Marker placement and resizing bug

[Meelad.Amouzgar@…]

Hello,

I found a bug. After I resize a placed marker using the mouse mode tool, I switch back to the "place marker on surface" to continue placing markers of the new, smaller size. However, the new markers that I place are of random sizes. They are always far larger than the resized marker, covering the entire chimeraX image area at times.  Thanks.

Best,
Meelad Amouzgar
Dumont Lab, UCSF

[Eric Pettersen]

From a later mail:

Here is the error report:

AttributeError: 'Atom' object has no attribute '_c_pointer_ref'

File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\core\atomic\molc.py", line 75, in get_prop
cget(self._c_pointer_ref, 1, v_ref)

See log for complete Python traceback.

If you wish to report this error, send mail to chimerax-bugs@… and describe what you were doing and include a copy of the contents of the log. Don't include any data you wish to remain private since a publicly viewable bug report will be created.

[goddard@…]

I tried placing markers on a 3d image surface, then resizing a marker, then placing markers on the surface, tried several repetitions and it always gave new markers of the same size as the previously resized marker.  So I don’t know how to reproduce the problem you describe.  Are you using the current ChimeraX daily build?  Are there any additional clues you could give me?  Does it work correctly on some maps but not others?

[Meelad.Amouzgar@…]

Hello, sorry for the response delay.

I switched to the new ChimeraX build and it continues to give resize errors. I am specifically using the "place marker on surface" setting. I have attached 3 screenshots that display the bug that occurs. 

1) I place a marker at surface.
2) I resize image.
3) I place multiple new markers. The new markers are of various sizes, and even the initial marker (marker 1 screenshot) changed shapes.

When I don't resize any markers, they remain the same size. This bug only occurs when I start using the resize option.

Best,
Meelad

-----Original Message-----
From: ChimeraX [mailto:ChimeraX-bugs-admin@cgl.ucsf.edu] 
Sent: Thursday, February 15, 2018 4:31 PM
To: Amouzgar, Meelad <Meelad.Amouzgar@ucsf.edu>; goddard@cgl.ucsf.edu
Subject: Re: [ChimeraX] #1036: Marker placement and resizing bug

#1036: Marker placement and resizing bug
----------------------------------------+----------------------
          Reporter:  Meelad.Amouzgar@…  |      Owner:  goddard
              Type:  defect             |     Status:  assigned
          Priority:  normal             |  Milestone:
         Component:  Volume Data        |    Version:
        Resolution:                     |   Keywords:
        Blocked By:                     |   Blocking:
Notify when closed:                     |   Platform:  all
           Project:  ChimeraX           |
----------------------------------------+----------------------

Comment (by goddard@…):

 {{{
 I tried placing markers on a 3d image surface, then resizing a marker,  then placing markers on the surface, tried several repetitions and it  always gave new markers of the same size as the previously resized marker.
 So I don’t know how to reproduce the problem you describe.  Are you using  the current ChimeraX daily build?  Are there any additional clues you  could give me?  Does it work correctly on some maps but not others?

 }}}

--
Ticket URL: <https://plato.cgl.ucsf.edu/trac/ChimeraX/ticket/1036#comment:2>
ChimeraX <http://www.rbvi.ucsf.edu/chimerax/>
ChimeraX Issue Tracker

Marker 1 Resized.PNG​

marker 1.PNG​

Multiple New Markers Placed.PNG​

[Meelad.Amouzgar@…]

Added by email2trac

[Meelad.Amouzgar@…]

Added by email2trac

[Meelad.Amouzgar@…]

Added by email2trac

[Tom Goddard]

I'm mystified. But you say "2) I resize image." Do you mean you resized the markers? I'm puzzled because your 3 attached images are all different sizes, so it looks as if you resized the window. But earlier you seem to clearly say you used the "resize marker" mode.

I think I've done exactly what you did, place markers on surface, and resize marker, and place more markers on surface, and it works correctly every time. So something must be different between what I do and what you do. Can you send me a ChimeraX session file of the randomly sized markers (command "save ~/Desktop/markertest.cxs") ?

[Meelad.Amouzgar@…]

Hi, 

Yes, I meant resize marker, not image. The image screenshots I sent you were manually made using the computer's snip tool...

I've attached the session file, and I've also attached a video showing exactly what I am doing, and one example of what happens. I do use the voxelsize feature in this video but I have tested it without using that command and it still bugs out.

And I receive this error message: 

AttributeError: 'Atom' object has no attribute 'radius'

File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\core\atomic\attr_registration.py", line 63, in get_attr
raise AttributeError("'%s' object has no attribute '%s'" % (self.class_.__name__, attr_name))


Thank you.

Best,
Meelad












-----Original Message-----
From: ChimeraX [mailto:ChimeraX-bugs-admin@cgl.ucsf.edu] 
Sent: Wednesday, February 21, 2018 6:40 PM
Cc: Amouzgar, Meelad <Meelad.Amouzgar@ucsf.edu>; goddard@cgl.ucsf.edu
Subject: Re: [ChimeraX] #1036: Marker placement and resizing bug

#1036: Marker placement and resizing bug
----------------------------------------+----------------------
          Reporter:  Meelad.Amouzgar@…  |      Owner:  goddard
              Type:  defect             |     Status:  assigned
          Priority:  normal             |  Milestone:
         Component:  Volume Data        |    Version:
        Resolution:                     |   Keywords:
        Blocked By:                     |   Blocking:
Notify when closed:                     |   Platform:  all
           Project:  ChimeraX           |
----------------------------------------+----------------------

Comment (by goddard):

 I'm mystified.  But you say "2) I resize image."  Do you mean you resized  the markers?  I'm puzzled because your 3 attached images are all different  sizes, so it looks as if you resized the window.  But earlier you seem to  clearly say you used the "resize marker" mode.

 I think I've done exactly what you did, place markers on surface, and  resize marker, and place more markers on surface, and it works correctly  every time.  So something must be different between what I do and what you  do.  Can you send me a ChimeraX session file of the randomly sized markers  (command "save ~/Desktop/markertest.cxs") ?

--
Ticket URL: <https://plato.cgl.ucsf.edu/trac/ChimeraX/ticket/1036#comment:4>
ChimeraX <http://www.rbvi.ucsf.edu/chimerax/>
ChimeraX Issue Tracker

markertest.cxs​

zoom_0.mp4​

[Meelad.Amouzgar@…]

Added by email2trac

[Meelad.Amouzgar@…]

Added by email2trac

[Tom Goddard]

Fixed in tonight's ChimeraX builds.

Thanks for movie and session file. I moved to a Windows machine and was able to reproduce the problem and fix it. The problem was that after you used the resize mode it was still trying to do resizing even after you switched out of that mode. I didn't cause any harm if you place a new marker without dragging the mouse. But on Windows, if you move the mouse even one pixel while placing a new marker it did a resize of the last atom you resized when you were in resize mode.

[Meelad.Amouzgar@…]

Perfect, thanks so much! I'll download the new build right away!

-----Original Message-----
From: ChimeraX [mailto:ChimeraX-bugs-admin@cgl.ucsf.edu] 
Sent: Thursday, February 22, 2018 6:05 PM
Cc: Amouzgar, Meelad <Meelad.Amouzgar@ucsf.edu>; goddard@cgl.ucsf.edu
Subject: Re: [ChimeraX] #1036: Marker placement and resizing bug

#1036: Marker placement and resizing bug
----------------------------------------+---------------------
          Reporter:  Meelad.Amouzgar@…  |      Owner:  goddard
              Type:  defect             |     Status:  closed
          Priority:  normal             |  Milestone:
         Component:  Volume Data        |    Version:
        Resolution:  fixed              |   Keywords:
        Blocked By:                     |   Blocking:
Notify when closed:                     |   Platform:  all
           Project:  ChimeraX           |
----------------------------------------+---------------------
Changes (by goddard):

 * status:  assigned => closed
 * resolution:   => fixed


Comment:

 Fixed in tonight's ChimeraX builds.

 Thanks for movie and session file.  I moved to a Windows machine and was  able to reproduce the problem and fix it.  The problem was that after you  used the resize mode it was still trying to do resizing even after you  switched out of that mode.  I didn't cause any harm if you place a new  marker without dragging the mouse.  But on Windows, if you move the mouse  even one pixel while placing a new marker it did a resize of the last atom  you resized when you were in resize mode.

--
Ticket URL: <https://plato.cgl.ucsf.edu/trac/ChimeraX/ticket/1036#comment:6>
ChimeraX <http://www.rbvi.ucsf.edu/chimerax/>
ChimeraX Issue Tracker