Promiscuous gesture scrolling

[788486@…]

The following bug report has been submitted:
Platform:        Darwin-18.6.0-x86_64-i386-64bit
ChimeraX Version: 0.9 (2019-06-06)
Description
Scrolling using the two-finger gesture in the Model Panel allows scrolling up and down in the panel, but it also moves the graphical model. The same effect is possible when using the two-finger gesture in the Side View.

Clicking in the Model Panel window and then scrolling doesn't fix the problem.

It seems to have stopped happening after I opened this bug-reporter window and tried to scroll.

I think it's a problem with focus.

Log:
UCSF ChimeraX version: 0.9 (2019-06-06)  
© 2016-2019 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> help help:quickstart

> toolshed show "Side View"

> open 3w7f

Summary of feedback from opening 3w7f fetched from pdb  
---  
notes | Fetching compressed mmCIF 3w7f from
http://files.rcsb.org/download/3w7f.cif  
Fetching CCD FPS from http://ligand-expo.rcsb.org/reports/F/FPS/FPS.cif  
Fetching CCD MG from http://ligand-expo.rcsb.org/reports/M/MG/MG.cif  
  
3w7f title:  
Crystal structure of the C(30) carotenoid dehydrosqualene synthase from
staphylococcus aureus complexed with farnesyl thiopyrophosphate [more info...]  
  
Chain information for 3w7f #1  
---  
Chain | Description  
A B | Dehydrosqualene synthase  
  
Non-standard residues in 3w7f #1  
---  
FPS — S-[(2E,6E)-3,7,11-trimethyldodeca-2,6,10-trienyl] trihydrogen
thiodiphosphate (farnesyl thiopyrophosphate)  
MG — magnesium ion  
  
3w7f mmCIF Assemblies  
---  
1| author_and_software_defined_assembly  
2| author_and_software_defined_assembly  
  
  

> delete /b

> view

> label ligand residues

> delete solvent

> ~select #1.1

Nothing selected  

> label @@display residues

> view

> view

> select /A:21@OG

1 atom selected  

> select /A:21@OG

1 atom selected  

> select /A:21@OG

1 atom selected  

> select /A:21@OG

1 atom selected  

> select /A:21@OG

1 atom selected  

> distance /A:21@OG /A:302@O1B

Distance between /A SER 21 OG and FPS 302 O1B: 2.405Å  

> view

> distance :248@OH :302@O1B

Distance between /A TYR 248 OH and FPS 302 O1B: 2.996Å  

> select :FPS

48 atoms, 46 bonds selected  

> hbonds sel restrict cross log true reveal true

    
    
    Finding intermodel H-bonds
    Finding intramodel H-bonds
    Constraints relaxed by 0.4 angstroms and 20 degrees
    Models used:
    	1 3w7f
    
    H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
    /A SER 19 OG    /A FPS 302 O2A  no hydrogen  2.886  N/A
    /A SER 21 N     /A FPS 302 O2B  no hydrogen  3.185  N/A
    /A SER 21 OG    /A FPS 302 O1B  no hydrogen  2.405  N/A
    /A SER 21 OG    /A FPS 302 O2B  no hydrogen  3.332  N/A
    /A TYR 41 OH    /A FPS 302 O2A  no hydrogen  2.585  N/A
    /A ARG 45 NH1   /A FPS 301 O2B  no hydrogen  3.428  N/A
    /A ARG 45 NH1   /A FPS 301 O3B  no hydrogen  2.585  N/A
    /A ARG 45 NH2   /A FPS 301 O2B  no hydrogen  3.175  N/A
    /A ARG 45 NH2   /A FPS 302 O1A  no hydrogen  3.052  N/A
    /A ARG 171 NH1  /A FPS 302 O1B  no hydrogen  2.685  N/A
    /A ARG 171 NH1  /A FPS 302 O3B  no hydrogen  3.412  N/A
    /A ARG 171 NH2  /A FPS 302 O3B  no hydrogen  3.129  N/A
    /A TYR 248 OH   /A FPS 302 O1B  no hydrogen  2.996  N/A
    

  
13 hydrogen bonds found  

> ~hbonds

> ~distance

> contacts sel test others reveal true log true select 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
    
    86 contacts
        atom1           atom2       overlap  distance
    /A FPS 301 C10  /A CYS 44 CB     0.472    3.288
    /A FPS 302 O2A  /A SER 19 CB     0.387    2.913
    /A FPS 301 PB   /A ARG 45 NH1    0.248    3.492
    /A FPS 302 O2A  /A SER 19 CA     0.242    3.058
    /A FPS 302 O1B  /A SER 21 CB     0.215    3.085
    /A FPS 302 C14  /A ALA 157 CB    0.208    3.552
    /A FPS 301 C7   /A CYS 44 CB     0.207    3.433
    /A FPS 302 C14  /A ALA 157 CA    0.191    3.569
    /A FPS 301 C6   /A ASP 48 CB     0.166    3.474
    /A FPS 301 C15  /A TYR 41 CD2    0.158    3.482
    /A FPS 301 O2A  /A MG 303 MG     0.156    1.834
    /A FPS 302 PB   /A ARG 171 NH1   0.139    3.601
    /A FPS 301 PA   /A ASN 168 ND2   0.116    3.624
    /A FPS 301 C14  /A LEU 141 CD1   0.106    3.654
    /A FPS 302 O1A  /A MG 304 MG     0.098    1.892
    /A FPS 301 C8   /A CYS 44 CB     0.097    3.393
    /A FPS 301 O2A  /A ASN 168 OD1   0.097    2.743
    /A FPS 301 O2A  /A ASP 172 OD2   0.088    2.752
    /A FPS 302 O1B  /A SER 21 OG     0.075    2.405
    /A FPS 301 O3B  /A ARG 45 NH1    0.075    2.585
    /A FPS 302 PB   /A SER 21 OG     0.073    3.487
    /A FPS 302 O3B  /A MG 304 MG     0.039    1.951
    /A FPS 301 C15  /A TYR 41 CE2    0.036    3.604
    /A FPS 302 C4   /A GLN 165 OE1   -0.007    3.307
    /A FPS 302 PA   /A ARG 45 NH2    -0.011    3.751
    /A FPS 301 C12  /A TYR 41 CD2    -0.015    3.535
    /A FPS 302 PB   /A SER 21 CB     -0.023    4.003
    /A FPS 302 O1B  /A ARG 171 NH1   -0.025    2.685
    /A FPS 302 C2   /A PHE 22 CE2    -0.038    3.558
    /A FPS 301 C12  /A VAL 137 CG1   -0.048    3.688
    /A FPS 301 O2B  /A MG 304 MG     -0.054    2.044
    /A FPS 301 C2   /A ASP 48 CG     -0.073    3.713
    /A FPS 302 C10  /A GLY 161 CA    -0.084    3.844
    /A FPS 301 C11  /A TYR 41 CD2    -0.091    3.611
    /A FPS 302 C5   /A ALA 134 CB    -0.095    3.855
    /A FPS 301 O1A  /A MG 304 MG     -0.097    2.087
    /A FPS 301 O3B  /A MG 305 MG     -0.103    2.093
    /A FPS 302 C5   /A LEU 164 CB    -0.104    3.864
    /A FPS 302 O2A  /A TYR 41 OH     -0.105    2.585
    /A FPS 301 O3B  /A ASP 48 OD2    -0.105    2.945
    /A FPS 301 C13  /A TYR 41 CD2    -0.106    3.476
    /A FPS 302 C15  /A LEU 145 CD1   -0.106    3.866
    /A FPS 301 C11  /A TYR 41 CE2    -0.107    3.627
    /A FPS 302 C12  /A LEU 160 CD2   -0.110    3.750
    /A FPS 301 C9   /A ARG 45 NH2    -0.149    3.669
    /A FPS 302 C11  /A LEU 164 CD1   -0.154    3.794
    /A FPS 301 C5   /A ASP 48 CG     -0.159    3.919
    /A FPS 302 C1   /A PHE 22 CE2    -0.161    3.681
    /A FPS 301 C9   /A TYR 41 CE2    -0.162    3.802
    /A FPS 302 C1   /A TYR 248 OH    -0.174    3.394
    /A FPS 301 C9   /A ARG 45 CA     -0.175    3.935
    /A FPS 302 C4   /A ASN 168 CB    -0.185    3.945
    /A FPS 302 PB   /A ARG 265 NH2   -0.191    3.931
    /A FPS 302 C14  /A PHE 233 CZ    -0.192    3.832
    /A FPS 302 C4   /A ASN 168 ND2   -0.193    3.713
    /A FPS 302 C15  /A LEU 141 CD1   -0.205    3.965
    /A FPS 302 C4   /A GLN 165 CA    -0.212    3.972
    /A FPS 301 C15  /A MET 15 CE     -0.215    3.975
    /A FPS 302 PA   /A SER 19 CB     -0.217    4.197
    /A FPS 302 O1B  /A TYR 248 CE2   -0.227    3.407
    /A FPS 302 C11  /A GLY 161 CA    -0.230    3.870
    /A FPS 302 C10  /A GLY 138 CA    -0.231    3.991
    /A FPS 302 PA   /A SER 19 CA     -0.232    4.212
    /A FPS 302 C12  /A GLY 138 CA    -0.237    3.877
    /A FPS 302 PA   /A SER 19 OG     -0.239    3.799
    /A FPS 301 C15  /A PHE 22 CD2    -0.249    3.889
    /A FPS 301 C5   /A ASP 48 CB     -0.250    4.010
    /A FPS 301 PA   /A ASN 168 OD1   -0.251    3.771
    /A FPS 302 PA   /A TYR 41 OH     -0.259    3.819
    /A FPS 302 C13  /A LEU 160 CD2   -0.264    3.754
    /A FPS 302 C15  /A LEU 160 CD2   -0.279    4.039
    /A FPS 301 C6   /A ASP 48 CG     -0.284    3.924
    /A FPS 301 C10  /A TYR 41 CD2    -0.296    3.936
    /A FPS 301 C9   /A ARG 45 CZ     -0.312    3.802
    /A FPS 302 C10  /A LEU 141 CD1   -0.317    4.077
    /A FPS 302 O2A  /A TYR 41 CE2    -0.327    3.507
    /A FPS 302 C7   /A ALA 134 CB    -0.333    3.973
    /A FPS 302 PB   /A TYR 248 OH    -0.356    3.916
    /A FPS 302 C10  /A GLY 138 N     -0.356    3.876
    /A FPS 301 O2A  /A ASN 168 CG    -0.361    3.391
    /A FPS 302 C7   /A GLY 161 CA    -0.379    4.019
    /A FPS 302 C14  /A PHE 233 CE1   -0.382    4.022
    /A FPS 302 O2A  /A HIS 18 O      -0.390    3.230
    /A FPS 302 C9   /A LEU 164 CD1   -0.390    4.150
    /A FPS 302 O1A  /A ARG 45 NH2    -0.392    3.052
    /A FPS 302 C6   /A ALA 134 CB    -0.396    4.036
    

  
86 contacts  

> ~select ligand

48 atoms selected  

> ~select ions

45 atoms selected  

> info residues sel

residue id /A:15 name MET index 20  
residue id /A:18 name HIS index 23  
residue id /A:19 name SER index 24  
residue id /A:21 name SER index 26  
residue id /A:22 name PHE index 27  
residue id /A:41 name TYR index 46  
residue id /A:44 name CYS index 49  
residue id /A:45 name ARG index 50  
residue id /A:48 name ASP index 53  
residue id /A:134 name ALA index 139  
residue id /A:137 name VAL index 142  
residue id /A:138 name GLY index 143  
residue id /A:141 name LEU index 146  
residue id /A:145 name LEU index 150  
residue id /A:157 name ALA index 162  
residue id /A:160 name LEU index 165  
residue id /A:161 name GLY index 166  
residue id /A:164 name LEU index 169  
residue id /A:165 name GLN index 170  
residue id /A:168 name ASN index 173  
residue id /A:171 name ARG index 176  
residue id /A:172 name ASP index 177  
residue id /A:233 name PHE index 238  
residue id /A:248 name TYR index 253  
residue id /A:265 name ARG index 270  

> mlp

Map values for surface "3w7f_A SES surface": minimum -45.1, mean -6.839,
maximum 24.8  

> ~ribbon

Unknown command: ~protein  

> ~display protein

> surface ligand @<6 visiblePatches 1

> view

Expected a keyword  

> style ligand sphere

Changed 48 atom styles  

> preset "initial styles" sticks

Preset implemented in Python; no expansion to individual ChimeraX commands
available.  

> style ligand sphere

Changed 48 atom styles  

> color byattribute bfactor

2443 atoms, 289 residues, 1 surfaces, atom bfactor range 18.3 to 95.2  

> open 2zco

Summary of feedback from opening 2zco fetched from pdb  
---  
note | Fetching compressed mmCIF 2zco from
http://files.rcsb.org/download/2zco.cif  
  
2zco title:  
Crystal structure of the C(30) carotenoid dehydrosqualene synthase from
Staphylococcus aureus [more info...]  
  
Chain information for 2zco #2  
---  
Chain | Description  
A | Dehydrosqualene synthase  
  
  

> preset original

Preset implemented in Python; no expansion to individual ChimeraX commands
available.  

> toolshed show "Model Panel"

> ~select #1.2

45 atoms selected  

> select #1.4

2392 atoms selected  

> ~select #1.1

2392 atoms selected  

> select #1.4

2392 atoms selected  

> hide #!1.1 models

> show #!1.1 models




OpenGL version: 4.1 INTEL-12.9.22
OpenGL renderer: Intel(R) Iris(TM) Graphics 6100
OpenGL vendor: Intel Inc.

[pett]

Reported by Michael Kenning

[Tom Goddard]

I'm not able to reproduce this on an iMac with magic trackpad, if I two finger drag with the pointer over the graphics window the model rotates, and then move the pointer to the model panel without clicking and two finger drag, then the Model Panel scrolls. I can go back and forth and it always works correctly. Tried in ChimeraX 0.9 (based on Qt 5.9 window toolkit) and ChimeraX daily (based on Qt 5.12).

Is there anything different about your setup? Are you using a magic mouse instead of a trackpad? Do you undock the model panel window (drag it out to be a separate window)? Are you able to consistently get the wrong behavior? Give exact steps.

[m.p.kenning.788486@…]

I am using a trackpad on my MacBook. All the panels are docked.

First of all I load my model, as in this case (obtained from a tutorial of a workshop today at Swansea University):

toolshed show "Side View” ; open 3w7f ; delete /b ; label ligand residues ; delete solvent ; label @@display residues ; distance :248@OH:302@O1B

The resolution on my computer is small enough such that there is a vertical scroll-bar in the Models panel. I discovered the bug when trying to scroll this up and down. I’ve tried expanding the window and this doesn’t change the bug.

To reproduce the error:


  1.  Ensure that ChimeraX is in full-screen mode (that it has its own desktop).
  2.  Focus ChimeraX on the graphical window (i.e., where the model is). I manipulated the model with the three-finger gesture to ensure this.
  3.  Use the four-finger gesture to switch desktops while ensuring that the cursor is on the graphical window. If you put the cursor in the window, it should shift the model slightly. I think that this is owing to the application detecting a three-finger gesture, as my little finger lifts up before the others briefly before completing the four-finger gesture. (I’m fairly sure this is another bug.)
  4.  Switch back to ChimeraX with the four-finger gesture.
  5.  Try scrolling up and down in the Models or Side View. This should rotate the model in the graphical view.

Earlier the bug was persistent, in spite of my clicking on the panels to shift the focus. Now it seems to stop after I have reproduced the bug and have lifted my fingers from the trackpad.

I’m sorry I couldn’t be more helpful. I hope you are able to reproduce it.


On 18 Jun 2019, at 19:23, ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu<mailto:ChimeraX-bugs-admin@cgl.ucsf.edu>> wrote:

#2092: Promiscuous gesture scrolling
---------------------------------------+----------------------
         Reporter:  788486@…          |      Owner:  goddard
             Type:  defect            |     Status:  assigned
         Priority:  normal            |  Milestone:
        Component:  General Controls  |    Version:
       Resolution:                    |   Keywords:
       Blocked By:                    |   Blocking:
Notify when closed:                    |   Platform:  all
          Project:  ChimeraX          |
---------------------------------------+----------------------

Comment (by goddard):

I'm not able to reproduce this on an iMac with magic trackpad, if I two
finger drag with the pointer over the graphics window the model rotates,
and then move the pointer to the model panel without clicking and two
finger drag, then the Model Panel scrolls.  I can go back and forth and it
always works correctly.  Tried in ChimeraX 0.9 (based on Qt 5.9 window
toolkit) and ChimeraX daily (based on Qt 5.12).

Is there anything different about your setup?  Are you using a magic mouse
instead of a trackpad?  Do you undock the model panel window (drag it out
to be a separate window)?  Are you able to consistently get the wrong
behavior?  Give exact steps.

--
Ticket URL: <https://plato.cgl.ucsf.edu/trac/ChimeraX/ticket/2092#comment:2>
ChimeraX <http://www.rbvi.ucsf.edu/chimerax/>
ChimeraX Issue Tracker

[Tom Goddard]

Thanks for the additional info. The problem is surely connected to using ChimeraX full-screen and switching desktops and doing that I was able to reproduce the scrolling in the wrong window. This is a Qt 5.9 window toolkit bug. Fortunately we just updated to Qt 5.12 in ChimeraX, it has been in the ChimeraX daily build for the last week and it does not have this problem.

You are using the older ChimeraX 0.9 which has another more serious bug where the molecules jump out of view sometimes when using the trackpad. This is also fixed in the ChimeraX daily builds. We always recommend people use the daily build for the latest fixes.