map jumps during mouse rotation / bad toolshed reporting

[rory.gordon.19@…]

The following bug report has been submitted:
Platform:        Darwin-19.5.0-x86_64-i386-64bit
ChimeraX Version: 1.0 (2020-06-04 23:15:07 UTC)
Description
left mouse button (settings, default) pressed down and rotating protein the map then jumps the inverse position (and opposite side of the protein). 

Log:
UCSF ChimeraX version: 1.0 (2020-06-04)  
© 2016-2020 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  
Some installed bundles are out of date. Please update the following bundles:

  * UI to version 1.2.1 (currently 1.0)
  * UI to version 1.2 (currently 1.0)

  

> open "/Users/rorygordon/Desktop/CYP158A1 LRET.3.pdb" format pdb

No such file/path: /Users/rorygordon/Desktop/CYP158A1 LRET.3.pdb  

> open "/Users/rorygordon/Desktop/MRes Project/Reference Enzymes/CYP158A1 -
> Streptomyces coellicolor/PDB/CYP158A1 - Biflaviolin.ent" format pdb

CYP158A1 - Biflaviolin.ent title:  
Structure and function studies of cytochrome P450 158A1 from streptomyces
coelicolor A3(2) [more info...]  
  
Chain information for CYP158A1 - Biflaviolin.ent #1  
---  
Chain | Description  
A B | cytochrome P450 CYP158A1  
  
Non-standard residues in CYP158A1 - Biflaviolin.ent #1  
---  
226 — naphthalene-1,2,4,5,7-pentol  
HEM — protoporphyrin IX containing Fe (HEME)  
  

> select /B

3279 atoms, 3246 bonds, 6 pseudobonds, 2 models selected  

> delete atoms (#!1 & sel)

> delete bonds (#!1 & sel)

> select /A

3314 atoms, 3246 bonds, 6 pseudobonds, 2 models selected  

> show (#!1 & sel) target ab

> select clear

> ui tool show Distances

> distance /A:291@NH1 /A:431@OAD

Distance between /A ARG 291 NH1 and 226 431 OAD: 2.777Å  
Must select one or more distances in the table  

> select clear

> select clear

> distance /A:291@NE /A:292@OG1

Distance between /A ARG 291 NE and THR 292 OG1: 6.523Å  

> ~distance /A:291@NE /A:292@OG1

> cartoon hide sel

> select /A

3314 atoms, 3246 bonds, 7 pseudobonds, 3 models selected  

> cartoon hide (#!1 & sel)

> select clear

> distance /A:291@NE /A:292@O

Distance between /A ARG 291 NE and THR 292 O: 2.987Å  

> distance /A:292@OG1 /A:293@N

Distance between /A THR 292 OG1 and SER 293 N: 3.066Å  

> distance /A:19@CZ2 /A:293@N

Distance between /A TRP 19 CZ2 and SER 293 N: 4.375Å  

> ~distance /A:292@OG1 /A:293@N

> select clear

> distance /A:290@NE2 /A:431@OAA

Distance between /A HIS 290 NE2 and 226 431 OAA: 3.123Å  

> distance /A:290@O /A:290@CD2

Distance between /A HIS 290 O and CD2: 3.721Å  

> ~distance /A:290@O /A:290@CD2

> distance /A:252@OD1 /A:290@ND1

Distance between /A ASN 252 OD1 and HIS 290 ND1: 3.248Å  

> distance /A:252@OD1 /A:255@NE2

Distance between /A ASN 252 OD1 and GLN 255 NE2: 5.830Å  

> distance /A:255@OE1 /A:255@NE2

Distance between /A GLN 255 OE1 and NE2: 2.244Å  

> distance /A:255@OE1 /A:391@CH2

Distance between /A GLN 255 OE1 and TRP 391 CH2: 4.305Å  

> select clear

> distance /A:290@O /A:290@ND1

Distance between /A HIS 290 O and ND1: 3.414Å  

> distance /A:255@NE2 /A:290@O

Distance between /A GLN 255 NE2 and HIS 290 O: 4.293Å  

> distance /A:290@O /A:398@NE

Distance between /A HIS 290 O and ARG 398 NE: 5.786Å  

> ~distance /A:19@CZ2 /A:293@N

> ~distance /A:290@O /A:398@NE




OpenGL version: 4.1 INTEL-14.6.18
OpenGL renderer: Intel HD Graphics 5000 OpenGL Engine
OpenGL vendor: Intel Inc.Hardware:

    Hardware Overview:

      Model Name: MacBook Air
      Model Identifier: MacBookAir6,2
      Processor Name: Dual-Core Intel Core i5
      Processor Speed: 1.4 GHz
      Number of Processors: 1
      Total Number of Cores: 2
      L2 Cache (per Core): 256 KB
      L3 Cache: 3 MB
      Hyper-Threading Technology: Enabled
      Memory: 4 GB
      Boot ROM Version: 121.0.0.0.0
      SMC Version (system): 2.13f15

Software:

    System Software Overview:

      System Version: macOS 10.15.5 (19F101)
      Kernel Version: Darwin 19.5.0
      Time since boot: 1 day 1:50

Graphics/Displays:

    Intel HD Graphics 5000:

      Chipset Model: Intel HD Graphics 5000
      Type: GPU
      Bus: Built-In
      VRAM (Dynamic, Max): 1536 MB
      Vendor: Intel
      Device ID: 0x0a26
      Revision ID: 0x0009
      Metal: Supported, feature set macOS GPUFamily1 v4
      Displays:
        Color LCD:
          Display Type: LCD
          Resolution: 1440 x 900 (Widescreen eXtended Graphics Array Plus)
          UI Looks like: 1440 x 900
          Framebuffer Depth: 24-Bit Color (ARGB8888)
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: No
          Connection Type: Internal

PyQt version: 5.12.3
Compiled Qt version: 5.12.4
Runtime Qt version: 5.12.8

[Eric Pettersen]

This ticket also shows two problems with the toolshed update mechanism:

1) It is reporting out-of-date packages when that code was supposed to be suppressed in the release

2) It reports both the 1.2 and 1.2.1 versions of UI when it should only show 1.2.1

[Tom Goddard]

In this bug report you talk about a protein structure and a map but the log only shows you have a PDB model open, not a map. Are you reporting the problem from some previous ChimeraX session?

Are the protein and map aligned with each other? Then when you say it jumps do they become unaligned? Or is it just that the view direction jumps and they are still aligned?

[rory.gordon.19@…]

Hi Tom,

Thanks for your email and apologies for the confusion caused by my email.

I was/am viewing a .pdb structures not a map. As I am rotating this map, the view seems to jump to the complex opposite side of the protein.

Not sure why, but it has happened on various different .pdb structures which I have been viewing.

Cheers,

Rory
________________________________
From: ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
Sent: 01 July 2020 17:56
Cc: chimera-staff@cgl.ucsf.edu <chimera-staff@cgl.ucsf.edu>; goddard@cgl.ucsf.edu <goddard@cgl.ucsf.edu>; Gordon, Rory <rory.gordon.19@ucl.ac.uk>
Subject: Re: [ChimeraX] #3463: map jumps during mouse rotation / bad toolshed reporting

#3463: map jumps during mouse rotation / bad toolshed reporting
---------------------------------------+-------------------------
          Reporter:  rory.gordon.19@…  |      Owner:  Tom 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 Tom Goddard):

 In this bug report you talk about a protein structure and a map but the
 log only shows you have a PDB model open, not a map.  Are you reporting
 the problem from some previous ChimeraX session?

 Are the protein and map aligned with each other?  Then when you say it
 jumps do they become unaligned?  Or is it just that the view direction
 jumps and they are still aligned?

--
Ticket URL: <https://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fplato.cgl.ucsf.edu%2Ftrac%2FChimeraX%2Fticket%2F3463%23comment%3A3&amp;data=02%7C01%7C%7C3e68d9a3ff6a4e7fe5dc08d81ddfc4ee%7C1faf88fea9984c5b93c9210a11d9a5c2%7C0%7C0%7C637292194206951372&amp;sdata=U5ufAHx6Olelwzya8BAMP8DaQboj%2Btirl4IoI4vvxx8%3D&amp;reserved=0>
ChimeraX <https://eur01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.rbvi.ucsf.edu%2Fchimerax%2F&amp;data=02%7C01%7C%7C3e68d9a3ff6a4e7fe5dc08d81ddfc4ee%7C1faf88fea9984c5b93c9210a11d9a5c2%7C0%7C0%7C637292194206951372&amp;sdata=I83HOJaHpkwL6gDUx%2FYqu7%2Fjx8L6oQfJ9sdUU7A%2BDZE%3D&amp;reserved=0>
ChimeraX Issue Tracker

[goddard@…]

Thanks.  I have on rare occasion seen this kind of jump when rotating.  Do you use a trackpad or a mouse when this happens?  If a trackpad, do you use two finger drag to rotate or do you click and drag with one finger to rotate?

I know in theory how this can happen, ChimeraX loses track of the trackpad/mouse position and then suddenly it looks like a big jump in position occurred.  I will look into what could trigger that.

[Tom Goddard]

Fixed.

When using Mac trackpad multifinger drags I sometimes observed a big jump in model position. I could get this to happen occasionally when rapidly tapping while dragging on the trackpad. Debugging showed that t.pos() and t.lastPos() where t is a Qt TouchPoint make a big jump. This seems like a Qt bug. I made ChimeraX code not use lastPos() and just use previous TouchPoint events. Then I was not able to get any large spurious model motions.

[rory.gordon.19@…]

Hi Tom,

I am using a wireless mouse with a fitted rollerball.

It is quite strange because it seems that it is taking me to the complete other side of the protein.

Cheers,

Rory
________________________________
From: ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
Sent: 02 July 2020 18:02
To: Gordon, Rory <rory.gordon.19@ucl.ac.uk>; goddard@cgl.ucsf.edu <goddard@cgl.ucsf.edu>
Cc: chimera-staff@cgl.ucsf.edu <chimera-staff@cgl.ucsf.edu>
Subject: Re: [ChimeraX] #3463: map jumps during mouse rotation / bad toolshed reporting

#3463: map jumps during mouse rotation / bad toolshed reporting
---------------------------------------+-------------------------
          Reporter:  rory.gordon.19@…  |      Owner:  Tom 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@…):

 {{{
 Thanks.  I have on rare occasion seen this kind of jump when rotating.  Do
 you use a trackpad or a mouse when this happens?  If a trackpad, do you
 use two finger drag to rotate or do you click and drag with one finger to
 rotate?

 I know in theory how this can happen, ChimeraX loses track of the
 trackpad/mouse position and then suddenly it looks like a big jump in
 position occurred.  I will look into what could trigger that.

 }}}

--
Ticket URL: <https://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fplato.cgl.ucsf.edu%2Ftrac%2FChimeraX%2Fticket%2F3463%23comment%3A5&amp;data=02%7C01%7C%7Ce739c12c2b6d41abe4a808d81ea9b4c1%7C1faf88fea9984c5b93c9210a11d9a5c2%7C0%7C0%7C637293061531677541&amp;sdata=TK%2B8xElW%2FR5Yr5PD9id1aFRZjgJ6YW%2BeH9Rt60IyaZI%3D&amp;reserved=0>
ChimeraX <https://eur01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.rbvi.ucsf.edu%2Fchimerax%2F&amp;data=02%7C01%7C%7Ce739c12c2b6d41abe4a808d81ea9b4c1%7C1faf88fea9984c5b93c9210a11d9a5c2%7C0%7C0%7C637293061531677541&amp;sdata=IUBQotPAgKe%2B9MHPuFs63f1iD8fW8STefRuW0sRBzAk%3D&amp;reserved=0>
ChimeraX Issue Tracker

[goddard@…]

Ok, my fix was only for multitouch trackpads.  Does the glitch happen when using the rollerball?  Or is it just when doing a mouse drag?  I have never seen this kind of glitch with a mouse.