Re: [COOT] Mac OS and Coot Update from CCP4
Hi Paul, On Sat, Sep 18, 2021 at 11:56:33AM +0100, Paul Emsley wrote: > Your message will make Clemens laugh - shadenfreude - or some such :-) Not at all: it's much better when software works exactly as intended - as Coot nearly always does! Cheers Clemens To unsubscribe from the COOT list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=COOT=1 This message was issued to members of www.jiscmail.ac.uk/COOT, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
Re: [COOT] Mac OS and Coot Update from CCP4
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
Re: [COOT] Mac OS and Coot Update from CCP4
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)
Re: [COOT] Mac OS and Coot Update from CCP4
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. Paul To unsubscribe from the COOT list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=COOT=1 This message was issued to members of www.jiscmail.ac.uk/COOT, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
Re: [COOT] Mac OS and Coot Update from CCP4
Hi, mine crashed from terminal once (not systematically) yesterday after getting the update (Linux Ubuntu). AS To unsubscribe from the COOT list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=COOT=1 This message was issued to members of www.jiscmail.ac.uk/COOT, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
[COOT] Mac OS and Coot Update from CCP4
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 ? Many thanks Best Xavier To unsubscribe from the COOT list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=COOT=1 This message was issued to members of www.jiscmail.ac.uk/COOT, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
