[Chimera-users] Sudden Chimera issues with OSX Mojave?
njr48 at cam.ac.uk
Thu Jun 27 04:14:41 PDT 2019
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
Many thanks for all your help and suggestions!
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
> Many thanks, I'll report my findings to this BB.
> 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.
>>> 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
>>> ("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,
>>> Dr. Neil Rzechorzek
>>> Senior Research Associate
>>> Department of Biochemistry
>>> University of Cambridge
>>> Sanger Building
>>> 80 Tennis Court Road
>>> Cambridge, UK
>>> CB2 1GA
>>> Biochemistry Enterprise Champion
>>> Advisory Chairman - Entrepreneurial Postdocs Of Cambridge
>>> Email: njr48 at cam.ac.uk
>>> Tel: +44 (0)1223 333652
>>> Chimera-users mailing list: Chimera-users at cgl.ucsf.edu
>>> Manage subscription:
Dr. Neil Rzechorzek
Senior Research Associate
Department of Biochemistry
University of Cambridge
80 Tennis Court Road
Biochemistry Enterprise Champion
Advisory Chairman - Entrepreneurial Postdocs Of Cambridge
Email: njr48 at cam.ac.uk
Tel: +44 (0)1223 333652
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