Undesirable center of rotation

[satyshur@…]

The following bug report has been submitted:
Platform:        Linux-3.10.0-1062.1.1.el7.x86_64-x86_64-with-redhat-7.7-Maipo
ChimeraX Version: 0.91 (2019-09-26)
Description
camera stereo
camera mono
camera stereo

Also, center of rotation in 3D is on the electron density and not the molceule so density is lost and molecule rotates out of view.

Log:
Startup Messages  
---  
warnings | 'clip' is a prefix of an existing command 'clipper'  
'rota' is a prefix of an existing command 'rotamers'  
  
UCSF ChimeraX version: 0.91 (2019-09-26)  
© 2016-2019 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open 6d52 structureFactors true

Summary of feedback from opening 6d52 fetched from pdb  
---  
warnings | Atom H1 is not in the residue template for GLU #1 in chain B  
Atom H1 is not in the residue template for GLU #1 in chain D  
Atom H1 is not in the residue template for GLU #1 in chain C  
Atom H1 is not in the residue template for GLU #1 in chain A  
notes | Resolution: 1.4280533552397077  
Reflection data provided as intensities. Performing French & Wilson scaling to
convert to amplitudes...  
  
6d52 title:  
Superoxide dismutase SodCI of Salmonella enterica serovar Typhimurium at 1.6
Angstrom resolution [more info...]  
  
Chain information for 6d52  
---  
Chain | Description  
1.3/A 1.3/B 1.3/C 1.3/D | Superoxide dismutase [Cu-Zn] 1  
  
Non-standard residues in 6d52 #1.3  
---  
CU — copper (II) ion  
ZN — zinc ion  
  
6d52 mmCIF Assemblies  
---  
1| author_and_software_defined_assembly  
2| author_and_software_defined_assembly  
  
  

> set bgColor white

> hide #!1.2 models

> hide #!1.3 models

> show #!1.3 models

> ui mousemode rightMode clip

> ui mousemode rightMode "clip rotate"

> camera stereo

> camera mono

> camera stereo

An error occurred in drawing the scene. Redrawing graphics is now stopped to
avoid a continuous stream of error messages. To restart graphics use the
command "graphics restart" after changing the settings that caused the error.  
  
Traceback (most recent call last):  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 73, in draw_new_frame  
view.draw(check_for_changes = False)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/core/graphics/view.py", line 166, in draw  
self._draw_scene(camera, drawings)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/core/graphics/view.py", line 205, in _draw_scene  
camera.set_render_target(vnum, r)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/core/graphics/camera.py", line 422, in set_render_target  
render.set_stereo_buffer(view_num)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/core/graphics/opengl.py", line 1171, in set_stereo_buffer  
GL.glDrawBuffer(b)  
File "src/errorchecker.pyx", line 53, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError  
OpenGL.error.GLError: GLError(  
err = 1282,  
description = b'invalid operation',  
baseOperation = glDrawBuffer,  
cArguments = (GL_BACK_RIGHT,)  
)  
  




OpenGL version: 3.3.0 NVIDIA 340.107
OpenGL renderer: Quadro FX 4800/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation

[Tom Goddard]

After "open 6d52 structurefactors true" I see the structure and density near the center of rotation and rotating correctly rotates about the center of the density and the cross-hair marker at the center of view. This seems to be working correctly for me (using Clipper tool vesrion 0.9.9 installed from toolshed).

You say the center of rotation is on the density but then rotating causes the density to be lost -- I don't understand your description.

The structure factor map display and center of rotation mode was implemented by Tristan Croll -- reassigning to him.

[Tristan Croll]

I’m afraid I haven’t tested Clipper with the stereo mode at all (don’t have a stereo machine to test it on). I also haven’t tested it with the clip rotate mouse mode. Apart from that, I do know of a bug affecting its interaction with the center of rotation - but it doesn’t look like this is that. If you do:

view <atom selection>

... the centre of rotation reverts to fixed. If you then translate the view somewhere and do:

cofr center

... then the cofr follows the view again, but is no longer at the centre of the screen (just starts moving from where it was at the moment of the view command). I’ve been meaning to track it down, but I’ve been distracted by back-to-back user workshops.

 

[Tristan Croll]

Oh - forgot to mention: that cofr bug only seems to appear when Clipper is active, which strongly suggests it’s my fault.
 

 

[Tristan Croll]

The culprit for the cofr bug was my clipping-adjusting zoom mode - it was changing the clipping plane points according to the vector between camera and cofr, rather than a point along the viewing direction vector.

[Tristan Croll]

I'm going to go ahead and tentatively close this as "fixed", since the bug causing Clipper to incorrectly move the centre of rotation has been taken care of. If you still run into problems, please let me know!