Image transparency

[cmurin@…]

Hi,

I am having a problem saving images on ChimeraX that have a transparent background. I am running ChimeraX-1.2.5. I am using the command “save image.png transparentBackground true”. Images save, but the background is solid. I’ve also tried other variations of this command and different file types (.tiff) and that doesn’t work. Whenever dropping into Photoshop, they have solid backgrounds. I’m running macOS Big Sur on a MacBook Pro (13” M1 2020) and just recently downloaded ChimeraX.

Thank you for any help you can provide,

Daniel

Charles D. Murin, Ph.D.
Staff Scientist
Department of Integrative Structural and
Computational Biology
(858) 784-7504
http://ward.scripps.edu/

10550 North Torrey Pines Road
La Jolla, CA 92037
TRY-21

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[cmurin@…]

Added by email2trac

[pett]

Reported by Charles Daniel Murin

[Tom Goddard]

Can you attach an example image saved with "save image.png transparentBackground true"? This works fine for me in ChimeraX 1.2.5 in macOS Big Sur. Maybe it just isn't clear in Photoshop that it is transparent. Just double clicking the image it is shown in Preview with a gray background since it is transparent even though I saved it as a black background.

[Tom Goddard]

No response from reporter.

[cmurin@…]

Hi,

So the problem randomly resolved itself, but I was able to reproduce by entering and errant command for image transparency. If entered incorrectly, then all subsequent images, even if the command was correct, would not be transparent. The problem seems to resolve if you start a new session. I think it may be some sort of bug?

Daniel

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________________________________
From: ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
Sent: Tuesday, August 3, 2021 11:27:23 PM
Cc: Daniel Murin <cmurin@scripps.edu>; goddard@cgl.ucsf.edu <goddard@cgl.ucsf.edu>
Subject: Re: [ChimeraX] #4925: Image transparency

#4925: Image transparency
--------------------------------------+-------------------------
          Reporter:  cmurin@…         |      Owner:  Tom Goddard
              Type:  defect           |     Status:  closed
          Priority:  normal           |  Milestone:
         Component:  Input/Output     |    Version:
        Resolution:  can't reproduce  |   Keywords:
        Blocked By:                   |   Blocking:
Notify when closed:                   |   Platform:  all
           Project:  ChimeraX         |
--------------------------------------+-------------------------
Changes (by Tom Goddard):

 * status:  assigned => closed
 * resolution:   => can't reproduce


Comment:

 No response from reporter.

--
Ticket URL: <https://www.rbvi.ucsf.edu/trac/ChimeraX/ticket/4925#comment:3>
ChimeraX <https://www.rbvi.ucsf.edu/chimerax/>
ChimeraX Issue Tracker

[Tom Goddard]

Sounds like a bug. But I don't think saving an image remembers anything about failed commands. Could you give me an example of the "errant" save image command that breaks subsequent transparent image saving?

[cmurin@…]

Hi,

For example if I type the command:

save image.png backgroundTransparent true

I get an error and then even if type it correctly:

save image.png transparentBackground true

the image is still non-transparent.

D

Charles D. Murin, Ph.D.
Staff Scientist
Department of Integrative Structural and
Computational Biology
(858) 784-7504
http://ward.scripps.edu/

10550 North Torrey Pines Road
La Jolla, CA 92037
TRY-21

[signature_911113635]

From: ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
Date: Wednesday, August 4, 2021 at 10:52 AM
To:
Cc: Daniel Murin <cmurin@scripps.edu>, goddard@cgl.ucsf.edu <goddard@cgl.ucsf.edu>
Subject: Re: [ChimeraX] #4925: Image transparency
#4925: Image transparency
--------------------------------------+-------------------------
          Reporter:  cmurin@…         |      Owner:  Tom Goddard
              Type:  defect           |     Status:  closed
          Priority:  normal           |  Milestone:
         Component:  Input/Output     |    Version:
        Resolution:  can't reproduce  |   Keywords:
        Blocked By:                   |   Blocking:
Notify when closed:                   |   Platform:  all
           Project:  ChimeraX         |
--------------------------------------+-------------------------

Comment (by Tom Goddard):

 Sounds like a bug.  But I don't think saving an image remembers anything
 about failed commands.  Could you give me an example of the "errant" save
 image command that breaks subsequent transparent image saving?

--
Ticket URL: <https://www.rbvi.ucsf.edu/trac/ChimeraX/ticket/4925#comment:5>
ChimeraX <https://www.rbvi.ucsf.edu/chimerax/>
ChimeraX Issue Tracker

[cmurin@…]

Added by email2trac

[Tom Goddard]

A mistyped command should have no effect on saving an transparent image. The command parsing that catches the bad argument has nothing to do with image saving code. I tested your mistyped and then correctly typed commands and the image saved correctly with transparency in ChimeraX 1.2.5 on macOS Big Sur 11.4 on a Mac Mini with Apple M1 cpu.

To debug this further save an image and use ChimeraX menu Help / Report a Bug... and include the saved image as an attachment. This will give me the info about your operating system, graphics driver, ....