Activity for Cell Paint

Adam Gardner posted a comment on ticket #16

Adam Gardner — Sun, 09 Feb 2025 23:35:58 -0000

Hi Lydia, The membrane has two orientations. If you draw it counter clockwise and close it the inside of the membrane faces out. Try drawing the membrane in a clockwise orientation. Then the membrane bound proteins should face out :). Let us know if you have any other problems! Good luck with your assignment! Best, Adam.

Lydia Reynolds created ticket #16

Lydia Reynolds — Sun, 09 Feb 2025 23:30:54 -0000

Coronavirus structure not working

Ludo posted a comment on ticket #15

Ludo — Wed, 16 Oct 2024 18:09:09 -0000

Indeed the problem came from the server. All fixed now. You can access illustrate either from cellpaint or directly through our web page : https://ccsb.scripps.edu/illustrate/. We also have a development version you can play with here https://mesoscope.scripps.edu/beta/cellPAINT_dev/. It has better performance.

Adam Gardner posted a comment on ticket #15

Adam Gardner — Wed, 16 Oct 2024 16:16:43 -0000

Hi Mathilde, Thank you for the kind words! It's possible the server is down or or misconfigured. And yes it is possible to load an image to circumvent that system or even just make something fun and unique. We tried to make cellPAINT work on most hardware, the only requirement for ingredient creation is an internet connection. I will send a tutorial later tonight. Cheers, Adam.

Mathilde COURTES created ticket #15

Mathilde COURTES — Wed, 16 Oct 2024 10:15:54 -0000

PDB structures are not loading

Adam Gardner posted a comment on ticket #14

Adam Gardner — Fri, 29 Sep 2023 04:05:22 -0000

Oh wow, I will look into that. Your complex must just be bigger than the texture we use. I will do a fix and update.

Brigandat Louis created ticket #14

Brigandat Louis — Thu, 28 Sep 2023 14:27:32 -0000

Can't load big complex

Jan Löwe created ticket #13

Jan Löwe — Tue, 23 Nov 2021 10:53:07 -0000

PDB import: rotations

Sebastian Tacke posted a comment on ticket #12

Sebastian Tacke — Thu, 07 Oct 2021 11:50:30 -0000

We have the same issue on our PCs. It seems that the scaling is totally of. The speckles seem to be the correct protein but the scale is wrong. On our MAC systems, however, this bug does not appear.

Baptiste Jammart posted a comment on ticket #10

Baptiste Jammart — Tue, 24 Aug 2021 13:06:31 -0000

Hi, Any news ? I'm eventually trying to determine whether I'll use this wonderfull tool with my students in september (and the online option is unfortunatelly not an option for me). Thanks. Best, Baptiste

Paul van Schayck posted a comment on ticket #12

Paul van Schayck — Fri, 20 Aug 2021 13:28:31 -0000

Maybe worth mentioning, that all of these machines do not have an issue rendering the web version.

Paul van Schayck created ticket #12

Paul van Schayck — Fri, 20 Aug 2021 13:22:10 -0000

CellPAINT 2.0.3 installation on Win10 not rendering properly

Andre Schwarz posted a comment on ticket #11

Andre Schwarz — Wed, 07 Jul 2021 16:14:14 -0000

Update Today I used the 'CoronavirusMarch_membrane' instead of the 'Human_Cell_membrane' and with this I was able to load save files the past few times I tried. Can't say yet definitively that that's the issue, but wanted to update nevertheless. Best, Andre

Andre Schwarz created ticket #11

Andre Schwarz — Tue, 06 Jul 2021 21:14:01 -0000

freezing while opening session

Baptiste Jammart posted a comment on ticket #10

Baptiste Jammart — Tue, 25 May 2021 08:14:16 -0000

Additional info : I've been testing the different CellPaint versions. So far, the first one (HIV) and the second one (exo) are working like a charm. This issue appears with the "coronavirus" build (2020-05), where the ingredients are on the left for the first time, and also for all the later builds. Best, Baptiste

Baptiste Jammart posted a comment on ticket #10

Baptiste Jammart — Tue, 25 May 2021 07:52:45 -0000

Hi, On my side, the problem cannot be solved this way. Actually, when I click on an ingredient using the web-based app, the painting tool is automatically selected, whereas using the offline software, nothing occurs for most ingredients (I can even highlight multiple ingredients in green but they never turn blue like on the web-based app ; see previous post for illustration). Here are the only ingredients that behave normally : 1. CoV membrane 2. CoV nucleocapsid 3. CoV M (but black, color can be...

Arie Horowitz posted a comment on ticket #9

Arie Horowitz — Tue, 25 May 2021 03:36:25 -0000

Hi Adam, Thank you for the effort you invested into trouble-shooting Cell Paint. I am away on vacation, but I’ll test it again once I am back. Best, Arie On May 24, 2021, at 17:04, Adam Gardner adamgardner@users.sourceforge.net wrote: Hi Arie, Sorry for the long delay. It took me a forever to figure out some of the codesigning problems and entitlements on MacOS. I think I solved it, there are some other issues namely highlight not working and it hasn't been fully tested, but if you download the latest...

Adam Gardner posted a comment on ticket #9

Adam Gardner — Tue, 25 May 2021 03:04:29 -0000

Hi Arie, Sorry for the long delay. It took me a forever to figure out some of the codesigning problems and entitlements on MacOS. I think I solved it, there are some other issues namely highlight not working and it hasn't been fully tested, but if you download the latest mac version it should work. fingers crossed! Best, Adam.

Adam Gardner posted a comment on ticket #10

Adam Gardner — Tue, 25 May 2021 02:59:18 -0000

If you change the background to white can you see the black proteins that were painted? I'm trying to recreate this error. But I haven't been able to. Best, Adam.

Cell Paint released /cellPAINT2D_Mac.zip

Cell Paint — Tue, 25 May 2021 02:56:03 -0000

Baptiste Jammart posted a comment on ticket #10

Baptiste Jammart — Wed, 19 May 2021 19:12:43 -0000

Hi, I'm a teacher (K-10 to K-12) and very interested in using CellPAINT in classroom. Unfortunately, it's far too long to load with the wifi of the school and I'm experiencing the same issue as Mr Tubiana when using it offline : When trying to run the app on Win10, most ingredients are black. Some can be clicked, color-edited and painted with, some other not (resulting in strange multiple selection on the ingredient panel but nothing being painted). Hope you can fix this. It would be great ! Baptiste...

Arie Horowitz posted a comment on ticket #9

Arie Horowitz — Wed, 05 May 2021 22:25:16 -0000

It's about a week after opening this ticket, and I still have no solution to opening the application on my iMac desktop (running the latest OS). Is there a chance this will be ever solved? Thank you

Thibault Tubiana created ticket #10

Thibault Tubiana — Wed, 05 May 2021 16:20:28 -0000

[WIN] No images in cellPAINT_data

Arie Horowitz posted a comment on ticket #9

Arie Horowitz — Sat, 01 May 2021 14:21:02 -0000

Oops, got it, thanks for the tip. I see that the web-based app is functional, but I still prefer to have one on my hard disk. Thanks

Arie Horowitz posted a comment on ticket #9

Arie Horowitz — Fri, 30 Apr 2021 21:03:17 -0000

I’ve also used the link. It eventually led me to the same webpage from where I downloaded CellPaint in the first time. On 04 30, 2021, at 15:06, Adam Gardner adamgardner@users.sourceforge.net wrote: Alternativly the web app is fully functional and doesn't require permissions to run. It just requires a browser like google chrome. https://ccsb.scripps.edu/cellpaint/ https://ccsb.scripps.edu/cellpaint/

Arie Horowitz posted a comment on ticket #9

Arie Horowitz — Fri, 30 Apr 2021 20:01:25 -0000

Hi again Adam, I realize that you are providing support as a volunteer, and that you may be busy with other activities. I would appreciate however if you could send further instructions so I can solve the CellPaint opening problem during the remainder of the day. I imagine it isn’t a difficult problem. If I am wrong, and/or if you are looking into this already, please disregard the preceding text. Thank you again for your help, Arie On Apr 30, 2021, at 15:02, Adam Gardner adamgardner@users.sourceforge.net...

Arie Horowitz posted a comment on ticket #9

Arie Horowitz — Fri, 30 Apr 2021 19:10:56 -0000

I am using Google Chrome, and have used it since it was still a beta version. On 04 30, 2021, at 15:06, Adam Gardner adamgardner@users.sourceforge.net wrote: Alternativly the web app is fully functional and doesn't require permissions to run. It just requires a browser like google chrome. https://ccsb.scripps.edu/cellpaint/ https://ccsb.scripps.edu/cellpaint/

Arie Horowitz posted a comment on ticket #9

Arie Horowitz — Fri, 30 Apr 2021 19:10:05 -0000

Hi Adam, I would also like to sign the app with Apple Gatekeeper, but I have no idea what it is. I am computer fluent and don’t mind trying new things. I just need the instructions (in full detail and exactly). When I try to open CellPaint again after running the terminal command, I get exactly the same alert as the one I attached, with or without holding the ctrl button. I didn’t encounter the behavior you described - no prompt to move to the trash, etc. I think that a bit more trouble shooting...

Adam Gardner posted a comment on ticket #9

Adam Gardner — Fri, 30 Apr 2021 19:06:37 -0000

Alternativly the web app is fully functional and doesn't require permissions to run. It just requires a browser like google chrome. https://ccsb.scripps.edu/cellpaint/

Adam Gardner posted a comment on ticket #9

Adam Gardner — Fri, 30 Apr 2021 19:02:26 -0000

Hi Arie, I think we have it on our Scripps page, but it's not on the sourceforge. I will add it. Ideally I would sign the app with the Apple Gatekeeper and avoid the problem alltogether. I think that last step may be unecessary. I tried on my laptop and when I ctrl + opended after the chmod step I got a message that prompted me to move the app to the trash. I hit cancel and then ctrl + opened again and got the same message but that time there was another button that allowed me to open the app. Does...

Arie Horowitz posted a comment on ticket #9

Arie Horowitz — Fri, 30 Apr 2021 17:33:19 -0000

Hi Adam, Thank you for your prompt reply. I followed your Terminal instructions - see the attached screenshot. I believe it ran correctly. When I tried to open CellPaint again, even with the Mac override command of , I still encounter the same error message. I opened ’security and privacy’, but the next step is unclear - what I am supposed to click? There was no prompt, and there are several tabs under ’security and privacy’. Your instruction isn’t specific enough - or maybe the...

Adam Gardner posted a comment on ticket #9

Adam Gardner — Fri, 30 Apr 2021 16:20:48 -0000

Hi Arie, Sorry for the inconvenience. It is due to the gate keeper on new macs, here is the solution: Open Terminal or iTerm and type "chmod -R 755 " and drag the .app into the window, which will bring the full path into Terminal or iTerm. It will look like this: chmod -R 755 Path\ to\ app\ file.app Press return Then, you can open the app file normally, but it will fail because gatekeeper won't be able to verify the file. From there, go into your "Security and Privacy" in "System Preferences" and...

Arie Horowitz created ticket #9

Arie Horowitz — Fri, 30 Apr 2021 14:23:54 -0000

Can't open cellPAINT2D_2.03_Mac

Ludo posted a comment on ticket #8

Ludo — Mon, 26 Apr 2021 18:45:51 -0000

The web app have been fixed according the unity forum. "find a line with this text, "p = /Mac OS X (10[._\d]+)/.exec(i)[1];", change it to "p = /Mac OS X (1[._\d][._\d]+)/.exec(i)[1];"

Ludo posted a comment on ticket #8

Ludo — Mon, 26 Apr 2021 18:40:58 -0000

Good catch, actually known from unity https://forum.unity.com/threads/bug-generated-unityloader-js-fails-in-ios-14-public-beta.942484/ I will check if its still the case and fix it otherwise. Ludo

Cell Paint released /cellPAINT2D_VaccineContest_Linux.zip

Cell Paint — Tue, 30 Mar 2021 22:05:03 -0000

Cell Paint released /cellPAINT2D_VaccineContest_Win.zip

Cell Paint — Tue, 30 Mar 2021 22:03:02 -0000

Cell Paint released /cellPAINT2D_VaccineContest_Mac.app.zip

Cell Paint — Tue, 30 Mar 2021 22:03:02 -0000

Cell Paint released /cellPAINT2D_VaccineContest_Linux.zip

Cell Paint — Tue, 30 Mar 2021 22:01:02 -0000

Cell Paint released /cellPAINT2D_2.03_Win.zip

Cell Paint — Tue, 02 Feb 2021 06:12:02 -0000

Cell Paint released /cellPAINT2D_2.03_Mac.app.zip

Cell Paint — Tue, 02 Feb 2021 06:11:03 -0000

Cell Paint released /cellPAINT2D_2.03_Linux.zip

Cell Paint — Tue, 02 Feb 2021 06:11:03 -0000

Christian Stolte created ticket #8

Christian Stolte — Thu, 28 Jan 2021 12:46:35 -0000

Web app won't load on MacOS 11

Cell Paint released /cellPAINT2D_v2.02_Win.zip

Cell Paint — Tue, 19 Jan 2021 21:47:32 -0000

Cell Paint released /cellPAINT2D_v2.02_Mac.app.zip

Cell Paint — Tue, 19 Jan 2021 21:47:32 -0000

Cell Paint released /libssl.dylib

Cell Paint — Tue, 19 Jan 2021 21:47:31 -0000

Cell Paint released /libmonobdwgc-2.0.dylib

Cell Paint — Tue, 19 Jan 2021 21:47:31 -0000

Cell Paint released /cellPAINT2D_v2.02dev_Mac.zip

Cell Paint — Tue, 19 Jan 2021 21:47:27 -0000

Cell Paint released /cellPAINT2D_2.01_Win.zip

Cell Paint — Tue, 15 Dec 2020 20:17:02 -0000

Cell Paint released /cellPAINT2D_2.01_Mac.app.zip

Cell Paint — Tue, 15 Dec 2020 20:15:03 -0000

Cell Paint released /cellPAINT2D_2.01_Linux.zip

Cell Paint — Tue, 15 Dec 2020 20:15:03 -0000

Cell Paint updated /cellPAINT2D_2.01_Mac.app.zip

Cell Paint — Mon, 14 Dec 2020 22:56:02 -0000

Cell Paint released /cellPAINT2D_2.01_Win.zip

Cell Paint — Mon, 14 Dec 2020 22:50:04 -0000

Cell Paint released /cellPAINT2D_2.01_Mac.app.zip

Cell Paint — Mon, 14 Dec 2020 22:50:04 -0000

Cell Paint released /cellPAINT2D_2.01_Linux.zip

Cell Paint — Mon, 14 Dec 2020 22:49:03 -0000

Cell Paint released /cellPAINT2D_2.01_Mac.zip

Cell Paint — Mon, 14 Dec 2020 22:46:03 -0000

Adam Gardner posted a comment on ticket #7

Adam Gardner — Wed, 09 Dec 2020 15:58:44 -0000

I will take a look at that. Would you be able to send me the save file? agardner@scripps.edu

Nicola posted a comment on ticket #7

Nicola — Wed, 09 Dec 2020 13:55:55 -0000

Version 2.0

Nicola created ticket #7

Nicola — Wed, 09 Dec 2020 13:54:29 -0000

Cannot load text files

Adam Gardner posted a comment on ticket #6

Adam Gardner — Wed, 09 Dec 2020 00:16:54 -0000

Hi Sarah, Its actually a very subtle effect. You will notice some of the chains are slightly darker grey. That way when you color the molecule its the same color but the alternate chains are slightly darker. We could do a feature request to make the chains colors more distinct or let you color them independently. Cheers, Adam.

Sarah Welsh created ticket #6

Sarah Welsh — Mon, 07 Dec 2020 20:49:28 -0000

Importing PDB file won't color by chain

Alberto Amatucci posted a comment on ticket #5

Alberto Amatucci — Mon, 07 Dec 2020 20:46:22 -0000

Hello, I managed to solve it with this command: "sudo chmod -R 755 Path\ to\ app\ file.app" I don't know why but I guess that the other suggestions I found online omitted the R operand and the numerical values (favoring letters, like x). Thanks

Adam Gardner posted a comment on ticket #5

Adam Gardner — Mon, 07 Dec 2020 19:58:06 -0000

Hmmm... Sorry for the difficulty! have you tried any solutions in this thread: https://developer.apple.com/forums/thread/666611 I will install Big Sur on our mac computer and see if I can recreate the issue.

Alberto Amatucci modified a comment on ticket #5

Alberto Amatucci — Mon, 07 Dec 2020 16:54:53 -0000

I am the only user of this computer. This problem occurs also on another computer owned by a different user. Please instruct me if you need any log from Console.app Regards

Alberto Amatucci posted a comment on ticket #5

Alberto Amatucci — Mon, 07 Dec 2020 16:54:33 -0000

I am the only user of this computer. This problem occurs on another computer owned by a different user. Please instruct me if you need any log from Console.app Regards

Adam Gardner posted a comment on ticket #5

Adam Gardner — Mon, 07 Dec 2020 16:29:44 -0000

I think you probably did the chmod correctly. However, I think the problem is your administrator privileges. Are you an administrator on the computer?

Alberto Amatucci created ticket #5

Alberto Amatucci — Sat, 05 Dec 2020 11:06:58 -0000

macOS - app requires privileges

Nick Ader posted a comment on ticket #4

Nick Ader — Fri, 04 Dec 2020 20:18:25 -0000

Thank you for the reply! I noticed someone else had posted the fix in an ealier ticket as well.

Nick Ader posted a comment on ticket #2

Nick Ader — Fri, 04 Dec 2020 20:17:36 -0000

This provides a way to fix: https://www.youtube.com/watch?v=i9TtoOJjGpU&ab_channel=VelociDrone

Adam Gardner posted a comment on ticket #4

Adam Gardner — Fri, 04 Dec 2020 20:16:38 -0000

It's not the easiest fix sorry, but the good news is that there is one. You need to go into the terminal and "chmod +x" the application. You can drag the executable into the terminal to get an exact path. Here is a more detailed explanation: https://superuser.com/questions/898124/the-application-someapp-app-can-t-be-opened If you still have a problem let me know :)

Nick Ader posted a comment on ticket #4

Nick Ader — Fri, 04 Dec 2020 20:12:00 -0000

Same exact problem. A fix would be appreciated.

Michelle Peckham posted a comment on ticket #4

Michelle Peckham — Tue, 01 Dec 2020 16:59:02 -0000

I have had the exact same problem - is there any advice?

Cell Paint released /cellPAINT2D_2.0_ReleaseCandidates/cellPAINT2D_2.0_ReleaseCandidate_Mac.app.zip

Cell Paint — Sat, 14 Nov 2020 17:15:03 -0000

Cell Paint updated /cellPAINT2D_2.0_ReleaseCandidates/cellPAINT2D_2.0_ReleaseCandidate_Linux.zip

Cell Paint — Sat, 14 Nov 2020 17:04:04 -0000

Cell Paint released /cellPAINT2D_2.0_ReleaseCandidates/cellPAINT2D_2.0_ReleaseCandidate_Linux.zip

Cell Paint — Sat, 14 Nov 2020 16:57:02 -0000

Cell Paint released /cellPAINT2D_2.0_ReleaseCandidates/cellPAINT2D_2.0_ReleaseCandidate_Win.zip

Cell Paint — Sat, 14 Nov 2020 16:30:02 -0000

gloria fuentes posted a comment on ticket #1

gloria fuentes — Mon, 24 Aug 2020 20:54:15 -0000

Hi there. I have found how to fix this issue. So from now on whoever can fix it after watching this youtube video. Have fun with cellPaint https://www.youtube.com/watch?v=i9TtoOJjGpU

gloria fuentes posted a comment on ticket #1

gloria fuentes — Thu, 20 Aug 2020 23:29:01 -0000

Hi Adam I am experiencing the same issue, and nothing fixes it. I tried with ctrl and open, and also from the System Prefrences to try to authorise it, but I failed. Is there something I am doing wrong? :( Thanks a lot in advance gloria

Evan Lester posted a comment on discussion General Discussion

Evan Lester — Thu, 16 Jul 2020 04:40:50 -0000

First I just wanted to say that CellPaint VR is awesome, I've been really hoping that someone would develop something like this and I hope you continue to build it out. It's a much more natural way to engage with biology and develop an intuition for the scale and relative sizes of components. I was wondering if there is any documentation on how to import new structures into CellPaint-VR. Do PDB or pymol structures work best? Thanks!

Javier Capilla posted a comment on ticket #3

Javier Capilla — Tue, 09 Jun 2020 17:20:06 -0000

I have the same problem, should I e-mail you?

Neha Varshney created ticket #4

Neha Varshney — Sun, 24 May 2020 03:36:47 -0000

Application can't be opened

Adam Gardner posted a comment on ticket #3

Adam Gardner — Sat, 09 May 2020 17:40:04 -0000

Hi Mattia, That might have to be solved with an update. It's actually the second time I've seen that bug, but I haven't been able to reproduce it on my end. Would you be able to send me an email to agardner@scripps.edu? I will send you a special build that saves a log file so we can get to the root of the error. Cheers, Adam.

Mattia Garavaglia created ticket #3

Mattia Garavaglia — Fri, 08 May 2020 17:44:45 -0000

Proteins size issues

Cell Paint updated /cellPAINT2D_Coronavirus_Linux.zip

Cell Paint — Mon, 04 May 2020 04:51:04 -0000

Cell Paint updated /cellPAINT2D_Coronavirus_Windows.zip

Cell Paint — Mon, 04 May 2020 04:49:03 -0000

Cell Paint updated /cellPAINT2D_Coronavirus_Apple.zip

Cell Paint — Mon, 04 May 2020 04:47:02 -0000

Kanika Khanna created ticket #2

Kanika Khanna — Fri, 01 May 2020 16:27:40 -0000

The application can't be opened

Adam Gardner posted a comment on ticket #1

Adam Gardner — Fri, 24 Apr 2020 16:51:22 -0000

Hi Connor, If you control click and select open from the dropdown it should add an exception for the app. There is an "untrusted developer" exception that we haven't been able to get around yet. However we don't add anything sketchy (besides the protein sketching part (^-^)) to our software so there is nothing to worry about anyway. Cheers, Adam.

Connor Rogerson created ticket #1

Connor Rogerson — Thu, 23 Apr 2020 13:58:48 -0000

The application “cellPAINT” can’t be opened.

Cell Paint released /cellPAINT2D_Coronavirus_Linux.zip

Cell Paint — Fri, 10 Apr 2020 18:37:03 -0000

Cell Paint released /cellPAINT2D_Coronavirus_Apple.zip

Cell Paint — Fri, 10 Apr 2020 17:16:03 -0000

Cell Paint released /cellPAINT2D_Coronavirus_Windows.zip

Cell Paint — Fri, 10 Apr 2020 17:16:03 -0000

Cell Paint released /cellPAINT_3D_Apple_DevBuild.app.zip

Cell Paint — Mon, 03 Feb 2020 23:00:04 -0000

Cell Paint released /AGO2.png