V 0.9 Pre drops the map out of display when going from mono to stereo. This
does not happen in 0.8 V. I have enclosed the output of coot from the run in
stereo.
thanks
kas
Kenneth A. Satyshur, M.S., Ph.D.
Senior Scientist,
Department of Bacteriology: College of Ag and Life Sciences;
Departments of Bio Molecular Chemistry,
Neuroscience, Oncology, and Carbone Cancer Center:
School of Medicine and Public Health;
and the School of Pharmacy
University of Wisconsin-Madison
Madison, Wisconsin, 53706
608-215-5207
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(coot-bin:27193): GLib-GObject-WARNING **: g_object_set_valist: object class
'GtkSettings' has no property named 'gtk-application-prefer-dark-theme'
INFO:: Using Standard CCP4 Refmac dictionary from CLIBD_MON:
/home/xray/ccp4/ccp4-7.0/lib/data/monomers/
There are 153 data in
/home/xray/ccp4/ccp4-7.0/lib/data/monomers/list/mon_lib_list.cif
There are 2 data in /home/xray/ccp4/ccp4-7.0/lib/data/monomers/a/ALA.cif
There are 2 data in /home/xray/ccp4/ccp4-7.0/lib/data/monomers/a/ASP.cif
There are 2 data in /home/xray/ccp4/ccp4-7.0/lib/data/monomers/a/ASN.cif
There are 2 data in /home/xray/ccp4/ccp4-7.0/lib/data/monomers/c/CYS.cif
There are 2 data in /home/xray/ccp4/ccp4-7.0/lib/data/monomers/g/GLN.cif
There are 2 data in /home/xray/ccp4/ccp4-7.0/lib/data/monomers/g/GLY.cif
There are 2 data in /home/xray/ccp4/ccp4-7.0/lib/data/monomers/g/GLU.cif
There are 2 data in /home/xray/ccp4/ccp4-7.0/lib/data/monomers/p/PHE.cif
There are 2 data in /home/xray/ccp4/ccp4-7.0/lib/data/monomers/h/HIS.cif
There are 2 data in /home/xray/ccp4/ccp4-7.0/lib/data/monomers/i/ILE.cif
There are 2 data in /home/xray/ccp4/ccp4-7.0/lib/data/monomers/l/LYS.cif
There are 2 data in /home/xray/ccp4/ccp4-7.0/lib/data/monomers/l/LEU.cif
There are 2 data in /home/xray/ccp4/ccp4-7.0/lib/data/monomers/m/MET.cif
There are 2 data in /home/xray/ccp4/ccp4-7.0/lib/data/monomers/m/MSE.cif
There are 2 data in /home/xray/ccp4/ccp4-7.0/lib/data/monomers/p/PRO.cif
There are 2 data in /home/xray/ccp4/ccp4-7.0/lib/data/monomers/a/ARG.cif
There are 2 data in /home/xray/ccp4/ccp4-7.0/lib/data/monomers/s/SER.cif
There are 2 data in /home/xray/ccp4/ccp4-7.0/lib/data/monomers/t/THR.cif
There are 2 data in /home/xray/ccp4/ccp4-7.0/lib/data/monomers/v/VAL.cif
There are 2 data in /home/xray/ccp4/ccp4-7.0/lib/data/monomers/t/TRP.cif
There are 2 data in /home/xray/ccp4/ccp4-7.0/lib/data/monomers/t/TYR.cif
There are 2 data in /home/xray/ccp4/ccp4-7.0/lib/data/monomers/p/PO4.cif
There are 2 data in /home/xray/ccp4/ccp4-7.0/lib/data/monomers/s/SO4.cif
There are 2 data in /home/xray/ccp4/ccp4-7.0/lib/data/monomers/g/GOL.cif
There are 2 data in /home/xray/ccp4/ccp4-7.0/lib/data/monomers/c/CIT.cif
There are 2 data in /home/xray/ccp4/ccp4-7.0/lib/data/monomers/e/EDO.cif
There are 2 data in /home/xray/ccp4/ccp4-7.0/lib/data/monomers/a/A.cif
There are 2 data in /home/xray/ccp4/ccp4-7.0/lib/data/monomers/c/C.cif
There are 2 data in /home/xray/ccp4/ccp4-7.0/lib/data/monomers/g/G.cif
There are 2 data in /home/xray/ccp4/ccp4-7.0/lib/data/monomers/u/U.cif
There are 2 data in /home/xray/ccp4/ccp4-7.0/lib/data/monomers/d/DA.cif
There are 2 data in /home/xray/ccp4/ccp4-7.0/lib/data/monomers/d/DC.cif
There are 2 data in /home/xray/ccp4/ccp4-7.0/lib/data/monomers/d/DG.cif
There are 2 data in /home/xray/ccp4/ccp4-7.0/lib/data/monomers/d/DT.cif
There are 2 data in /home/xray/ccp4/ccp4-7.0/lib/data/monomers/h/HOH.cif
There are 2 data in /home/xray/ccp4/ccp4-7.0/lib/data/monomers/n/NA.cif
INFO:: Reading coordinate file:
/home/CryoEM/ccpEM/ccpem-1.4.1/share/coot/standard-residues.pdb
PDBINFO:: file /home/CryoEM/ccpEM/ccpem-1.4.1/share/coot/standard-residues.pdb
has been read.
Spacegroup: P 1
initalize graphics molecules...done.
(filter-fileselection-filenames-state)
(get-active-map-drag-flag)
(use-graphics-interface-state)
INFO:: coot.py imported
** (coot-bin:27193): WARNING **: Trying to register gtype 'GMountMountFlags' as
enum when in fact it is of type 'GFlags'
** (coot-bin:27193): WARNING **: Trying to register gtype 'GDriveStartFlags' as
enum when in fact it is of type 'GFlags'
** (coot-bin:27193): WARNING **: Trying to register gtype 'GSocketMsgFlags' as
enum when in fact it is of type 'GFlags'
INFO:: coot_python initialized
Running python script
/home/CryoEM/ccpEM/ccpem-1.4.1/lib/python2.7/site-packages/coot/coot_load_modules.py
Good Afternoon Person with no name, Welcome to Coot version 0.9-pre
(set-display-intro-string "Good Afternoon Person with no name, Welcome to Coot
version 0.9-pre")
Coot Python Scripting GUI code found and loaded.
Coot Python Scripting GUI code found and loaded.
(use-graphics-interface-state)
Running python script /home/satyshur/.coot-preferences/coot_toolbuttons.py
(filter-fileselection-filenames-state)
(get-active-map-drag-flag)
(use-graphics-interface-state)
Coot Scheme Scripting GUI code found and loaded.
Good afternoon . Welcome to Coot 0.9-pre.
(set-display-intro-string "Good afternoon . Welcome to Coot 0.9-pre")
(set-display-lists-for-maps 1)
load /home/satyshur/.coot-preferences/coot-preferences.scm
(set-filter-fileselection-filenames 0)
(unset-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 30.60)
(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)
(filter-fileselection-filenames-state)
(get-active-map-drag-flag)
(use-graphics-interface-state)
(set-graphics-window-size 1605 999)
(set-graphics-window-position 0 24)
(set-clipping-front 0.00)
(set-clipping-back 0.00)
(set-density-size 50.00)
(set-colour-map-rotation-on-read-pdb 21.00)
(set-colour-map-rotation-on-read-pdb-flag 1)
(set-colour-map-rotation-on-read-pdb-c-only-flag 1)
(set-swap-difference-map-colours 0)
(set-symmetry-size 13.00)
(set-symmetry-colour-merge 0.50)
(set-symmetry-colour 0.10 0.20 0.80)
(set-symmetry-atom-labels-expanded 0)
(set-active-map-drag-flag 1)
(handle-read-draw-molecule-with-recentre "ken-test_real_space_refined.pdb" 1)
INFO:: Reading coordinate file: ken-test_real_space_refined.pdb
PDBINFO:: file ken-test_real_space_refined.pdb has been read.
Spacegroup: P 1
INFO:: Found 1 models
Model 1 had 0 links
in add_molecular_symmetry_matrices() made 0 biomt matrices
INFO:: NCS chain comparison 19/582
INFO:: NCS chain comparison 19/582
INFO:: NCS chain comparison 10/388
Molecule 0 read successfully
DEBUG:: there were 0 types with no dictionary
(set-molecule-bonds-colour-map-rotation 0 21.00)
(set-draw-hydrogens 0 1)
INFO:: map file type was determined to be CCP4 type
INFO:: attempting to read CCP4 map:
/home/satyshur/CG-NY/cryosparc_P5_J100_map_sharp.mrc
.......................... grid sampling Nuvw = ( 256, 256, 256)
Map statistics: mean: 0.000126348 st.d: 0.0125927
Map statistics: min: -0.118614, max: 0.331444
-0.112988 14
-0.101737 28
-0.0904852 66
-0.0792338 205
-0.0679823 644
-0.0567309 2826
-0.0454794 10696
-0.034228 40521
-0.0229765 171653
-0.0117251 1075873
-0.000473601 14564328
0.0107779 721703
0.0220293 26917
0.0332808 21435
0.0445322 17815
0.0557837 14991
0.0670351 13370
0.0782866 11773
0.089538 10286
0.100789 9429
0.112041 8477
0.123292 7399
0.134544 6746
0.145795 6216
0.157047 5597
0.168298 4913
0.17955 4472
0.190801 3977
0.202053 3379
0.213304 2847
0.224556 2442
0.235807 1969
0.247058 1459
0.25831 1130
0.269561 733
0.280813 446
0.292064 249
0.303316 126
0.314567 53
0.325819 12
0.33707 1
INFO:: n grid points: 16777216
INFO:: mean before filtering: 0.000126348
INFO:: variance before filtering: 0.000158577
INFO:: filter by ignoring 93475 of 16777216 counts ( = 0.5572%) with values
around -0.0001361 from bin 2632 of 10000
Map extents: ..... 256 256 256
Map mean: ........ 0.0001278
Map rmsd: ........ 0.01263
Map maximum: ..... 0.3314
Map minimum: ..... -0.1186
(set-last-map-contour-level 0.04)
(set-last-map-sigma-step 0.40)
(set-show-symmetry-master 0)
(set-go-to-atom-molecule 0)
(set-rotation-centre 141.42 142.02 139.59)
INFO:: backup file
coot-backup/ken-test_real_space_refined.pdb_Tue_Feb_25_14:43:51_2020_modification_0.pdb.gz
INFO:: (result) ASP swapped atoms in [spec: 1 "A" 8 ""] ASP
INFO:: (result) TYR swapped atoms in [spec: 1 "A" 11 ""] TYR
INFO:: (result) ASP swapped atoms in [spec: 1 "A" 24 ""] ASP
INFO:: (result) TYR swapped atoms in [spec: 1 "A" 60 ""] TYR
INFO:: (result) TYR swapped atoms in [spec: 1 "A" 85 ""] TYR
INFO:: (result) ASP swapped atoms in [spec: 1 "A" 139 ""] ASP
INFO:: (result) PHE swapped atoms in [spec: 1 "A" 141 ""] PHE
INFO:: (result) TYR swapped atoms in [spec: 1 "A" 155 ""] TYR
INFO:: (result) PHE swapped atoms in [spec: 1 "A" 369 ""] PHE
INFO:: (result) TYR swapped atoms in [spec: 1 "A" 456 ""] TYR
INFO:: (result) ASP swapped atoms in [spec: 1 "A" 492 ""] ASP
INFO:: (result) PHE swapped atoms in [spec: 1 "A" 503 ""] PHE
INFO:: (result) ASP swapped atoms in [spec: 1 "A" 552 ""] ASP
INFO:: (result) ASP swapped atoms in [spec: 1 "A" 570 ""] ASP
INFO:: (result) TYR swapped atoms in [spec: 1 "B" 69 ""] TYR
INFO:: (result) TYR swapped atoms in [spec: 1 "B" 82 ""] TYR
INFO:: (result) PHE swapped atoms in [spec: 1 "B" 89 ""] PHE
INFO:: (result) PHE swapped atoms in [spec: 1 "B" 94 ""] PHE
INFO:: (result) TYR swapped atoms in [spec: 1 "B" 128 ""] TYR
INFO:: (result) PHE swapped atoms in [spec: 1 "B" 131 ""] PHE
INFO:: (result) PHE swapped atoms in [spec: 1 "B" 134 ""] PHE
INFO:: (result) PHE swapped atoms in [spec: 1 "B" 140 ""] PHE
INFO:: (result) TYR swapped atoms in [spec: 1 "B" 148 ""] TYR
INFO:: (result) ASP swapped atoms in [spec: 1 "B" 150 ""] ASP
INFO:: (result) ASP swapped atoms in [spec: 1 "B" 165 ""] ASP
INFO:: (result) PHE swapped atoms in [spec: 1 "B" 171 ""] PHE
INFO:: (result) TYR swapped atoms in [spec: 1 "B" 199 ""] TYR
INFO:: (result) TYR swapped atoms in [spec: 1 "B" 203 ""] TYR
INFO:: (result) PHE swapped atoms in [spec: 1 "B" 264 ""] PHE
INFO:: (result) PHE swapped atoms in [spec: 1 "B" 330 ""] PHE
INFO:: (result) TYR swapped atoms in [spec: 1 "B" 338 ""] TYR
INFO:: (result) PHE swapped atoms in [spec: 1 "B" 361 ""] PHE
INFO:: (result) TYR swapped atoms in [spec: 1 "C" 127 ""] TYR
INFO:: (result) TYR swapped atoms in [spec: 1 "C" 137 ""] TYR
INFO:: (result) TYR swapped atoms in [spec: 1 "C" 145 ""] TYR
INFO:: (result) PHE swapped atoms in [spec: 1 "C" 289 ""] PHE
INFO:: 36 residues had their atoms swapped
(stereo-mode-state)
INFO:: Hardware stereo widget opened successfully
ERROR:: using display list 0 when main_or_secondary is 1
ERROR:: using display list 0 when main_or_secondary is 1
(hardware-stereo-mode)
ERROR:: using display list 0 when main_or_secondary is 1
ERROR:: using display list 0 when main_or_secondary is 1
ERROR:: using display list 0 when main_or_secondary is 1
ERROR:: using display list 0 when main_or_secondary is 1
ERROR:: using display list 0 when main_or_secondary is 1
ERROR:: using display list 0 when main_or_secondary is 1
ERROR:: using display list 0 when main_or_secondary is 1
ERROR:: using display list 0 when main_or_secondary is 1
ERROR:: using display list 0 when main_or_secondary is 1
ERROR:: using display list 0 when main_or_secondary is 1
ERROR:: using display list 0 when main_or_secondary is 1
ERROR:: using display list 0 when main_or_secondary is 1
ERROR:: using display list 0 when main_or_secondary is 1
ERROR:: using display list 0 when main_or_secondary is 1
ERROR:: using display list 0 when main_or_secondary is 1
ERROR:: using display list 0 when main_or_secondary is 1
ERROR:: using display list 0 when main_or_secondary is 1
ERROR:: using display list 0 when main_or_secondary is 1
ERROR:: using display list 0 when main_or_secondary is 1
ERROR:: using display list 0 when main_or_secondary is 1
ERROR:: using display list 0 when main_or_secondary is 1
ERROR:: using display list 0 when main_or_secondary is 1
ERROR:: using display list 0 when main_or_secondary is 1
ERROR:: using display list 0 when main_or_secondary is 1
ERROR:: using display list 0 when main_or_secondary is 1
ERROR:: using display list 0 when main_or_secondary is 1
ERROR:: using display list 0 when main_or_secondary is 1
ERROR:: using display list 0 when main_or_secondary is 1
ERROR:: using display list 0 when main_or_secondary is 1
ERROR:: using display list 0 when main_or_secondary is 1
ERROR:: using display list 0 when main_or_secondary is 1
ERROR:: using display list 0 when main_or_secondary is 1
ERROR:: using display list 0 when main_or_secondary is 1
ERROR:: using display list 0 when main_or_secondary is 1
ERROR:: using display list 0 when main_or_secondary is 1
ERROR:: using display list 0 when main_or_secondary is 1
ERROR:: using display list 0 when main_or_secondary is 1
ERROR:: using display list 0 when main_or_secondary is 1
ERROR:: using display list 0 when main_or_secondary is 1
ERROR:: using display list 0 when main_or_secondary is 1
ERROR:: using display list 0 when main_or_secondary is 1
ERROR:: using display list 0 when main_or_secondary is 1
ERROR:: using display list 0 when main_or_secondary is 1
ERROR:: using display list 0 when main_or_secondary is 1
ERROR:: using display list 0 when main_or_secondary is 1
ERROR:: using display list 0 when main_or_secondary is 1
ERROR:: using display list 0 when main_or_secondary is 1
ERROR:: using display list 0 when main_or_secondary is 1
ERROR:: using display list 0 when main_or_secondary is 1
ERROR:: using display list 0 when main_or_secondary is 1
ERROR:: using display list 0 when main_or_secondary is 1
ERROR:: using display list 0 when main_or_secondary is 1
ERROR:: using display list 0 when main_or_secondary is 1
ERROR:: using display list 0 when main_or_secondary is 1
ERROR:: using display list 0 when main_or_secondary is 1
ERROR:: using display list 0 when main_or_secondary is 1
ERROR:: using display list 0 when main_or_secondary is 1
ERROR:: using display list 0 when main_or_secondary is 1
ERROR:: using display list 0 when main_or_secondary is 1
ERROR:: using display list 0 when main_or_secondary is 1
ERROR:: using display list 0 when main_or_secondary is 1
ERROR:: using display list 0 when main_or_secondary is 1
ERROR:: using display list 0 when main_or_secondary is 1
ERROR:: using display list 0 when main_or_secondary is 1
ERROR:: using display list 0 when main_or_secondary is 1
ERROR:: using display list 0 when main_or_secondary is 1
ERROR:: using display list 0 when main_or_secondary is 1
ERROR:: using display list 0 when main_or_secondary is 1
ERROR:: using display list 0 when main_or_secondary is 1
ERROR:: using display list 0 when main_or_secondary is 1
ERROR:: using display list 0 when main_or_secondary is 1
ERROR:: using display list 0 when main_or_secondary is 1
ERROR:: using display list 0 when main_or_secondary is 1
ERROR:: using display list 0 when main_or_secondary is 1
ERROR:: using display list 0 when main_or_secondary is 1
ERROR:: using display list 0 when main_or_secondary is 1
ERROR:: using display list 0 when main_or_secondary is 1
ERROR:: using display list 0 when main_or_secondary is 1
ERROR:: using display list 0 when main_or_secondary is 1
ERROR:: using display list 0 when main_or_secondary is 1
ERROR:: using display list 0 when main_or_secondary is 1
ERROR:: using display list 0 when main_or_secondary is 1
ERROR:: using display list 0 when main_or_secondary is 1
ERROR:: using display list 0 when main_or_secondary is 1
ERROR:: using display list 0 when main_or_secondary is 1
ERROR:: using display list 0 when main_or_secondary is 1
ERROR:: using display list 0 when main_or_secondary is 1
ERROR:: using display list 0 when main_or_secondary is 1
ERROR:: using display list 0 when main_or_secondary is 1
ERROR:: using display list 0 when main_or_secondary is 1
ERROR:: using display list 0 when main_or_secondary is 1
ERROR:: using display list 0 when main_or_secondary is 1
ERROR:: using display list 0 when main_or_secondary is 1
ERROR:: using display list 0 when main_or_secondary is 1
(stereo-mode-state)
INFO:: switch to mono_mode succeeded
Elapsed time for map contouring: 180ms
(mono-mode)
(coot-checked-exit 0)
(clear-backups-maybe)
(stereo-mode-state)
(stereo-mode-state)
(save-state)
[satyshur@xingxtal ~/CG-NY]$
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