Selection outline issues

[taohsin.chang@…]

The following bug report has been submitted:
Platform:        Darwin-18.6.0-x86_64-i386-64bit
ChimeraX Version: 0.91 (2019-07-10)
Description
(Describe the actions that caused this problem to occur here)
Selection does not show green line very well. Very strange. It is sometime OK, but it usually shows isolated green patches.

Thank you very much!

Log:
Startup Messages  
---  
warning | 'clip' is a prefix of an existing command 'clipper'  
  
UCSF ChimeraX version: 0.91 (2019-07-10)  
© 2016-2019 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open "/Users/tao-hsin/OneDrive - Johns Hopkins University/2019-S2C2-modeling
workshop/chimerax_tutorial/6n2y.cif"

6n2y.cif title:  
Bacillus PS3 ATP synthase class 1 [more info...]  
  
Chain information for 6n2y.cif #1  
---  
Chain | Description  
A B C | ATP synthase subunit α  
D E F | ATP synthase subunit β  
G | ATP synthase γ chain  
H | ATP synthase ε chain  
I | ATP synthase subunit δ  
a | ATP synthase subunit a  
b1 | ATP synthase subunit b  
b2 | ATP synthase subunit b  
c0 c1 c2 c3 c4 c5 c6 c7 c8 c9 | ATP synthase subunit c  
  
Non-standard residues in 6n2y.cif #1  
---  
ADP — adenosine-5'-diphosphate  
ATP — adenosine-5'-triphosphate  
MG — magnesium ion  
PO4 — phosphate ion  
  

> select /A:2-501

3827 atoms, 3888 bonds, 1 model selected  

> select /A:2-501

3827 atoms, 3888 bonds, 1 model selected  

> select /B:2-501

3787 atoms, 3846 bonds, 1 model selected  

> select /B:2-501

3787 atoms, 3846 bonds, 1 model selected  




OpenGL version: 4.1 ATI-2.9.26
OpenGL renderer: AMD Radeon Pro Vega 16 OpenGL Engine
OpenGL vendor: ATI Technologies Inc.

[Tom Goddard]

Strike that last comment. The fix was for a different ticket.

[Tom Goddard]

I suspect this is a graphics driver problem. I just ordered a new Mac laptop that has Radeon Vega Pro 20 graphics that will probably have the same problem as the laptop in this report with Radeon Vega Pro 16 graphics. It will probably arrive in a week or two and I can then do testing.

My old MacBook Pro laptop (circa 2012, Nvidia Geforce GT 650M) displays the selection outlines correctly.

[tchang37@…]

Hi Tom,

Thank you very much! I remember the chimera X that works fine in your old Macbook during the tutorial.
I like your lecture for the chimera X very much. It is super useful to let me start using Chimera X rather than always using PyMol and Coot.

BTW, I am very happy for my new MacBook Pro 2019 (except the graphic card issue for Chimera X). I hope you will enjoy your new one as well.

See you next time.

Best wishes,
Tao-Hsin

Tao-Hsin Chang, DPhil
Human Frontier Science Program Postdoctoral Fellow
Department of Molecular Biology and Genetics
Howard Hughes Medical Institute
805 PCTB
725 North Wolfe Street
Johns Hopkins Medical School
Baltimore, MD 21205
Laboratory of Jeremy Nathans, MD/PhD
410-955-4679
tchang37@jhmi.edu<mailto:tchang37@jhmi.edu>
https://www.ndm.ox.ac.uk/tao-hsin-chang



On Jul 12, 2019, at 6:09 PM, ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu<mailto:ChimeraX-bugs-admin@cgl.ucsf.edu>> wrote:

#2216: Selection outline issues
--------------------------------------+----------------------
         Reporter:  taohsin.chang@…  |      Owner:  goddard
             Type:  defect           |     Status:  assigned
         Priority:  normal           |  Milestone:
        Component:  Graphics         |    Version:
       Resolution:                   |   Keywords:
       Blocked By:                   |   Blocking:
Notify when closed:                   |   Platform:  all
          Project:  ChimeraX         |
--------------------------------------+----------------------

Comment (by goddard):

I suspect this is a graphics driver problem.  I just ordered a new Mac
laptop that has Radeon Vega Pro 20 graphics that will probably have the
same problem as the laptop in this report with Radeon Vega Pro 16
graphics.  It will probably arrive in a week or two and I can then do
testing.

My old MacBook Pro laptop (circa 2012, Nvidia Geforce GT 650M) displays
the selection outlines correctly.

--
Ticket URL: <https://plato.cgl.ucsf.edu/trac/ChimeraX/ticket/2216#comment:4>
ChimeraX <http://www.rbvi.ucsf.edu/chimerax/>
ChimeraX Issue Tracker

[Tom Goddard]

Fixed.

My new laptop with Radeon Pro Vega 20 graphics had the same fragmented selection outlines. It appears the problem is that copying the default framebuffer depth values to an offscreen buffer for rendering the selection gets the wrong depth values. If the original rendering is done offscreen then the depth buffer copy works as expected and outlines are correct. So I put in a specific check for Mac Radeon Pro Vega graphics that uses offscreen rendering for outlines. The depth buffer is copied with glBlitFramebuffer() and the OpenGL documentation says that if the source and destination depth buffers have incompatible formats then glBlitFramebuffer() gives an INVALID_OPERATION error. We don't get that error, so supposedly the depth buffers are compatible. This looks like a bug in the OpenGL graphics driver.

[taohsin.chang@…]

Hi Tom,

I was wondering how can I fix the problem in my side? Just download the latest released ChimeraX?
Thank you. 
Have a nice weekend.

Best wishes,
Tao-Hsin

[goddard@…]

Yes, the current daily build should draw correct selection outlines on your mac laptop.