1.2.0
filelock: 3.9.0
fonttools: 4.39.3
funcparserlib: 1.0.1
grako: 3.16.5
h5py: 3.8.0
html2text: 2020.1.16
idna: 3.4
ihm: 0.35
imagecodecs: 2022.9.26
imagesize: 1.4.1
importlib-metadata: 6.6.0
ipykernel: 6.21.1
ipython: 8.10.0
ipython-genutils: 0.2.0
ipywidgets: 8.0.6
jedi: 0.18.2
Jinja2: 3.1.2
jupyter-client: 8.0.2
jupyter-core: 5.3.0
jupyterlab-widgets: 3.0.7
kiwisolver: 1.4.4
line-profiler: 4.0.2
lxml: 4.9.2
lz4: 4.3.2
MarkupSafe: 2.1.2
matplotlib: 3.6.3
matplotlib-inline: 0.1.6
msgpack: 1.0.4
nest-asyncio: 1.5.6
netCDF4: 1.6.2
networkx: 2.8.8
nibabel: 5.0.1
nptyping: 2.5.0
numexpr: 2.8.4
numpy: 1.23.5
openvr: 1.23.701
packaging: 21.3
ParmEd: 3.4.3
parso: 0.8.3
pep517: 0.13.0
pexpect: 4.8.0
pickleshare: 0.7.5
Pillow: 9.3.0
pip: 23.0
pkginfo: 1.9.6
platformdirs: 3.5.0
prompt-toolkit: 3.0.38
psutil: 5.9.4
ptyprocess: 0.7.0
pure-eval: 0.2.2
pycollada: 0.7.2
pydicom: 2.3.0
Pygments: 2.14.0
pynrrd: 1.0.0
PyOpenGL: 3.1.5
PyOpenGL-accelerate: 3.1.5
pyparsing: 3.0.9
pyproject-hooks: 1.0.0
PyQt6-commercial: 6.4.2
PyQt6-Qt6: 6.4.3
PyQt6-sip: 13.4.1
PyQt6-WebEngine-commercial: 6.4.0
PyQt6-WebEngine-Qt6: 6.4.3
python-dateutil: 2.8.2
pytz: 2023.3
pyzmq: 25.0.2
qtconsole: 5.4.0
QtPy: 2.3.1
RandomWords: 0.4.0
requests: 2.28.2
scipy: 1.9.3
setuptools: 67.4.0
setuptools-scm: 7.0.5
sfftk-rw: 0.7.3
six: 1.16.0
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
soupsieve: 2.4.1
sphinx: 6.1.3
sphinx-autodoc-typehints: 1.22
sphinxcontrib-applehelp: 1.0.4
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 1.0.2
sphinxcontrib-htmlhelp: 2.0.1
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 1.0.3
sphinxcontrib-serializinghtml: 1.1.5
stack-data: 0.6.2
tables: 3.7.0
tcia-utils: 1.2.0
tifffile: 2022.10.10
tinyarray: 1.2.4
tomli: 2.0.1
tornado: 6.3.1
traitlets: 5.9.0
typing-extensions: 4.5.0
tzdata: 2023.3
urllib3: 1.26.15
wcwidth: 0.2.6
webcolors: 1.12
wheel: 0.38.4
wheel-filename: 1.4.1
widgetsnbextension: 4.0.7
zipp: 3.15.0
File attachment: 2023-06-01 bug report session ponatinib and asciminib.cxs
Attachments (1)
Change History (3)
by , 2 years ago
| Attachment: | 2023-06-01 bug report session ponatinib and asciminib.cxs added |
|---|
comment:1 by , 2 years ago
| Component: | Unassigned → Depiction |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → Hiding/showing model changes lighting |
comment:2 by , 2 years ago
| Resolution: | → limitation |
|---|---|
| Status: | assigned → closed |
You are using the "soft" lighting mode which approximates ambient shadows cast from all directions. But the approximation is limited and I believe it is the limitations of the ambient light that cause the strange behavior you see. Transparent surfaces do not cast shadows by default because the code is not sophisticated enough. So only the two ligands are casting shadows. And hiding either is going to change the shadowing across the entire surface. It is weird that hiding it makes the surface darker in some spots. If the ambient shadows were an ideal calculation the surface should only get lighter when you remove an object that casts shadows.
I'd suggest you have the transparent surface also cast a shadow. Use command "material transparentCastShadows true". This looks much better and more natural to me. The drawback is that the surface shadows the ligands so they don't appear as bright. You can make the ligands not accept shadows -- see https://rbvi.github.io/chimerax-recipes/shadows/shadows.html for an example.
I also tried playing with the ambient lighting parameters (use the lighting command), number of shadow casting directions (default 64) and multishadow map size (default 128) and did not see an improvement in the unexpected darkening you see. I don't understand it, but there are so many approximations being made to render ambient shadows in real time I am not too surprised. But the fact that the transparent surface does not cast shadows means the lighting is not going to be intuitive in any sense. The shadow graphics code has no idea how to handle transparency -- if you enable casting shadows from a transparent surface the shadows are completely dark. That is why it is not enabled by default.
Hope these clues help.
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