Dear Chimera users, Has anyone else started seeing issues with the latest stable version of Chimera on OSX Mojave? We have two new identical systems that were running perfectly as recently as 48 hours ago, but now Chimera is constantly crashing whenever we do something as trivial as File>Open or if we attempt to save a map. To our knowledge there has been no update to Mojave, and we haven't changed our Chimera installation. An example of the error log generated by Chimera when trying to, for example, save a map is: while executing "4642906592_scrollBothNow" ("after" script) File>Open windows do not scroll properly, and will instantly crash the entire program unless we change preferences to 'Open dialog starts in directory from last session = false' Does anyone know of any recent (last ~36 hours...) changes to any supporting software? We're wondering whether there has been some silent security update at Apple that has interefered with, for example, the windowing toolkit? Many thanks, Neil -- Dr. Neil Rzechorzek Senior Research Associate Department of Biochemistry University of Cambridge Sanger Building 80 Tennis Court Road Cambridge, UK CB2 1GA www.bioc.cam.ac.uk Biochemistry Enterprise Champion www.enterprise.cam.ac.uk Advisory Chairman - Entrepreneurial Postdocs Of Cambridge www.epoc.group.cam.ac.uk Email: njr48@cam.ac.uk Tel: +44 (0)1223 333652
Hi Neil, I don’t know why your systems would have started having problems in the last 48 hours. Nonetheless, I suggest you try using the daily build instead of the production release. The daily build uses a newer version of the Tk windowing toolkit that Chimera relies on to draw windows, handle scrolling, etc. and that newer version in particular has some fixes for bad scrolling behavior. If the daily build fails to remedy the problem, try using Chimera’s Help→Report a Bug to make a bug report. The bug report will include many details of your hardware and software setup that will help us investigate the problem. —Eric Eric Pettersen UCSF Computer Graphics Lab
On Jun 26, 2019, at 9:11 AM, Neil Rzechorzek <njr48@cam.ac.uk> wrote:
Dear Chimera users,
Has anyone else started seeing issues with the latest stable version of Chimera on OSX Mojave? We have two new identical systems that were running perfectly as recently as 48 hours ago, but now Chimera is constantly crashing whenever we do something as trivial as File>Open or if we attempt to save a map.
To our knowledge there has been no update to Mojave, and we haven't changed our Chimera installation.
An example of the error log generated by Chimera when trying to, for example, save a map is:
while executing "4642906592_scrollBothNow" ("after" script)
File>Open windows do not scroll properly, and will instantly crash the entire program unless we change preferences to 'Open dialog starts in directory from last session = false'
Does anyone know of any recent (last ~36 hours...) changes to any supporting software? We're wondering whether there has been some silent security update at Apple that has interefered with, for example, the windowing toolkit?
Many thanks,
Neil
-- Dr. Neil Rzechorzek Senior Research Associate Department of Biochemistry University of Cambridge Sanger Building 80 Tennis Court Road Cambridge, UK CB2 1GA www.bioc.cam.ac.uk
Biochemistry Enterprise Champion www.enterprise.cam.ac.uk
Advisory Chairman - Entrepreneurial Postdocs Of Cambridge www.epoc.group.cam.ac.uk
Email: njr48@cam.ac.uk Tel: +44 (0)1223 333652
_______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
Thanks for this Eric, I've given the daily build (25th June) a go and it does seem to improve things. I'm now able to open files from File>Open and the window that is generated seems fine. I'll test more fully tomorrow. One additional symptom that I neglected to mention before but which still persists now (albeit to a lesser extent) is that some of the pop-up windows go black when interacted with. As an example, when using 'Fit in Map', if I change either of the two drop-down selection boxes the whole window will turn black as soon as I make a selection. This clears as soon as I move the mouse again, unless I move the mouse before the selection is properly registered (i.e. click a model name and move the mouse straight away). In this case, the window only returns to normal again if I position the mouse cursor over the window size control tab in the bottom right-hand corner. A minor 'feature', but something worth noting in case it hints at an underlying issue. I'll submit a bug report on this shortly. Many thanks for your help! Neil On 26/06/2019 18:58, Eric Pettersen wrote:
Hi Neil, I don’t know why your systems would have started having problems in the last 48 hours. Nonetheless, I suggest you try using the daily build instead of the production release. The daily build uses a newer version of the Tk windowing toolkit that Chimera relies on to draw windows, handle scrolling, etc. and that newer version in particular has some fixes for bad scrolling behavior. If the daily build fails to remedy the problem, try using Chimera’s Help→Report a Bug to make a bug report. The bug report will include many details of your hardware and software setup that will help us investigate the problem.
—Eric
Eric Pettersen UCSF Computer Graphics Lab
On Jun 26, 2019, at 9:11 AM, Neil Rzechorzek <njr48@cam.ac.uk <mailto:njr48@cam.ac.uk>> wrote:
Dear Chimera users,
Has anyone else started seeing issues with the latest stable version of Chimera on OSX Mojave? We have two new identical systems that were running perfectly as recently as 48 hours ago, but now Chimera is constantly crashing whenever we do something as trivial as File>Open or if we attempt to save a map.
To our knowledge there has been no update to Mojave, and we haven't changed our Chimera installation.
An example of the error log generated by Chimera when trying to, for example, save a map is:
while executing "4642906592_scrollBothNow" ("after" script)
File>Open windows do not scroll properly, and will instantly crash the entire program unless we change preferences to 'Open dialog starts in directory from last session = false'
Does anyone know of any recent (last ~36 hours...) changes to any supporting software? We're wondering whether there has been some silent security update at Apple that has interefered with, for example, the windowing toolkit?
Many thanks,
Neil
-- Dr. Neil Rzechorzek Senior Research Associate Department of Biochemistry University of Cambridge Sanger Building 80 Tennis Court Road Cambridge, UK CB2 1GA www.bioc.cam.ac.uk <http://www.bioc.cam.ac.uk>
Biochemistry Enterprise Champion www.enterprise.cam.ac.uk
Advisory Chairman - Entrepreneurial Postdocs Of Cambridge www.epoc.group.cam.ac.uk
Email: njr48@cam.ac.uk Tel: +44 (0)1223 333652
_______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
-- Dr. Neil Rzechorzek Senior Research Associate Department of Biochemistry University of Cambridge Sanger Building 80 Tennis Court Road Cambridge, UK CB2 1GA www.bioc.cam.ac.uk Biochemistry Enterprise Champion www.enterprise.cam.ac.uk Advisory Chairman - Entrepreneurial Postdocs Of Cambridge www.epoc.group.cam.ac.uk Email: njr48@cam.ac.uk Tel: +44 (0)1223 333652
Hi Neil, If macOS didn't change and Chimera didn't change but Chimera is crashing now there are two possibilities I can think of. One is that something in Chimera preferences got set that is causing the problem. You could rename your ~/.chimera/preferences file so Chimera starts with default preferences to test that idea. One other possibility since you mention that changing the setting about what directory the Open dialog starts in has an effect -- maybe you have external drives or network mounted drives on this computer and those extra file systems somehow are causing the crashes when trying to open a file in Chimera. Tom
On Jun 26, 2019, at 9:11 AM, Neil Rzechorzek wrote:
Dear Chimera users,
Has anyone else started seeing issues with the latest stable version of Chimera on OSX Mojave? We have two new identical systems that were running perfectly as recently as 48 hours ago, but now Chimera is constantly crashing whenever we do something as trivial as File>Open or if we attempt to save a map.
To our knowledge there has been no update to Mojave, and we haven't changed our Chimera installation.
An example of the error log generated by Chimera when trying to, for example, save a map is:
while executing "4642906592_scrollBothNow" ("after" script)
File>Open windows do not scroll properly, and will instantly crash the entire program unless we change preferences to 'Open dialog starts in directory from last session = false'
Does anyone know of any recent (last ~36 hours...) changes to any supporting software? We're wondering whether there has been some silent security update at Apple that has interefered with, for example, the windowing toolkit?
Many thanks,
Neil
-- Dr. Neil Rzechorzek Senior Research Associate Department of Biochemistry University of Cambridge Sanger Building 80 Tennis Court Road Cambridge, UK CB2 1GA www.bioc.cam.ac.uk
Biochemistry Enterprise Champion www.enterprise.cam.ac.uk
Advisory Chairman - Entrepreneurial Postdocs Of Cambridge www.epoc.group.cam.ac.uk
Email: njr48@cam.ac.uk Tel: +44 (0)1223 333652
_______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
Hi Tom, Thanks for these - both good suggestions. I'll explore both more fully tomorrow, though the bit I don't get is why both systems suddenly had these problems at the same time. While I'm a frequent Chimera user, the other machine had not had Chimera running for a while. I'm not sure how both sets of preferences could have changed simultaneously, but I will test it nonetheless. The second suggestion is perhaps more intriguing. To my knowledge, the only common externally mounted drive/network drive on both systems is Dropbox. While we're not directly reading from/writing to this, it is possible that something there has changed and is causing issues. I'll see if sync pausing or quitting Dropbox altogether has any effect.... Many thanks, I'll report my findings to this BB. Neil On 26/06/2019 20:25, Tom Goddard wrote:
Hi Neil,
If macOS didn't change and Chimera didn't change but Chimera is crashing now there are two possibilities I can think of. One is that something in Chimera preferences got set that is causing the problem. You could rename your ~/.chimera/preferences file so Chimera starts with default preferences to test that idea. One other possibility since you mention that changing the setting about what directory the Open dialog starts in has an effect -- maybe you have external drives or network mounted drives on this computer and those extra file systems somehow are causing the crashes when trying to open a file in Chimera.
Tom
On Jun 26, 2019, at 9:11 AM, Neil Rzechorzek wrote:
Dear Chimera users,
Has anyone else started seeing issues with the latest stable version of Chimera on OSX Mojave? We have two new identical systems that were running perfectly as recently as 48 hours ago, but now Chimera is constantly crashing whenever we do something as trivial as File>Open or if we attempt to save a map.
To our knowledge there has been no update to Mojave, and we haven't changed our Chimera installation.
An example of the error log generated by Chimera when trying to, for example, save a map is:
while executing "4642906592_scrollBothNow" ("after" script)
File>Open windows do not scroll properly, and will instantly crash the entire program unless we change preferences to 'Open dialog starts in directory from last session = false'
Does anyone know of any recent (last ~36 hours...) changes to any supporting software? We're wondering whether there has been some silent security update at Apple that has interefered with, for example, the windowing toolkit?
Many thanks,
Neil
-- Dr. Neil Rzechorzek Senior Research Associate Department of Biochemistry University of Cambridge Sanger Building 80 Tennis Court Road Cambridge, UK CB2 1GA www.bioc.cam.ac.uk
Biochemistry Enterprise Champion www.enterprise.cam.ac.uk
Advisory Chairman - Entrepreneurial Postdocs Of Cambridge www.epoc.group.cam.ac.uk
Email: njr48@cam.ac.uk Tel: +44 (0)1223 333652
_______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
-- Dr. Neil Rzechorzek Senior Research Associate Department of Biochemistry University of Cambridge Sanger Building 80 Tennis Court Road Cambridge, UK CB2 1GA www.bioc.cam.ac.uk Biochemistry Enterprise Champion www.enterprise.cam.ac.uk Advisory Chairman - Entrepreneurial Postdocs Of Cambridge www.epoc.group.cam.ac.uk Email: njr48@cam.ac.uk Tel: +44 (0)1223 333652
Dear all, I promised an update. Renaming my preferences file does revert stable Chimera back to basic settings (window launches are smaller for a start), but does not remove the problem of crashing when trying to save a map. Pausing syncing on Dropbox also has no effect on the usability of the current daily build (June 25th). My colleague who has the identical machine to mine has now also played with this daily build, and in his hands he has an interesting effect where the main text in his File>Open window turns upside-down when he navigates to the Desktop! This does not happen with other folders... I've also just had a crash when trying to re-size a File>Open window, though this would appear to be a one-off... Eric has noted that a new version of the windowing software (Tk) should be available soon, so we'll hold out until this is released. My suspicion is that a silent Apple update (they do this for security fixes and other bits) has somehow interefered with things. I can't find anything alluding to this online yet, but will see what tomorrow brings... I would be interested to know if any other users start experiencing problems. Many thanks for all your help and suggestions! Neil On 26/06/2019 20:48, Neil Rzechorzek wrote:
Hi Tom,
Thanks for these - both good suggestions.
I'll explore both more fully tomorrow, though the bit I don't get is why both systems suddenly had these problems at the same time. While I'm a frequent Chimera user, the other machine had not had Chimera running for a while. I'm not sure how both sets of preferences could have changed simultaneously, but I will test it nonetheless.
The second suggestion is perhaps more intriguing. To my knowledge, the only common externally mounted drive/network drive on both systems is Dropbox. While we're not directly reading from/writing to this, it is possible that something there has changed and is causing issues. I'll see if sync pausing or quitting Dropbox altogether has any effect....
Many thanks, I'll report my findings to this BB.
Neil
On 26/06/2019 20:25, Tom Goddard wrote:
Hi Neil,
If macOS didn't change and Chimera didn't change but Chimera is crashing now there are two possibilities I can think of. One is that something in Chimera preferences got set that is causing the problem. You could rename your ~/.chimera/preferences file so Chimera starts with default preferences to test that idea. One other possibility since you mention that changing the setting about what directory the Open dialog starts in has an effect -- maybe you have external drives or network mounted drives on this computer and those extra file systems somehow are causing the crashes when trying to open a file in Chimera.
Tom
On Jun 26, 2019, at 9:11 AM, Neil Rzechorzek wrote:
Dear Chimera users,
Has anyone else started seeing issues with the latest stable version of Chimera on OSX Mojave? We have two new identical systems that were running perfectly as recently as 48 hours ago, but now Chimera is constantly crashing whenever we do something as trivial as File>Open or if we attempt to save a map.
To our knowledge there has been no update to Mojave, and we haven't changed our Chimera installation.
An example of the error log generated by Chimera when trying to, for example, save a map is:
while executing "4642906592_scrollBothNow" ("after" script)
File>Open windows do not scroll properly, and will instantly crash the entire program unless we change preferences to 'Open dialog starts in directory from last session = false'
Does anyone know of any recent (last ~36 hours...) changes to any supporting software? We're wondering whether there has been some silent security update at Apple that has interefered with, for example, the windowing toolkit?
Many thanks,
Neil
-- Dr. Neil Rzechorzek Senior Research Associate Department of Biochemistry University of Cambridge Sanger Building 80 Tennis Court Road Cambridge, UK CB2 1GA www.bioc.cam.ac.uk
Biochemistry Enterprise Champion www.enterprise.cam.ac.uk
Advisory Chairman - Entrepreneurial Postdocs Of Cambridge www.epoc.group.cam.ac.uk
Email: njr48@cam.ac.uk Tel: +44 (0)1223 333652
_______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
-- Dr. Neil Rzechorzek Senior Research Associate Department of Biochemistry University of Cambridge Sanger Building 80 Tennis Court Road Cambridge, UK CB2 1GA www.bioc.cam.ac.uk Biochemistry Enterprise Champion www.enterprise.cam.ac.uk Advisory Chairman - Entrepreneurial Postdocs Of Cambridge www.epoc.group.cam.ac.uk Email: njr48@cam.ac.uk Tel: +44 (0)1223 333652
participants (3)
-
Eric Pettersen -
Neil Rzechorzek -
Tom Goddard