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Opened 5 years ago
Closed 5 years ago
#3255 closed defect (fixed)
labels for hidden objects not auto-hiding
| Reported by: | Elaine Meng | Owned by: | Tom Goddard |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Graphics | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: Darwin-18.7.0-x86_64-i386-64bit
ChimeraX Version: 1.0rc202005180441 (2020-05-18 04:41:25 UTC)
Description
labels no longer go away when you hide the residue
open 2gbp
label solvent
hide solvent
....HOH labels are still there. They are supposed to go away, right? They go away in 0.93.
Log:
> contacts :sti makePseudobonds false reveal true log true
Allowed overlap: -0.4
H-bond overlap reduction: 0.4
Ignore contacts between atoms separated by 4 bonds or less
Detect intra-residue contacts: False
Detect intra-molecule contacts: True
87 contacts
atom1 atom2 overlap distance
/A STI 600 C52 /A ASP 381 OD2 0.332 2.968
/A STI 600 C52 /A HIS 361 O 0.321 2.979
/A STI 600 C53 /A ASP 381 OD2 0.265 3.035
/A STI 600 C11 /A PHE 382 CD2 0.225 3.295
/A STI 600 N10 /A PHE 382 CD2 0.206 3.194
/A STI 600 C20 /A ALA 269 CB 0.140 3.620
/A STI 600 C50 /A ILE 360 O 0.121 3.179
/A STI 600 C54 /A ILE 360 O 0.104 3.196
/A STI 600 N3 /A PHE 317 CD1 0.070 3.330
/A STI 600 C18 /A LYS 271 CB 0.057 3.583
/A STI 600 C11 /A VAL 256 CG1 0.052 3.588
/A STI 600 C2 /A MET 318 O 0.038 3.142
/A STI 600 C2 /A PHE 317 CE1 0.034 3.486
/A STI 600 O29 /A VAL 299 CG1 0.022 3.278
/A STI 600 N21 /A MET 290 CE 0.021 3.499
/A STI 600 N10 /A PHE 382 CE2 0.017 3.383
/A STI 600 C46 /A VAL 289 CG1 -0.013 3.773
/A STI 600 C54 /A HIS 361 O -0.021 3.321
/A STI 600 C11 /A PHE 382 CE2 -0.027 3.547
/A STI 600 C2 /A PHE 317 CD1 -0.038 3.558
/A STI 600 C46 /A ILE 293 CD1 -0.041 3.801
/A STI 600 N3 /A MET 318 N -0.057 2.937
/A STI 600 N51 /A ILE 360 O -0.063 2.723
/A STI 600 C17 /A HOH 146 O -0.064 3.284
/A STI 600 C6 /A LEU 370 CD2 -0.073 3.713
/A STI 600 C49 /A VAL 289 CG1 -0.074 3.834
/A STI 600 C20 /A LYS 271 N -0.089 3.609
/A STI 600 C25 /A ASP 381 CB -0.112 3.752
/A STI 600 C20 /A ALA 269 C -0.136 3.626
/A STI 600 C20 /A ALA 269 O -0.137 3.437
/A STI 600 C16 /A HOH 146 O -0.141 3.211
/A STI 600 C5 /A LEU 248 CD1 -0.142 3.632
/A STI 600 C9 /A PHE 382 CE2 -0.143 3.513
/A STI 600 C17 /A MET 290 SD -0.146 3.676
/A STI 600 C17 /A MET 290 CE -0.146 3.786
/A STI 600 C6 /A LEU 248 CD1 -0.150 3.790
/A STI 600 C54 /A ARG 362 CD -0.168 3.928
/A STI 600 C29 /A MET 290 CE -0.174 3.814
/A STI 600 C6 /A TYR 253 CE1 -0.176 3.696
/A STI 600 C54 /A ARG 362 CG -0.186 3.946
/A STI 600 C23 /A ASP 381 CB -0.187 3.677
/A STI 600 C53 /A ASP 381 CG -0.190 3.950
/A STI 600 C22 /A ASP 381 O -0.190 3.220
/A STI 600 C18 /A ILE 313 CG2 -0.192 3.832
/A STI 600 C20 /A LYS 271 CB -0.193 3.953
/A STI 600 N8 /A ALA 269 CB -0.206 3.726
/A STI 600 N3 /A PHE 317 CA -0.215 3.735
/A STI 600 C29 /A ASP 381 CB -0.216 3.856
/A STI 600 C25 /A ASP 381 N -0.217 3.617
/A STI 600 O29 /A ALA 380 CB -0.227 3.527
/A STI 600 C5 /A LEU 370 CD2 -0.239 3.729
/A STI 600 N21 /A MET 290 SD -0.245 3.255
/A STI 600 C17 /A GLU 286 OE2 -0.246 3.426
/A STI 600 C49 /A ILE 360 O -0.277 3.577
/A STI 600 C52 /A HOH 87 O -0.277 3.617
/A STI 600 C12 /A VAL 256 CG1 -0.285 3.925
/A STI 600 C12 /A TYR 253 CG -0.288 3.658
/A STI 600 C53 /A ASP 381 CB -0.289 4.049
/A STI 600 C14 /A THR 315 CG2 -0.297 3.787
/A STI 600 C16 /A MET 290 SD -0.301 3.681
/A STI 600 C12 /A TYR 253 CD2 -0.302 3.822
/A STI 600 N3 /A MET 318 CA -0.307 3.827
/A STI 600 N13 /A THR 315 OG1 -0.314 3.014
/A STI 600 C12 /A LEU 248 CD1 -0.314 3.954
/A STI 600 C11 /A TYR 253 CB -0.315 3.955
/A STI 600 C12 /A TYR 253 CD1 -0.316 3.836
/A STI 600 O29 /A ASP 381 N -0.321 2.981
/A STI 600 C15 /A VAL 299 CG1 -0.321 3.961
/A STI 600 O29 /A ALA 380 CA -0.328 3.628
/A STI 600 C4 /A LEU 370 CD1 -0.329 3.969
/A STI 600 C2 /A MET 318 N -0.333 3.733
/A STI 600 C12 /A PHE 382 CE2 -0.335 3.855
/A STI 600 C20 /A VAL 256 CG1 -0.343 4.103
/A STI 600 C4 /A LEU 370 CD2 -0.348 3.988
/A STI 600 C17 /A ILE 313 CG2 -0.349 3.989
/A STI 600 C1 /A GLY 321 CA -0.356 3.996
/A STI 600 C20 /A THR 315 OG1 -0.357 3.697
/A STI 600 C22 /A ASP 381 N -0.359 3.609
/A STI 600 C7 /A LEU 248 CD1 -0.361 3.851
/A STI 600 C1 /A LEU 370 CD2 -0.372 4.012
/A STI 600 N3 /A PHE 317 CE1 -0.377 3.777
/A STI 600 C26 /A ASP 381 CB -0.382 4.022
/A STI 600 C15 /A THR 315 CG2 -0.382 4.022
/A STI 600 C14 /A THR 315 OG1 -0.386 3.456
/A STI 600 C53 /A HIS 361 O -0.387 3.687
/A STI 600 C19 /A THR 315 CG2 -0.388 3.878
/A STI 600 C52 /A ASP 381 CG -0.393 4.153
87 contacts
> label @@display
> hide solvent
> contacts :sti makePseudobonds false reveal true log true
Allowed overlap: -0.4
H-bond overlap reduction: 0.4
Ignore contacts between atoms separated by 4 bonds or less
Detect intra-residue contacts: False
Detect intra-molecule contacts: True
87 contacts
atom1 atom2 overlap distance
/A STI 600 C52 /A ASP 381 OD2 0.332 2.968
/A STI 600 C52 /A HIS 361 O 0.321 2.979
/A STI 600 C53 /A ASP 381 OD2 0.265 3.035
/A STI 600 C11 /A PHE 382 CD2 0.225 3.295
/A STI 600 N10 /A PHE 382 CD2 0.206 3.194
/A STI 600 C20 /A ALA 269 CB 0.140 3.620
/A STI 600 C50 /A ILE 360 O 0.121 3.179
/A STI 600 C54 /A ILE 360 O 0.104 3.196
/A STI 600 N3 /A PHE 317 CD1 0.070 3.330
/A STI 600 C18 /A LYS 271 CB 0.057 3.583
/A STI 600 C11 /A VAL 256 CG1 0.052 3.588
/A STI 600 C2 /A MET 318 O 0.038 3.142
/A STI 600 C2 /A PHE 317 CE1 0.034 3.486
/A STI 600 O29 /A VAL 299 CG1 0.022 3.278
/A STI 600 N21 /A MET 290 CE 0.021 3.499
/A STI 600 N10 /A PHE 382 CE2 0.017 3.383
/A STI 600 C46 /A VAL 289 CG1 -0.013 3.773
/A STI 600 C54 /A HIS 361 O -0.021 3.321
/A STI 600 C11 /A PHE 382 CE2 -0.027 3.547
/A STI 600 C2 /A PHE 317 CD1 -0.038 3.558
/A STI 600 C46 /A ILE 293 CD1 -0.041 3.801
/A STI 600 N3 /A MET 318 N -0.057 2.937
/A STI 600 N51 /A ILE 360 O -0.063 2.723
/A STI 600 C17 /A HOH 146 O -0.064 3.284
/A STI 600 C6 /A LEU 370 CD2 -0.073 3.713
/A STI 600 C49 /A VAL 289 CG1 -0.074 3.834
/A STI 600 C20 /A LYS 271 N -0.089 3.609
/A STI 600 C25 /A ASP 381 CB -0.112 3.752
/A STI 600 C20 /A ALA 269 C -0.136 3.626
/A STI 600 C20 /A ALA 269 O -0.137 3.437
/A STI 600 C16 /A HOH 146 O -0.141 3.211
/A STI 600 C5 /A LEU 248 CD1 -0.142 3.632
/A STI 600 C9 /A PHE 382 CE2 -0.143 3.513
/A STI 600 C17 /A MET 290 SD -0.146 3.676
/A STI 600 C17 /A MET 290 CE -0.146 3.786
/A STI 600 C6 /A LEU 248 CD1 -0.150 3.790
/A STI 600 C54 /A ARG 362 CD -0.168 3.928
/A STI 600 C29 /A MET 290 CE -0.174 3.814
/A STI 600 C6 /A TYR 253 CE1 -0.176 3.696
/A STI 600 C54 /A ARG 362 CG -0.186 3.946
/A STI 600 C23 /A ASP 381 CB -0.187 3.677
/A STI 600 C53 /A ASP 381 CG -0.190 3.950
/A STI 600 C22 /A ASP 381 O -0.190 3.220
/A STI 600 C18 /A ILE 313 CG2 -0.192 3.832
/A STI 600 C20 /A LYS 271 CB -0.193 3.953
/A STI 600 N8 /A ALA 269 CB -0.206 3.726
/A STI 600 N3 /A PHE 317 CA -0.215 3.735
/A STI 600 C29 /A ASP 381 CB -0.216 3.856
/A STI 600 C25 /A ASP 381 N -0.217 3.617
/A STI 600 O29 /A ALA 380 CB -0.227 3.527
/A STI 600 C5 /A LEU 370 CD2 -0.239 3.729
/A STI 600 N21 /A MET 290 SD -0.245 3.255
/A STI 600 C17 /A GLU 286 OE2 -0.246 3.426
/A STI 600 C49 /A ILE 360 O -0.277 3.577
/A STI 600 C52 /A HOH 87 O -0.277 3.617
/A STI 600 C12 /A VAL 256 CG1 -0.285 3.925
/A STI 600 C12 /A TYR 253 CG -0.288 3.658
/A STI 600 C53 /A ASP 381 CB -0.289 4.049
/A STI 600 C14 /A THR 315 CG2 -0.297 3.787
/A STI 600 C16 /A MET 290 SD -0.301 3.681
/A STI 600 C12 /A TYR 253 CD2 -0.302 3.822
/A STI 600 N3 /A MET 318 CA -0.307 3.827
/A STI 600 N13 /A THR 315 OG1 -0.314 3.014
/A STI 600 C12 /A LEU 248 CD1 -0.314 3.954
/A STI 600 C11 /A TYR 253 CB -0.315 3.955
/A STI 600 C12 /A TYR 253 CD1 -0.316 3.836
/A STI 600 O29 /A ASP 381 N -0.321 2.981
/A STI 600 C15 /A VAL 299 CG1 -0.321 3.961
/A STI 600 O29 /A ALA 380 CA -0.328 3.628
/A STI 600 C4 /A LEU 370 CD1 -0.329 3.969
/A STI 600 C2 /A MET 318 N -0.333 3.733
/A STI 600 C12 /A PHE 382 CE2 -0.335 3.855
/A STI 600 C20 /A VAL 256 CG1 -0.343 4.103
/A STI 600 C4 /A LEU 370 CD2 -0.348 3.988
/A STI 600 C17 /A ILE 313 CG2 -0.349 3.989
/A STI 600 C1 /A GLY 321 CA -0.356 3.996
/A STI 600 C20 /A THR 315 OG1 -0.357 3.697
/A STI 600 C22 /A ASP 381 N -0.359 3.609
/A STI 600 C7 /A LEU 248 CD1 -0.361 3.851
/A STI 600 C1 /A LEU 370 CD2 -0.372 4.012
/A STI 600 N3 /A PHE 317 CE1 -0.377 3.777
/A STI 600 C26 /A ASP 381 CB -0.382 4.022
/A STI 600 C15 /A THR 315 CG2 -0.382 4.022
/A STI 600 C14 /A THR 315 OG1 -0.386 3.456
/A STI 600 C53 /A HIS 361 O -0.387 3.687
/A STI 600 C19 /A THR 315 CG2 -0.388 3.878
/A STI 600 C52 /A ASP 381 CG -0.393 4.153
87 contacts
> hide solvent
> label delete solvent
> label :hoh@o atoms
OpenGL version: 4.1 INTEL-12.10.17
OpenGL renderer: Intel Iris Pro OpenGL Engine
OpenGL vendor: Intel Inc.Hardware:
Hardware Overview:
Model Name: MacBook Pro
Model Identifier: MacBookPro11,4
Processor Name: Intel Core i7
Processor Speed: 2.2 GHz
Number of Processors: 1
Total Number of Cores: 4
L2 Cache (per Core): 256 KB
L3 Cache: 6 MB
Hyper-Threading Technology: Enabled
Memory: 16 GB
Boot ROM Version: 197.0.0.0.0
SMC Version (system): 2.29f24
Software:
System Software Overview:
System Version: macOS 10.14.6 (18G4032)
Kernel Version: Darwin 18.7.0
Time since boot: 9:20
Graphics/Displays:
Intel Iris Pro:
Chipset Model: Intel Iris Pro
Type: GPU
Bus: Built-In
VRAM (Dynamic, Max): 1536 MB
Vendor: Intel
Device ID: 0x0d26
Revision ID: 0x0008
Metal: Supported, feature set macOS GPUFamily1 v4
Displays:
Color LCD:
Display Type: Built-In Retina LCD
Resolution: 2880 x 1800 Retina
Framebuffer Depth: 24-Bit Color (ARGB8888)
Main Display: Yes
Mirror: Off
Online: Yes
Rotation: Supported
Automatically Adjust Brightness: No
PyQt version: 5.12.3
Compiled Qt version: 5.12.4
Runtime Qt version: 5.12.8
Change History (2)
comment:1 by , 5 years ago
| Component: | Unassigned → Graphics |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → labels for hidden objects not auto-hiding |
comment:2 by , 5 years ago
| Resolution: | → fixed |
|---|---|
| Status: | assigned → closed |
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Fixed.
Changed tracking of atom display changed 7 weeks ago (#3000) as an optimization and caused atom hide to not cause any change notice. The specific atoms hidden are no longer tracked, but a "display change" reason is recorded with no atoms and that was being ignored.