Opened 5 years ago

Closed 5 years ago

Last modified 5 years ago

#4237 closed defect (not a bug)

Ribbons: spline normal computation for straight line

Reported by: mmaldo@… Owned by: Tom Goddard
Priority: normal Milestone:
Component: Depiction Version:
Keywords: Cc:
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description 

The following bug report has been submitted:
Platform:        Darwin-18.7.0-x86_64-i386-64bit
ChimeraX Version: 0.91 (2019-12-23)
Description
I'm not sure what caused this problem. It happens when I open the file or try to select the chains. The file does open, but then chain commands are not responsive, e.g. select, color, etc. Thanks!

Log:
UCSF ChimeraX version: 0.91 (2019-12-23)  
© 2016-2019 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open
> /Volumes/cloud.mcb.ucdavis.edu/mcb_labs/letts/Model_Building/T.thermophila/SCI+III2/Maps/CIMAdistal-
> focused_cryosparc_P15_J424_007_volume_map_sharp-fit.mrc

Opened CIMAdistal-focused_cryosparc_P15_J424_007_volume_map_sharp-fit.mrc,
grid size 600,600,600, pixel 0.835, shown at level 0.318, step 4, values
float32  

> open
> /Volumes/cloud.mcb.ucdavis.edu/mcb_labs/letts/Model_Building/T.thermophila/SCI+III2/Initial_model/CI_Modelling/MA_fitted_J424-MA-
> focused_202110210_mm-coot-10.pdb

Summary of feedback from opening
/Volumes/cloud.mcb.ucdavis.edu/mcb_labs/letts/Model_Building/T.thermophila/SCI+III2/Initial_model/CI_Modelling/MA_fitted_J424-MA-
focused_202110210_mm-coot-10.pdb  
---  
warning | Start residue of secondary structure not found: HELIX 57 57 THR D 90
PHE D 94 1 5  
  
Chain information for MA_fitted_J424-MA-focused_202110210_mm-coot-10.pdb #2  
---  
Chain | Description  
| No description available  
1 | No description available  
2 | No description available  
3 | No description available  
4 | No description available  
5 | No description available  
6 | No description available  
7 | No description available  
8 | 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  
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  
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  
  

> hide all

> show #2 cartoons

Traceback (most recent call last):  
File
"/programs/i386-mac/chimerax/0.91/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File
"/programs/i386-mac/chimerax/0.91/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/structure.py", line 2661, in
_update_graphics_if_needed  
s[i]._update_graphics_if_needed()  
File
"/programs/i386-mac/chimerax/0.91/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/structure.py", line 304, in
_update_graphics_if_needed  
self._create_ribbon_graphics()  
File
"/programs/i386-mac/chimerax/0.91/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/structure.py", line 773, in _create_ribbon_graphics  
self._use_spline_normals)  
File
"/programs/i386-mac/chimerax/0.91/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/ribbon.py", line 50, in __init__  
atom_normals = self._compute_normals_from_control_points(coords)  
File
"/programs/i386-mac/chimerax/0.91/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/ribbon.py", line 246, in
_compute_normals_from_control_points  
raise RuntimeError("spline normal computation for straight line")  
RuntimeError: spline normal computation for straight line  
  
Error processing trigger "graphics update":  
RuntimeError: spline normal computation for straight line  
  
File
"/programs/i386-mac/chimerax/0.91/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/ribbon.py", line 246, in
_compute_normals_from_control_points  
raise RuntimeError("spline normal computation for straight line")  
  
See log for complete Python traceback.  
  

> hide #!1 models

> show #!1 models

> volume #1 step 1

> volume #1 level 0.404

> volume #1 level 0.3639

> preset "initial styles" "space-filling (single color)"

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

> undo

> show #!1 models

> lighting full

> color zone #1 near #2 distance 3

> hide #!1 models

> show #!1 models

> color zone #1 near #2 distance 3

> view

> volume #1 level 0.4499

> turn y 90

> turn y 30

> turn y -15

> movie record

> turn y 2 180

> wait 180

> movie encode /Users/mmaldo/Desktop/movie2.mp4

Movie saved to /Users/mmaldo/Desktop/movie2.mp4  
  

> hide #!1 models

> show #!1 models

> hide #!1 models

> ui mousemode rightMode select

Traceback (most recent call last):  
File
"/programs/i386-mac/chimerax/0.91/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 477, in <lambda>  
gw.mouseReleaseEvent = lambda e, s=self: s._dispatch_mouse_event(e,
"mouse_up")  
File
"/programs/i386-mac/chimerax/0.91/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 402, in
_dispatch_mouse_event  
f(MouseEvent(event, modifiers=modifiers))  
File
"/programs/i386-mac/chimerax/0.91/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/mouse_modes/std_modes.py", line 56, in mouse_up  
mouse_drag_select(self.mouse_down_position, event, mode, self.session,
self.view)  
File
"/programs/i386-mac/chimerax/0.91/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/mouse_modes/std_modes.py", line 191, in mouse_drag_select  
pick = view.rectangle_intercept(sx,sy,x,y,exclude=unpickable)  
File
"/programs/i386-mac/chimerax/0.91/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/graphics/view.py", line 809, in rectangle_intercept  
picks = self.drawing.planes_pick(planes, exclude=exclude)  
File
"/programs/i386-mac/chimerax/0.91/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/graphics/drawing.py", line 1107, in planes_pick  
picks.extend(d.planes_pick(pplanes, exclude))  
File
"/programs/i386-mac/chimerax/0.91/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/graphics/drawing.py", line 1107, in planes_pick  
picks.extend(d.planes_pick(pplanes, exclude))  
File
"/programs/i386-mac/chimerax/0.91/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/graphics/drawing.py", line 1107, in planes_pick  
picks.extend(d.planes_pick(pplanes, exclude))  
File
"/programs/i386-mac/chimerax/0.91/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/structure.py", line 2213, in planes_pick  
t2r = self.parent.parent._ribbon_t2r[self]  
KeyError: <chimerax.atomic.structure.RibbonDrawing object at 0x137d4c410>  
  
KeyError:  
  
File
"/programs/i386-mac/chimerax/0.91/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/structure.py", line 2213, in planes_pick  
t2r = self.parent.parent._ribbon_t2r[self]  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/programs/i386-mac/chimerax/0.91/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 475, in <lambda>  
gw.mousePressEvent = lambda e, s=self: s._dispatch_mouse_event(e,
"mouse_down")  
File
"/programs/i386-mac/chimerax/0.91/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 396, in
_dispatch_mouse_event  
lm.mouse_up(MouseEvent(event, modifiers=modifiers))  
File
"/programs/i386-mac/chimerax/0.91/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/mouse_modes/std_modes.py", line 56, in mouse_up  
mouse_drag_select(self.mouse_down_position, event, mode, self.session,
self.view)  
File
"/programs/i386-mac/chimerax/0.91/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/mouse_modes/std_modes.py", line 191, in mouse_drag_select  
pick = view.rectangle_intercept(sx,sy,x,y,exclude=unpickable)  
File
"/programs/i386-mac/chimerax/0.91/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/graphics/view.py", line 809, in rectangle_intercept  
picks = self.drawing.planes_pick(planes, exclude=exclude)  
File
"/programs/i386-mac/chimerax/0.91/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/graphics/drawing.py", line 1107, in planes_pick  
picks.extend(d.planes_pick(pplanes, exclude))  
File
"/programs/i386-mac/chimerax/0.91/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/graphics/drawing.py", line 1107, in planes_pick  
picks.extend(d.planes_pick(pplanes, exclude))  
File
"/programs/i386-mac/chimerax/0.91/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/graphics/drawing.py", line 1107, in planes_pick  
picks.extend(d.planes_pick(pplanes, exclude))  
File
"/programs/i386-mac/chimerax/0.91/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/structure.py", line 2213, in planes_pick  
t2r = self.parent.parent._ribbon_t2r[self]  
KeyError: <chimerax.atomic.structure.RibbonDrawing object at 0x137d4c410>  
  
KeyError:  
  
File
"/programs/i386-mac/chimerax/0.91/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/structure.py", line 2213, in planes_pick  
t2r = self.parent.parent._ribbon_t2r[self]  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/programs/i386-mac/chimerax/0.91/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 477, in <lambda>  
gw.mouseReleaseEvent = lambda e, s=self: s._dispatch_mouse_event(e,
"mouse_up")  
File
"/programs/i386-mac/chimerax/0.91/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 402, in
_dispatch_mouse_event  
f(MouseEvent(event, modifiers=modifiers))  
File
"/programs/i386-mac/chimerax/0.91/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/mouse_modes/std_modes.py", line 56, in mouse_up  
mouse_drag_select(self.mouse_down_position, event, mode, self.session,
self.view)  
File
"/programs/i386-mac/chimerax/0.91/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/mouse_modes/std_modes.py", line 191, in mouse_drag_select  
pick = view.rectangle_intercept(sx,sy,x,y,exclude=unpickable)  
File
"/programs/i386-mac/chimerax/0.91/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/graphics/view.py", line 809, in rectangle_intercept  
picks = self.drawing.planes_pick(planes, exclude=exclude)  
File
"/programs/i386-mac/chimerax/0.91/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/graphics/drawing.py", line 1107, in planes_pick  
picks.extend(d.planes_pick(pplanes, exclude))  
File
"/programs/i386-mac/chimerax/0.91/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/graphics/drawing.py", line 1107, in planes_pick  
picks.extend(d.planes_pick(pplanes, exclude))  
File
"/programs/i386-mac/chimerax/0.91/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/graphics/drawing.py", line 1107, in planes_pick  
picks.extend(d.planes_pick(pplanes, exclude))  
File
"/programs/i386-mac/chimerax/0.91/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/structure.py", line 2213, in planes_pick  
t2r = self.parent.parent._ribbon_t2r[self]  
KeyError: <chimerax.atomic.structure.RibbonDrawing object at 0x137d4c410>  
  
KeyError:  
  
File
"/programs/i386-mac/chimerax/0.91/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/structure.py", line 2213, in planes_pick  
t2r = self.parent.parent._ribbon_t2r[self]  
  
See log for complete Python traceback.  
  




OpenGL version: 4.1 NVIDIA-12.0.24 355.11.10.50.10.103
OpenGL renderer: NVIDIA GeForce GT 750M OpenGL Engine
OpenGL vendor: NVIDIA Corporation

Attachments (1)

SBgrid_test_newer.pdb​ (4.7 MB ) - added by mmaldo@… 5 years ago.
Added by email2trac

Change History (15)

comment:1 by Eric Pettersen, 5 years ago

Component: Unassigned → Depiction
Owner: set to Tom Goddard
Platform: → all
Project: → ChimeraX
Status: new → assigned
Summary: ChimeraX bug report submission → Ribbons: spline normal computation for straight line

Reported by Maria Maldonado

comment:2 by Tom Goddard, 5 years ago

Apparently your structure has atoms on exactly a straight line and sadly ChimeraX ribbon code fails because it can't figure out what normal vector to use. I can try to fix this, but I am not sure I can make an example file that reproduces the problem. Can you email the PDB file that causes the error?

/Volumes/cloud.mcb.ucdavis.edu/mcb_labs/letts/Model_Building/T.thermophila/SCI+III2/Initial_model/CI_Modelling/MA_fitted_J424-MA-focused_202110210_mm-coot-10.pdb

in reply to:  3 ; comment:3 by mmaldo@…, 5 years ago 

Hello Tom,

Thank you very much for getting back to me. The pdb is attached.

Thanks,
Maria 

On 2/11/21, 3:05 PM, "ChimeraX" <ChimeraX-bugs-admin@cgl.ucsf.edu> wrote:

    #4237: Ribbons: spline normal computation for straight line
    --------------------------------+-------------------------
              Reporter:  mmaldo@…   |      Owner:  Tom Goddard
                  Type:  defect     |     Status:  assigned
              Priority:  normal     |  Milestone:
             Component:  Depiction  |    Version:
            Resolution:             |   Keywords:
            Blocked By:             |   Blocking:
    Notify when closed:             |   Platform:  all
               Project:  ChimeraX   |
    --------------------------------+-------------------------

    Comment (by Tom Goddard):

     Apparently your structure has atoms on exactly a straight line and sadly
     ChimeraX ribbon code fails because it can't figure out what normal vector
     to use.  I can try to fix this, but I am not sure I can make an example
     file that reproduces the problem.  Can you email the PDB file that causes
     the error?

     /Volumes/cloud.mcb.ucdavis.edu/mcb_labs/letts/Model_Building/T.thermophila/SCI+III2/Initial_model/CI_Modelling/MA_fitted_J424
     -MA-focused_202110210_mm-coot-10.pdb

    --
    Ticket URL: <https://plato.cgl.ucsf.edu/trac/ChimeraX/ticket/4237#comment:2>
    ChimeraX <http://www.rbvi.ucsf.edu/chimerax/>
    ChimeraX Issue Tracker

SBgrid_test_newer.pdb​

by mmaldo@…, 5 years ago

Attachment: SBgrid_test_newer.pdb​ added

Added by email2trac

in reply to:  5 comment:4 by goddard@…, 5 years ago 

Thanks.  But this PDB structure does not give the error you reported

open SBGrid_test_newer.pdb
show #1 cartoon

No error.

Oh!  I see you are using ChimeraX version 0.91.  That is very old.  Please try with the current ChimeraX 1.1.  The ribbon code was changed a lot.

in reply to:  6 ; comment:5 by mmaldo@…, 5 years ago 

Ok, thank you. I'm using the Chimerax on Sbgrid, I thought it was updated regularly.

Best,
Maria 

On 2/11/21, 3:57 PM, "ChimeraX" <ChimeraX-bugs-admin@cgl.ucsf.edu> wrote:

    #4237: Ribbons: spline normal computation for straight line
    --------------------------------+-------------------------
              Reporter:  mmaldo@…   |      Owner:  Tom Goddard
                  Type:  defect     |     Status:  assigned
              Priority:  normal     |  Milestone:
             Component:  Depiction  |    Version:
            Resolution:             |   Keywords:
            Blocked By:             |   Blocking:
    Notify when closed:             |   Platform:  all
               Project:  ChimeraX   |
    --------------------------------+-------------------------

    Comment (by goddard@…):

     {{{
     Thanks.  But this PDB structure does not give the error you reported

     open SBGrid_test_newer.pdb
     show #1 cartoon

     No error.

     Oh!  I see you are using ChimeraX version 0.91.  That is very old.  Please
     try with the current ChimeraX 1.1.  The ribbon code was changed a lot.
     }}}

    --
    Ticket URL: <https://plato.cgl.ucsf.edu/trac/ChimeraX/ticket/4237#comment:4>
    ChimeraX <http://www.rbvi.ucsf.edu/chimerax/>
    ChimeraX Issue Tracker

in reply to:  7 ; comment:6 by goddard@…, 5 years ago 

Thanks!  I'll talk to SBGrid about that.

in reply to:  8 ; comment:7 by goddard@…, 5 years ago 

The SBGrid ChimeraX page says the current version is 1.1.1 on macOS.

	https://sbgrid.org/software/titles/chimerax <https://sbgrid.org/software/titles/chimerax>

I don't know how SBGrid software is updated.  That page says you run "sbgrid-cli install chimerax" to install it.  Do you know who does the SBGrid update or install for your machine?

in reply to:  9 ; comment:8 by mmaldo@…, 5 years ago 

I’m not sure how the updates work, I assumed they happened automatically in the background and then I got the most updated versions by initializing sbgrid and running the programme. Jason Key is the person we normally talk to at SBGrid.

From: Tom Goddard <goddard@sonic.net>
Date: Thursday, February 11, 2021 at 5:12 PM
To: Maria Maldonado <mmaldo@ucdavis.edu>
Cc: "ChimeraX-bugs@cgl.ucsf.edu" <ChimeraX-bugs@cgl.ucsf.edu>
Subject: Re: [ChimeraX] #4237: Ribbons: spline normal computation for straight line

The SBGrid ChimeraX page says the current version is 1.1.1 on macOS.

https://sbgrid.org/software/titles/chimerax

I don't know how SBGrid software is updated.  That page says you run "sbgrid-cli install chimerax" to install it.  Do you know who does the SBGrid update or install for your machine?

comment:9 by Tom Goddard, 5 years ago

The PDB file you sent has not-a-number values for coordinates:

ATOM 56959 O ALA t 19 180.357 270.851 173.912 1.00 50.00 O
ATOM 56960 CB ALA t 19 181.267 274.063 175.347 1.00 50.00 C
ATOM 56961 N ALA i 2 nan nan nan 1.00 50.00 N
ATOM 56962 C ALA i 2 nan nan nan 1.00 50.00 C
ATOM 56963 CA ALA i 2 nan nan nan 1.00 50.00 C
ATOM 56964 O ALA i 2 nan nan nan 1.00 50.00 O
...

You can be sure that will cause havoc. Current ChimeraX does not give an error and remarkably does show a ribbon for this structure, but weird stuff happens, for instance if you undisplay the atoms then the ribbon vanishes too because the ribbon gets NaN coordinates and the ribbon bounds are then unknown and cause the graphics to goof up.

comment:10 by Tom Goddard, 5 years ago

This SBGrid page says that for the macOS GUI SBGrid installer updates are "managed by the user". So it sounds like they are not automatic.

​https://sbgrid.org/wiki/installation_overview

"The MacOS GUI installation manager allows users to select the applications they need when they need them through a MacOS-native graphical application. Applications are updated on a rolling basis and are available to the user at their convenience. Updates are reported when available, but are managed by the user."

in reply to:  12 comment:11 by mmaldo@…, 5 years ago 

Oh, wow, ok! Thanks for letting me know! Sorry about that.

On 2/11/21, 5:24 PM, "ChimeraX" <ChimeraX-bugs-admin@cgl.ucsf.edu> wrote:

    #4237: Ribbons: spline normal computation for straight line
    --------------------------------+-------------------------
              Reporter:  mmaldo@…   |      Owner:  Tom Goddard
                  Type:  defect     |     Status:  assigned
              Priority:  normal     |  Milestone:
             Component:  Depiction  |    Version:
            Resolution:             |   Keywords:
            Blocked By:             |   Blocking:
    Notify when closed:             |   Platform:  all
               Project:  ChimeraX   |
    --------------------------------+-------------------------

    Comment (by Tom Goddard):

     This SBGrid page says that for the macOS GUI SBGrid installer updates are
     "managed by the user".  So it sounds like they are not automatic.

     https://sbgrid.org/wiki/installation_overview

     "The MacOS GUI installation manager allows users to select the
     applications they need when they need them through a MacOS-native
     graphical application. Applications are updated on a rolling basis and are
     available to the user at their convenience. Updates are reported when
     available, but are managed by the user."

    --
    Ticket URL: <https://plato.cgl.ucsf.edu/trac/ChimeraX/ticket/4237#comment:10>
    ChimeraX <http://www.rbvi.ucsf.edu/chimerax/>
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comment:12 by Tom Goddard, 5 years ago

Resolution: → not a bug
Status: assigned → closed

No problem.

in reply to:  14 comment:13 by mmaldo@…, 5 years ago 

Thank you! Do you know how that could have happened in Coot? I did a google search but it does not come up. It's a model started by somebody else, so not sure what may have happened to them.

Thanks,
Maria 

On 2/11/21, 5:19 PM, "ChimeraX" <ChimeraX-bugs-admin@cgl.ucsf.edu> wrote:

    #4237: Ribbons: spline normal computation for straight line
    --------------------------------+-------------------------
              Reporter:  mmaldo@…   |      Owner:  Tom Goddard
                  Type:  defect     |     Status:  assigned
              Priority:  normal     |  Milestone:
             Component:  Depiction  |    Version:
            Resolution:             |   Keywords:
            Blocked By:             |   Blocking:
    Notify when closed:             |   Platform:  all
               Project:  ChimeraX   |
    --------------------------------+-------------------------

    Comment (by Tom Goddard):

     The PDB file you sent has not-a-number values for coordinates:

     ATOM  56959  O   ALA t  19     180.357 270.851 173.912  1.00 50.00
     O
     ATOM  56960  CB  ALA t  19     181.267 274.063 175.347  1.00 50.00
     C
     ATOM  56961  N   ALA i   2         nan     nan     nan  1.00 50.00
     N
     ATOM  56962  C   ALA i   2         nan     nan     nan  1.00 50.00
     C
     ATOM  56963  CA  ALA i   2         nan     nan     nan  1.00 50.00
     C
     ATOM  56964  O   ALA i   2         nan     nan     nan  1.00 50.00
     O
     ...

     You can be sure that will cause havoc.  Current ChimeraX does not give an
     error and remarkably does show a ribbon for this structure, but weird
     stuff happens, for instance if you undisplay the atoms then the ribbon
     vanishes too because the ribbon gets NaN coordinates and the ribbon bounds
     are then unknown and cause the graphics to goof up.

    --
    Ticket URL: <https://plato.cgl.ucsf.edu/trac/ChimeraX/ticket/4237#comment:9>
    ChimeraX <http://www.rbvi.ucsf.edu/chimerax/>
    ChimeraX Issue Tracker

in reply to:  15 ; comment:14 by goddard@…, 5 years ago 

I don't know how Coot could have produced NaN coordinates.  Seems like a bug in Coot.  But maybe the starting model fed into Coot had the NaN.  I was surprised that our PDB reader even accepted the file.  But I guess the standard number parsing code allows "nan" as a legal value.
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