On 18/09/2021 05:54, Xavier Brazzolotto wrote:
Hi Paul,
My apologies, was bit in a rush with new data to analyze.
For more informations : Mac OS Big Sur 11.5.2, XQuartz 2.8.1 (xorg-server 1.20.11), Coot 0.9.6 (updated via
CCP4 (7.1.016).
Here is the terminal output (if I downgrade back to coot 0.9.6, uninstalling the last ccp4 update, then coot
does not crash)
Hope it will help
Xavier
INFO:: Using Standard CCP4 Refmac dictionary from CLIBD_MON:
/Applications/ccp4-7.1/lib/data/monomers/
There are 244 data in
/Applications/ccp4-7.1/lib/data/monomers/list/mon_lib_list.cif
There are 2 data in /Applications/ccp4-7.1/lib/data/monomers/a/ALA.cif
There are 2 data in /Applications/ccp4-7.1/lib/data/monomers/a/ASP.cif
There are 2 data in /Applications/ccp4-7.1/lib/data/monomers/a/ASN.cif
There are 2 data in /Applications/ccp4-7.1/lib/data/monomers/c/CYS.cif
There are 2 data in /Applications/ccp4-7.1/lib/data/monomers/g/GLN.cif
There are 2 data in /Applications/ccp4-7.1/lib/data/monomers/g/GLY.cif
There are 2 data in /Applications/ccp4-7.1/lib/data/monomers/g/GLU.cif
There are 2 data in /Applications/ccp4-7.1/lib/data/monomers/p/PHE.cif
There are 2 data in /Applications/ccp4-7.1/lib/data/monomers/h/HIS.cif
There are 2 data in /Applications/ccp4-7.1/lib/data/monomers/i/ILE.cif
There are 2 data in /Applications/ccp4-7.1/lib/data/monomers/l/LYS.cif
There are 2 data in /Applications/ccp4-7.1/lib/data/monomers/l/LEU.cif
There are 2 data in /Applications/ccp4-7.1/lib/data/monomers/m/MET.cif
There are 2 data in /Applications/ccp4-7.1/lib/data/monomers/m/MSE.cif
There are 2 data in /Applications/ccp4-7.1/lib/data/monomers/p/PRO.cif
There are 2 data in /Applications/ccp4-7.1/lib/data/monomers/a/ARG.cif
There are 2 data in /Applications/ccp4-7.1/lib/data/monomers/s/SER.cif
There are 2 data in /Applications/ccp4-7.1/lib/data/monomers/t/THR.cif
There are 2 data in /Applications/ccp4-7.1/lib/data/monomers/v/VAL.cif
There are 2 data in /Applications/ccp4-7.1/lib/data/monomers/t/TRP.cif
There are 2 data in /Applications/ccp4-7.1/lib/data/monomers/t/TYR.cif
There are 2 data in /Applications/ccp4-7.1/lib/data/monomers/p/PO4.cif
There are 2 data in /Applications/ccp4-7.1/lib/data/monomers/s/SO4.cif
There are 2 data in /Applications/ccp4-7.1/lib/data/monomers/g/GOL.cif
There are 2 data in /Applications/ccp4-7.1/lib/data/monomers/c/CIT.cif
There are 2 data in /Applications/ccp4-7.1/lib/data/monomers/e/EDO.cif
There are 2 data in /Applications/ccp4-7.1/lib/data/monomers/a/A.cif
There are 2 data in /Applications/ccp4-7.1/lib/data/monomers/c/C.cif
There are 2 data in /Applications/ccp4-7.1/lib/data/monomers/g/G.cif
There are 2 data in /Applications/ccp4-7.1/lib/data/monomers/u/U.cif
There are 2 data in /Applications/ccp4-7.1/lib/data/monomers/d/DA.cif
There are 2 data in /Applications/ccp4-7.1/lib/data/monomers/d/DC.cif
There are 2 data in /Applications/ccp4-7.1/lib/data/monomers/d/DG.cif
There are 2 data in /Applications/ccp4-7.1/lib/data/monomers/d/DT.cif
There are 2 data in /Applications/ccp4-7.1/lib/data/monomers/h/HOH.cif
There are 2 data in /Applications/ccp4-7.1/lib/data/monomers/n/NA.cif
Spacegroup: P 1
*(filter-fileselection-filenames-state)*
*(get-active-map-drag-flag)*
*(use-graphics-interface-state)*
INFO:: coot.py imported
** (coot-bin:22238): WARNING **: Trying to register gtype 'GMountMountFlags' as enum when in fact it is of
type 'GFlags'
** (coot-bin:22238): WARNING **: Trying to register gtype 'GDriveStartFlags' as enum when in fact it is of
type 'GFlags'
** (coot-bin:22238): WARNING **: Trying to register gtype 'GSocketMsgFlags' as enum when in fact it is of
type 'GFlags'
INFO:: coot_python initialized
Running python script
/Applications/ccp4-7.1/lib/python2.7/site-packages/coot/coot_load_modules.py
Good Morning Xavier, Welcome to Coot version 0.9.6
*(set-display-intro-string "Good Morning Xavier, Welcome to Coot version
0.9.6")*
Coot Python Scripting GUI code found and loaded.
Coot Python Scripting GUI code found and loaded.
*(use-graphics-interface-state)*
Running python script /Users/xbrazzolotto/.coot-preferences/coot_preferences.py
*(set-filter-fileselection-filenames 1)*
*(set-sticky-sort-by-date)*
*(set-colour-map-rotation-on-read-pdb 21.00)*
*(set-colour-map-rotation-on-read-pdb-c-only-flag 1)*
*(set-density-size 17.00)*
*(set-swap-difference-map-colours 0)*
*(set-colour-map-rotation-for-map 14.00)*
*(set-active-map-drag-flag 1)*
*(set-idle-function-rotate-angle 1.00)*
Running python script /Users/xbrazzolotto/.coot-preferences/xenops_symmetry.py
*(set-show-symmetry-master 1)*
*(filter-fileselection-filenames-state)*
*(get-active-map-drag-flag)*
Loading ~/.coot.py...
Running python script /Users/xbrazzolotto/.coot.py
*(use-graphics-interface-state)*
Coot Scheme Scripting GUI code found and loaded.
Good morning Xavier Brazzolotto. Welcome to Coot 0.9.6.
*(set-display-intro-string "Good morning Xavier. Welcome to Coot 0.9.6")*
*(set-display-lists-for-maps 0)*
load /Users/xbrazzolotto/.coot-preferences/coot-preferences.scm
*(set-filter-fileselection-filenames 1)*
*(set-sticky-sort-by-date)*
*(set-colour-map-rotation-on-read-pdb 21.00)*
*(set-colour-map-rotation-on-read-pdb-c-only-flag 1)*
*(set-density-size 17.00)*
*(set-swap-difference-map-colours 0)*
*(set-colour-map-rotation-for-map 14.00)*
*(set-active-map-drag-flag 1)*
Backtrace:
In /Users/xbrazzolotto/.coot-preferences/coot-preferences.scm:
68: 0* (no-coot-tips)
/Users/xbrazzolotto/.coot-preferences/coot-preferences.scm:68:1: In expression
(no-coot-tips):
/Users/xbrazzolotto/.coot-preferences/coot-preferences.scm:68:1: Unbound
variable: no-coot-tips
. ------ Coot crashed - trying to diagnose -----
Guile 1.8.8
Copyright (c) 1995, 1996, 1997, 2000, 2001, 2002, 2003, 2004, 2005, 2006, 2007,
2008 Free Software Foundation
Guile may be distributed under the terms of the GNU General Public Licence;
certain other uses are permitted as well. For details, see the file
`COPYING', which is included in the Guile distribution.
There is no warranty, to the extent permitted by law.
catching the crash log:
coot-exe: "/Applications/ccp4-7.1/libexec/coot-bin"
/bin/ls
-rwxr-xr-x 1 root admin 9877812 Sep 18 06:37
/Applications/ccp4-7.1/libexec/coot-bin
coot-version:
/Applications/ccp4-7.1/libexec/coot-bin
Builder_info: CCP4, Oxfordshire, UK
Enabled: Enhanced-ligand-tools C++-11 Threads Boost-based-thread-pool Goocanvas
GSL LibCurl
Binary type: Darwin-MacOSX-10.9.5-x86_64-python-gtk2
git commit: 0b823e493e00c1199103369ddab6641e14560d00
Builder_info: CCP4, Oxfordshire, UK
[with python 2.7.16 embedded]
[with guile 1.8.8 embedded]
0.9.6 (revision-count 10625)
platform:
/usr/bin/uname
Darwin macbook-pro-de-xavier-brazzolotto-9.local 20.6.0 Darwin Kernel Version 20.6.0: Wed Jun 23 00:26:31
PDT 2021; root:xnu-7195.141.2~5/RELEASE_X86_64 x86_64
core: #f
No core file found. No debugging
Le 18 sept. 2021 à 03:22, Paul Emsley <pems...@mrc-lmb.cam.ac.uk
<mailto:pems...@mrc-lmb.cam.ac.uk>> a écrit :
On 17/09/2021 09:17, Xavier Brazzolotto wrote:
I am using Coot on a Mac (Big Sur)
I’ve lately updated my CCP4 (7.1.016) which includes the latest Coot version, but after this update Coot
systematically crashes (From Phenix or directly from my terminal).
I’ve downgraded to CCP4 7.1.015, to get my Coot to work again.
Any of you experiment such crashes ?
How to solve this ?
If this is not a bug report, then I have nothing to say (Coot does not
systematically crash for me).
If it *is* a bug report, then I do...
How do you know that it crashed?
It would be helpful to see the crash catcher log.
It would be less helpful, but it would at least be something, to see the
terminal output.
But with no log at all and no recipe to reproduce, you have given us litterally nothing to go on. That's
not helful.
Hi Xavier,
Your message will make Clemens laugh - shadenfreude - or some such :-)
It is indeed not a crash - Coot terminates with an error message (but the crash-catcher thinks that it *has*
crashed, inconstantly).
For now, remove (no-coot-tips) from your ~/.coot or any .scm files in ~/.coot-preferences - in your case
~/.coot-preferences/coot-preferences.scm
This issue will be addressed in the shortly-to-be-released 0.9.6.2.
Thanks,
Paul.
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