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Opened 6 years ago
Closed 6 years ago
#2251 closed defect (fixed)
Label (picking) wrong on second screen
| Reported by: | 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-18.6.0-x86_64-i386-64bit ChimeraX Version: 0.91 (2019-07-07) Description When moving my chimeraX screen to a different monitor with different resolution something messes up with the coordinate system (i think?). When mousing over residues the label that pops up is wrong, like it thinks my mouse is somewhere else.(Describe the actions that caused this problem to occur here) Log: Startup Messages --- note | available bundle cache has not been initialized yet UCSF ChimeraX version: 0.91 (2019-07-07) © 2016-2019 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open "/Users/fredward/Google Drive/P7A7 Manuscript/Figures/fred_misc_figs/4ybb_A2_50S_wchains.pdb" "/Users/fredward/Google Drive/P7A7 Manuscript/Figures/fred_misc_figs/lp8-pp-j172.mrc" Summary of feedback from opening files --- warning | Ignored bad PDB record found on line 1 HEADER RIBOSOME 2015-02-18 XXXX Opened lp8-pp-j172.mrc, grid size 296,296,296, pixel 1.11, shown at level 0.00572, step 2, values float32 Chain information for 4ybb_A2_50S_wchains.pdb --- Chain | Description 1.2/I | No description available 1.2/J | No description available 1.2/K | No description available 1.2/L | No description available 1.2/M | No description available 1.2/N | No description available 1.2/O | No description available 1.2/P | No description available 1.2/Q | No description available 1.2/R | No description available 1.2/S | No description available 1.2/T | No description available 1.2/U | No description available 1.2/V | No description available 1.2/W | No description available 1.2/X | No description available 1.2/Y | No description available 1.2/Z | No description available 1.2/a | No description available 1.2/b | No description available 1.2/c | No description available 1.2/d | No description available 1.2/e | No description available 1.2/f | No description available 1.2/g | No description available 1.2/h | No description available 1.2/i | No description available 1.2/j | No description available 1.2/k | No description available 1.2/l | No description available 1.2/m | No description available > ui mousemode rightMode "translate selected models" > select #1.1 2 models selected > toolshed show "Fit in Map" Fit molecule 4ybb_A2_50S_wchains.pdb (#1.2) to map lp8-pp-j172.mrc (#1.1) using 91720 atoms average map value = 0.004616, steps = 132 shifted from previous position = 14.5 rotated from previous position = 7.43 degrees atoms outside contour = 57648, contour level = 0.0057154 Position of 4ybb_A2_50S_wchains.pdb (#1.2) relative to lp8-pp-j172.mrc (#1.1) coordinates: Matrix rotation and translation 0.99220217 0.11773499 -0.04090626 30.20381683 -0.11907654 0.99236717 -0.03206529 -129.47115467 0.03681883 0.03668622 0.99864833 -157.48715765 Axis 0.26591274 -0.30062017 -0.91592463 Axis point -613.22492816 134.68185386 0.00000000 Rotation angle (degrees) 7.42767471 Shift along axis 191.19958722 > style selAtoms stick Changed 0 atom styles > ~select #1.1 Nothing selected > select #1.2 91720 atoms, 98933 bonds, 1 pseudobond, 2 models selected > style selAtoms stick Changed 91720 atom styles > style selAtoms stick Changed 91720 atom styles > ~select #1.2 Nothing selected > select #1.2 91720 atoms, 98933 bonds, 1 pseudobond, 2 models selected > show selAtoms ribbons > hide selAtoms > ~select #1.2 Nothing selected > ui mousemode rightMode zoom > open "/Users/fredward/Google Drive/P7A7 Manuscript/Figures/fred_misc_figs/WT_lp8.mrc" Opened WT_lp8.mrc, grid size 296,296,296, pixel 1.11, shown at level 0.00873, step 2, values float32 > select #2 2 models selected > ui mousemode rightMode "translate selected models" Fit map WT_lp8.mrc in map lp8-pp-j172.mrc using 259346 points correlation = 0.9415, correlation about mean = 0.2392, overlap = 16.65 steps = 184, shift = 27.8, angle = 9.21 degrees Position of WT_lp8.mrc (#2) relative to lp8-pp-j172.mrc (#1.1) coordinates: Matrix rotation and translation 0.98857400 0.15014638 0.01332307 -198.07888041 -0.14920724 0.98727356 -0.05502836 -131.87093525 -0.02141583 0.05241171 0.99839590 -178.24192929 Axis 0.33581130 0.10857882 -0.93565026 Axis point -1068.32916744 1430.14198003 0.00000000 Rotation angle (degrees) 9.20520677 Shift along axis 85.93659031 > ~select #2 Nothing selected > undo Fit map WT_lp8.mrc in map lp8-pp-j172.mrc using 875390 points correlation = 0.9185, correlation about mean = 0.5303, overlap = 30.55 steps = 76, shift = 9.6, angle = 0.0214 degrees Position of WT_lp8.mrc (#2) relative to lp8-pp-j172.mrc (#1.1) coordinates: Matrix rotation and translation 0.98858622 0.15004850 0.01351759 -198.09531637 -0.14909277 0.98727399 -0.05533002 -131.84433645 -0.02164775 0.05268312 0.99837661 -178.22695969 Axis 0.33755927 0.10989762 -0.93486697 Axis point -1069.27427740 1430.67893440 0.00000000 Rotation angle (degrees) 9.20639458 Shift along axis 85.26020802 > ~select #2 Nothing selected > ui mousemode rightMode zoom > select /I:2611 20 atoms, 21 bonds, 1 model selected > select #1 91720 atoms, 98933 bonds, 1 pseudobond, 5 models selected > ~select #1 Nothing selected > select #1/I:2444-2576 2846 atoms, 3181 bonds, 1 model selected > select #1.2 91720 atoms, 98933 bonds, 1 pseudobond, 2 models selected > ~select #1.2 Nothing selected > color #1/I:2444-2576 blue > color #1/I:2444-2576 green > open "/Users/fredward/Google Drive/P7A7 Manuscript/Figures/fred_misc_figs/ref_job_170_CDmap.mrc" Opened ref_job_170_CDmap.mrc, grid size 296,296,296, pixel 1.11, shown at level 0.00484, step 2, values float32 > select #3 2 models selected > ui mousemode rightMode "translate selected models" Fit map ref_job_170_CDmap.mrc in map lp8-pp-j172.mrc using 123277 points correlation = 0.9011, correlation about mean = 0.4099, overlap = 6.403 steps = 124, shift = 16.1, angle = 0.0111 degrees Position of ref_job_170_CDmap.mrc (#3) relative to lp8-pp-j172.mrc (#1.1) coordinates: Matrix rotation and translation 0.99999999 -0.00000340 -0.00013302 -164.80425458 0.00000342 0.99999999 0.00014192 -164.82303865 0.00013302 -0.00014192 0.99999998 -164.82682342 Axis -0.72948245 -0.68377541 0.01750847 Axis point 0.00000000 -1189818.12954880 52966.33209374 Rotation angle (degrees) 0.01114658 Shift along axis 230.03788705 > ~select #3 Nothing selected > hide #!1.1 models > ui mousemode rightMode zoom > hide #!3 models > show #!3 models > close #3 > open "/Users/fredward/Google Drive/P7A7 Manuscript/Figures/fred_misc_figs/postprocess.mrc" Opened postprocess.mrc, grid size 296,296,296, pixel 1.11, shown at level 0.0129, step 2, values float32 > select #3 2 models selected > ui mousemode rightMode "translate selected models" Fit map postprocess.mrc in map lp8-pp-j172.mrc using 32484 points correlation = 0.8848, correlation about mean = 0.4956, overlap = 3.171 steps = 108, shift = 13.6, angle = 0.0111 degrees Position of postprocess.mrc (#3) relative to lp8-pp-j172.mrc (#1.1) coordinates: Matrix rotation and translation 0.99999998 -0.00017442 0.00007499 -164.77619851 0.00017441 0.99999998 0.00003749 -164.84466674 -0.00007499 -0.00003748 1.00000000 -164.79791530 Axis -0.19370345 0.38750819 0.90128595 Axis point 544021.21713069 -1145234.63304580 0.00000000 Rotation angle (degrees) 0.01108776 Shift along axis -180.49098697 > ui mousemode rightMode zoom > ~select #3 Nothing selected > show #!2 models > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > show #!1.1 models > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > hide #!2 models > hide #!1.1 models > hide #!3 models > select clear > select clear > select clear > select clear > show #!1.1 models > show #!2 models > hide #!2 models > show #!3 models > hide #!1.1 models > hide #!1 models > show #!1 models > show #!1.1 models > hide #!1.1 models > toolshed show "Show Volume Menu" > show #!1.1 models > hide #!3 models > color #1/I:2057-2063 blue > hide #!1.1 models > show #!1.1 models > select #1.1 2 models selected > select #1.1 2 models selected > ~select #1.1 Nothing selected Expected an integer >= 1 or a keyword > view #1/I:2057-2063 > hide #!1.1 models > select #1/I:2057-2063 154 atoms, 173 bonds, 1 model selected > select #1/I:2057 23 atoms, 25 bonds, 1 model selected > show #!1.1 models > hide #!1.1 models > show #!1.1 models > clip off > select up 62229 atoms, 69695 bonds, 1 model selected > select up 63076 atoms, 69695 bonds, 1 model selected > select up 91720 atoms, 98933 bonds, 1 model selected > select up 91720 atoms, 98933 bonds, 3 models selected > select up 91720 atoms, 98933 bonds, 4 models selected > select up 91720 atoms, 98933 bonds, 8 models selected > select down 91720 atoms, 98933 bonds, 4 models selected > select down 91720 atoms, 98933 bonds, 3 models selected > select down 91720 atoms, 98933 bonds, 1 model selected > select down 63076 atoms, 69695 bonds, 1 model selected > select down 62229 atoms, 69695 bonds, 1 model selected > select down 23 atoms, 25 bonds, 1 model selected > select clear > color #1/I:2578-2613 red > select /J:70 20 atoms, 21 bonds, 1 model selected > select #1.1 2 models selected > select #1.1 2 models selected > select #1.1 2 models selected > select /N:148 11 atoms, 10 bonds, 1 model selected > select #1.1 2 models selected > select #1.1 2 models selected > save session "/Users/fredward/Google Drive/P7A7 Manuscript/Figures/fred_misc_figs/base_tab_session.cxs" > close session > open "/Users/fredward/Google Drive/P7A7 Manuscript/Figures/fred_misc_figs/base_tab_session.cxs" format session opened ChimeraX session > close #3 > hide #!1.2 models > show #!1.2 models > hide #!1.1 models > close #1.2 > open "/Users/fredward/Google Drive/P7A7 Manuscript/Figures/fred_misc_figs/4ybb_A2_50S_wchains.pdb" Summary of feedback from opening /Users/fredward/Google Drive/P7A7 Manuscript/Figures/fred_misc_figs/4ybb_A2_50S_wchains.pdb --- warning | Ignored bad PDB record found on line 1 HEADER RIBOSOME 2015-02-18 XXXX Chain information for 4ybb_A2_50S_wchains.pdb #3 --- Chain | Description I | No description available J | No description available K | No description available L | No description available M | No description available N | No description available O | No description available P | No description available Q | No description available R | No description available S | No description available T | No description available U | No description available V | No description available W | No description available X | No description available Y | No description available Z | No description available a | No description available b | No description available c | No description available d | No description available e | No description available f | No description available g | No description available h | No description available i | No description available j | No description available k | No description available l | No description available m | No description available > hide selAtoms > show selAtoms ribbons > show #!1.1 models > toolshed show "Fit in Map" Fit molecule 4ybb_A2_50S_wchains.pdb (#3) to map lp8-pp-j172.mrc (#1.1) using 91720 atoms average map value = 0.004616, steps = 132 shifted from previous position = 14.5 rotated from previous position = 7.43 degrees atoms outside contour = 30738, contour level = 0.0036522 Position of 4ybb_A2_50S_wchains.pdb (#3) relative to lp8-pp-j172.mrc (#1.1) coordinates: Matrix rotation and translation 0.99220217 0.11773499 -0.04090626 30.20381683 -0.11907654 0.99236717 -0.03206529 -129.47115467 0.03681883 0.03668622 0.99864833 -157.48715765 Axis 0.26591274 -0.30062017 -0.91592463 Axis point -613.22492816 134.68185386 0.00000000 Rotation angle (degrees) 7.42767471 Shift along axis 191.19958722 > color #1/I:2578-2613 red > color #3/I:2578-2613 red > select clear > select clear > select clear OpenGL version: 4.1 NVIDIA-12.0.23 355.11.10.50.10.103 OpenGL renderer: NVIDIA GeForce GT 750M OpenGL Engine OpenGL vendor: NVIDIA Corporation
Change History (7)
comment:1 by , 6 years ago
| Component: | Unassigned → Graphics |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → Label (picking) wrong on second screen |
comment:2 by , 6 years ago
Is one display a Mac retina display and the other conventional resolution? I can imagine that will cause problems because there is a "display scaling" factor ChimeraX uses from the Qt window toolkit that is 2 for retina displays and 1 for lower resolution displays.
comment:3 by , 6 years ago
Hovering the mouse over an atom shows the correct atom name when I move the ChimeraX window back and forth on an iMac between a 5K and an HD display. In my test the second display was connected to an eGPU so that may be the reason it works for me but not for you. I don't have the needed adapter (HDM to USBC) to connect the external display with the eGPU.
I also don't think the display scaling factor should matter because the atom that the mouse is over is computed directly in ChimeraX, not using the graphics rendering. So if it is wrong that suggests that the mouse x,y position reported by Qt in the graphics window is wrong.
Does the problem go away if you resize the ChimeraX window?
follow-up: 4 comment:4 by , 6 years ago
The issues seemed to clear up if I move the window back to my laptop screen and then back again, or resize the window. Of course it's not reproducing as well the next day... In any case it seems like things work with a movement or resizing. Thanks for the quick response, Fred On Thu, Jul 25, 2019 at 12:16 PM ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu> wrote:
comment:5 by , 6 years ago
I suspect this is a Qt window toolkit bug where it is not reporting the correct mouse position after you move to the new screen until you resize the window. I probably won't be able to fix that. But I will test it tomorrow on my Mac laptop with an external display (don't have the laptop now) to see if that is really the problem.
comment:6 by , 6 years ago
I was able to reproduce this bug using a retina Mac laptop connected by hdmi to an HD display.
When the ChimeraX window is moved from the Retina display to HD display the molecule view shows only one quadrant of the original view on the Retina display. This is wrong and is because the change in display scaling was not noticed by ChimeraX. If I resize the window then the correct view is shown and the new display scaling is used. If I move the window back from HD display to retina it again shows the wrong view this time only using the lower left quadrant of the graphics area to show the molecule. Same problem, not detecting the change in display scale, and resizing the window by hand fixes it.
Need to add some code that detects the change in display scale when the window is moved so that the graphics is correctly shown.
comment:7 by , 6 years ago
| Resolution: | → fixed |
|---|---|
| Status: | assigned → closed |
Fixed.
Made ChimeraX detect when it moves to a display with a different pixel scale.
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Reported by Fred Ward