Hello everybody,
On my computer (Ubuntu (xubuntu) 24.04.2 LTS), Coot 1.1.15 is unable to display
the symmetry-related molecules.
I used the Coot 1 installation provided with the CCP4 suite.
As you will see in the logfile below, there is a "WARNING:: No symmetry
available for this molecule" message. This message (as well as the
impossibility to display symmetry-related molecules) is encountered no matter
the PDB file I am working with.
The logfile below has been obtained using the files from the tutorial.
Do you have any idea how I could correct this behavior ?
Thank you very much in advance for your help and your support !
Fontconfig error: Cannot load default config file: No such file: (null)
INFO:: built with GTK 4.10.4
pdd /usr/xtal/CCP4_9.0/ccp4-9/coot_py3/share/coot
INFO:: Using Standard CCP4 Refmac dictionary from CLIBD_MON:
/usr/xtal/CCP4_9.0/ccp4-9/lib/data/monomers/
There are 247 data in
/usr/xtal/CCP4_9.0/ccp4-9/lib/data/monomers/list/mon_lib_list.cif
There are 2 data in /usr/xtal/CCP4_9.0/ccp4-9/lib/data/monomers/a/ALA.cif
There are 2 data in /usr/xtal/CCP4_9.0/ccp4-9/lib/data/monomers/a/ASP.cif
There are 2 data in /usr/xtal/CCP4_9.0/ccp4-9/lib/data/monomers/a/ASN.cif
There are 2 data in /usr/xtal/CCP4_9.0/ccp4-9/lib/data/monomers/c/CYS.cif
There are 2 data in /usr/xtal/CCP4_9.0/ccp4-9/lib/data/monomers/g/GLN.cif
There are 2 data in /usr/xtal/CCP4_9.0/ccp4-9/lib/data/monomers/g/GLY.cif
There are 2 data in /usr/xtal/CCP4_9.0/ccp4-9/lib/data/monomers/g/GLU.cif
There are 2 data in /usr/xtal/CCP4_9.0/ccp4-9/lib/data/monomers/p/PHE.cif
There are 2 data in /usr/xtal/CCP4_9.0/ccp4-9/lib/data/monomers/h/HIS.cif
There are 2 data in /usr/xtal/CCP4_9.0/ccp4-9/lib/data/monomers/i/ILE.cif
There are 2 data in /usr/xtal/CCP4_9.0/ccp4-9/lib/data/monomers/l/LYS.cif
There are 2 data in /usr/xtal/CCP4_9.0/ccp4-9/lib/data/monomers/l/LEU.cif
There are 2 data in /usr/xtal/CCP4_9.0/ccp4-9/lib/data/monomers/m/MET.cif
There are 2 data in /usr/xtal/CCP4_9.0/ccp4-9/lib/data/monomers/m/MSE.cif
There are 2 data in /usr/xtal/CCP4_9.0/ccp4-9/lib/data/monomers/p/PRO.cif
There are 2 data in /usr/xtal/CCP4_9.0/ccp4-9/lib/data/monomers/a/ARG.cif
There are 2 data in /usr/xtal/CCP4_9.0/ccp4-9/lib/data/monomers/s/SER.cif
There are 2 data in /usr/xtal/CCP4_9.0/ccp4-9/lib/data/monomers/t/THR.cif
There are 2 data in /usr/xtal/CCP4_9.0/ccp4-9/lib/data/monomers/v/VAL.cif
There are 2 data in /usr/xtal/CCP4_9.0/ccp4-9/lib/data/monomers/t/TRP.cif
There are 2 data in /usr/xtal/CCP4_9.0/ccp4-9/lib/data/monomers/t/TYR.cif
There are 2 data in /usr/xtal/CCP4_9.0/ccp4-9/lib/data/monomers/p/PO4.cif
There are 2 data in /usr/xtal/CCP4_9.0/ccp4-9/lib/data/monomers/s/SO4.cif
There are 2 data in /usr/xtal/CCP4_9.0/ccp4-9/lib/data/monomers/g/GOL.cif
There are 2 data in /usr/xtal/CCP4_9.0/ccp4-9/lib/data/monomers/c/CIT.cif
There are 2 data in /usr/xtal/CCP4_9.0/ccp4-9/lib/data/monomers/e/EDO.cif
There are 2 data in /usr/xtal/CCP4_9.0/ccp4-9/lib/data/monomers/a/A.cif
There are 2 data in /usr/xtal/CCP4_9.0/ccp4-9/lib/data/monomers/c/C.cif
There are 2 data in /usr/xtal/CCP4_9.0/ccp4-9/lib/data/monomers/g/G.cif
There are 2 data in /usr/xtal/CCP4_9.0/ccp4-9/lib/data/monomers/u/U.cif
There are 2 data in /usr/xtal/CCP4_9.0/ccp4-9/lib/data/monomers/d/DA.cif
There are 2 data in /usr/xtal/CCP4_9.0/ccp4-9/lib/data/monomers/d/DC.cif
There are 2 data in /usr/xtal/CCP4_9.0/ccp4-9/lib/data/monomers/d/DG.cif
There are 2 data in /usr/xtal/CCP4_9.0/ccp4-9/lib/data/monomers/d/DT.cif
There are 2 data in /usr/xtal/CCP4_9.0/ccp4-9/lib/data/monomers/h/HOH.cif
There are 2 data in /usr/xtal/CCP4_9.0/ccp4-9/lib/data/monomers/n/NA.cif
DEBUG:: get_atom_selection() with file
"/usr/xtal/CCP4_9.0/ccp4-9/coot_py3/share/coot/standard-residues.pdb"
use_gemmi: 0
DEBUG:: in setup_python_basic() pydirectory is
/usr/xtal/CCP4_9.0/ccp4-9/coot_py3/lib/python3.9/site-packages
DEBUG:: in setup_python_basic() pkgpydirectory is
/usr/xtal/CCP4_9.0/ccp4-9/coot_py3/lib/python3.9/site-packages/coot
DEBUG:: in setup_python_basic(): d_main 0x7ee0fc54b680
DEBUG:: in setup_python_basic(): sys imported
DEBUG:: in setup_python_coot_module() appending to sys path:
/usr/xtal/CCP4_9.0/ccp4-9/coot_py3/lib/python3.9/site-packages
DEBUG:: in setup_python_coot_module() appending to sys path:
/usr/xtal/CCP4_9.0/ccp4-9/coot_py3/lib/python3.9/site-packages/coot
INFO:: Using Standard CCP4 Refmac dictionary from CLIBD_MON:
/usr/xtal/CCP4_9.0/ccp4-9/lib/data/monomers/
There are 247 data in
/usr/xtal/CCP4_9.0/ccp4-9/lib/data/monomers/list/mon_lib_list.cif
There are 2 data in /usr/xtal/CCP4_9.0/ccp4-9/lib/data/monomers/a/ALA.cif
There are 2 data in /usr/xtal/CCP4_9.0/ccp4-9/lib/data/monomers/a/ASP.cif
There are 2 data in /usr/xtal/CCP4_9.0/ccp4-9/lib/data/monomers/a/ASN.cif
There are 2 data in /usr/xtal/CCP4_9.0/ccp4-9/lib/data/monomers/c/CYS.cif
There are 2 data in /usr/xtal/CCP4_9.0/ccp4-9/lib/data/monomers/g/GLN.cif
There are 2 data in /usr/xtal/CCP4_9.0/ccp4-9/lib/data/monomers/g/GLY.cif
There are 2 data in /usr/xtal/CCP4_9.0/ccp4-9/lib/data/monomers/g/GLU.cif
There are 2 data in /usr/xtal/CCP4_9.0/ccp4-9/lib/data/monomers/p/PHE.cif
There are 2 data in /usr/xtal/CCP4_9.0/ccp4-9/lib/data/monomers/h/HIS.cif
There are 2 data in /usr/xtal/CCP4_9.0/ccp4-9/lib/data/monomers/i/ILE.cif
There are 2 data in /usr/xtal/CCP4_9.0/ccp4-9/lib/data/monomers/l/LYS.cif
There are 2 data in /usr/xtal/CCP4_9.0/ccp4-9/lib/data/monomers/l/LEU.cif
There are 2 data in /usr/xtal/CCP4_9.0/ccp4-9/lib/data/monomers/m/MET.cif
There are 2 data in /usr/xtal/CCP4_9.0/ccp4-9/lib/data/monomers/m/MSE.cif
There are 2 data in /usr/xtal/CCP4_9.0/ccp4-9/lib/data/monomers/p/PRO.cif
There are 2 data in /usr/xtal/CCP4_9.0/ccp4-9/lib/data/monomers/a/ARG.cif
There are 2 data in /usr/xtal/CCP4_9.0/ccp4-9/lib/data/monomers/s/SER.cif
There are 2 data in /usr/xtal/CCP4_9.0/ccp4-9/lib/data/monomers/t/THR.cif
There are 2 data in /usr/xtal/CCP4_9.0/ccp4-9/lib/data/monomers/v/VAL.cif
There are 2 data in /usr/xtal/CCP4_9.0/ccp4-9/lib/data/monomers/t/TRP.cif
There are 2 data in /usr/xtal/CCP4_9.0/ccp4-9/lib/data/monomers/t/TYR.cif
There are 2 data in /usr/xtal/CCP4_9.0/ccp4-9/lib/data/monomers/p/PO4.cif
There are 2 data in /usr/xtal/CCP4_9.0/ccp4-9/lib/data/monomers/s/SO4.cif
There are 2 data in /usr/xtal/CCP4_9.0/ccp4-9/lib/data/monomers/g/GOL.cif
There are 2 data in /usr/xtal/CCP4_9.0/ccp4-9/lib/data/monomers/c/CIT.cif
There are 2 data in /usr/xtal/CCP4_9.0/ccp4-9/lib/data/monomers/e/EDO.cif
There are 2 data in /usr/xtal/CCP4_9.0/ccp4-9/lib/data/monomers/a/A.cif
There are 2 data in /usr/xtal/CCP4_9.0/ccp4-9/lib/data/monomers/c/C.cif
There are 2 data in /usr/xtal/CCP4_9.0/ccp4-9/lib/data/monomers/g/G.cif
There are 2 data in /usr/xtal/CCP4_9.0/ccp4-9/lib/data/monomers/u/U.cif
There are 2 data in /usr/xtal/CCP4_9.0/ccp4-9/lib/data/monomers/d/DA.cif
There are 2 data in /usr/xtal/CCP4_9.0/ccp4-9/lib/data/monomers/d/DC.cif
There are 2 data in /usr/xtal/CCP4_9.0/ccp4-9/lib/data/monomers/d/DG.cif
There are 2 data in /usr/xtal/CCP4_9.0/ccp4-9/lib/data/monomers/d/DT.cif
There are 2 data in /usr/xtal/CCP4_9.0/ccp4-9/lib/data/monomers/h/HOH.cif
There are 2 data in /usr/xtal/CCP4_9.0/ccp4-9/lib/data/monomers/n/NA.cif
DEBUG:: get_atom_selection() with file
"/usr/xtal/CCP4_9.0/ccp4-9/coot_py3/share/coot/standard-residues.pdb"
use_gemmi: 0
INFO:: monitor 1 no description
INFO:: monitor 1 connection DP-0
INFO:: monitor 1 refresh rate 59950 mHz
INFO:: monitor 1 scale_factor 1
INFO:: monitor 2 no description
INFO:: monitor 2 connection DP-2
INFO:: monitor 2 refresh rate 59950 mHz
INFO:: monitor 2 scale_factor 1
INFO:: GL Version: 3.2.0 NVIDIA 550.163.01
INFO:: GL Shading Language Version: 1.50 NVIDIA via Cg compiler
INFO:: GL Renderer: NVIDIA T1000 8GB/PCIe/SSE2
INFO:: GL Vendor: NVIDIA Corporation
Shader compile texture-meshes.shader success
Shader compile outline-of-active-residue.shader success
Shader compile map.shader success
Shader compile draw-map-cap.shader success
Shader compile model.shader success
Shader compile central-cube.shader success
Shader compile central-cube.shader success
Shader compile hud-text.shader success
Shader compile hud-bars.shader success
Shader compile hud-labels.shader success
Shader compile hud-image-texture.shader success
Shader compile atom-label.shader success
Shader compile moleculestotriangles.shader success
Shader compile lines.shader success
Shader compile lines-pulse.shader success
Shader compile rama-balls.shader success
Shader compile particles.shader success
Shader compile instanced-objects.shader success
Shader compile extra-distance-restraints.shader success
Shader compile hud-geometry-tooltip-text.shader success
Shader compile residue-markers.shader success
Shader compile ligand-view.shader success
Shader compile model-as-mesh.shader success
Shader compile symmetry-atoms-lines.shader success
Shader compile hud-bars.shader success
Shader compile rama-plot-axes-and-ticks.shader success
Shader compile rama-plot-phi-psi-markers.shader success
Shader compile hud-lines.shader success
Shader compile background-image.shader success
Shader compile meshes.shader success
Shader compile texture-meshes.shader success
Shader compile residue-markers-for-ssao.shader success
Shader compile meshes-with-shadows.shader success
Shader compile meshes-for-shadow-map.shader success
Shader compile instanced-meshes-for-shadow-map.shader success
Shader compile meshes-for-ssao.shader success
Shader compile instanced-meshes-for-ssao.shader success
Shader compile texture-meshes-for-ssao.shader success
Shader compile texture-meshes-with-shadows.shader success
Shader compile texture-meshes-shadow-map.shader success
Shader compile shadow-map-image-texture.shader success
Shader compile 9.ssao_geometry.shader success
Shader compile 9.ssao.shader success
Shader compile 9.ssao_blur.shader success
Shader compile instanced-meshes-with-shadows.shader success
Shader compile effects.shader success
Shader compile blur-x.shader success
Shader compile blur-y.shader success
Shader compile depth-of-field.shader success
Shader compile rotation-centre-cross-hairs-for-ssao.shader success
DEBUG:: in setup_python_with_coot_modules() pkgpydirectory:
/usr/xtal/CCP4_9.0/ccp4-9/coot_py3/lib/python3.9/site-packages/coot
DEBUG:: in setup_python_with_coot_modules() pydirectory:
/usr/xtal/CCP4_9.0/ccp4-9/coot_py3/lib/python3.9/site-packages
DEBUG:: in setup_python_with_coot_modules() appending to sys path:
/usr/xtal/CCP4_9.0/ccp4-9/coot_py3/lib/python3.9/site-packages
DEBUG:: in setup_python_with_coot_modules() appending to sys path:
/usr/xtal/CCP4_9.0/ccp4-9/coot_py3/lib/python3.9/site-packages/coot
DEBUG:: in setup_python_with_coot_modules() sys imported
DEBUG:: in setup_python_with_coot_modules() PyImport_ImportModule() coot:
0x7ee0fc451720
DEBUG:: in setup_python_with_coot_modules() PyImport_ImportModule() coot_utils:
0x7ee0fc2ea860
Coot Python Scripting GUI code found and loaded.
DEBUG:: in setup_python_with_coot_modules() PyImport_ImportModule() for
gui_module: 0x7ee0fc2cd590
** (coot-1:3841713): WARNING **: 09:56:50.807:
set_vertical_toolbar_internal_alignment: Toolbar item 0x1540cc40 of type
GtkToggleButton: The parent widget that wraps GtkToggleButton::child is not a
GtkBox but a GtkToggleButton. GtkToggleButton::child however is a GtkBox.
Attempt will be made to align it. It might not work.
Load python config script /home/lionel/.config/Coot/coot_preferences.py
DEBUG:: get_atom_selection() with file
"/usr/xtal/CCP4_9.0/ccp4-9/coot_py3/share/coot/data/tutorial-modern.pdb"
use_gemmi: 0
INFO:: Reading coordinate file:
/usr/xtal/CCP4_9.0/ccp4-9/coot_py3/share/coot/data/tutorial-modern.pdb
INFO:: file
/usr/xtal/CCP4_9.0/ccp4-9/coot_py3/share/coot/data/tutorial-modern.pdb has been
read.
INFO:: Found 1 models
Model 1 had 0 links
WARNING:: No symmetry available for this molecule
DEBUG:: start display_control_molecule_combo_box()
DEBUG:: text: "Bonds (Colour by Atom)" user data (imol) 0
----- refresh_validation_graph_model_list adding label 0
..._py3/share/coot/data/tutorial-modern.pdb
----------------------- refresh_ramachandran_plot_model_list ---------
----- refresh_ramachandran_plot_model_list adding label 0
..._py3/share/coot/data/tutorial-modern.pdb
----------------------- done refresh_ramachandran_plot_model_list ---------
WARNING:: No Symmetry for this model
INFO:: fill_ghost_info Constructed 1 ghosts
Ghost 0 name: "NCS found from matching Chain B onto Chain A"
GL ERROR:: in make_glsl_bonds_type_checked() --- start ---
Molecule 0 read successfully
INFO:: making map from mtz filename
/usr/xtal/CCP4_9.0/ccp4-9/coot_py3/share/coot/data/rnasa-1.8-all_refmac1.mtz
INFO:: Number of observed reflections: 17554
INFO:: finding ASU unique map points with sampling rate 2.5
INFO:: grid sampling...Nuvw = ( 180, 216, 108)
Map extents: ..... 180 216 108
Map mean: ........ 4.7689e-05
Map sigma: ....... 0.373505
Map maximum: ..... 3.47348
Map minimum: ..... -1.25991
GL ERROR:: Mesh::setup_glsl_map_rendering() Pos A1 GL_INVALID_OPERATION
INFO:: Stored refmac parameters: FGMP18 SIGFGMP18 FreeR_flag is sensible.
GL ERROR:: Mesh::setup_glsl_map_rendering() Pos A1 GL_INVALID_OPERATION
GL ERROR:: Mesh::setup_glsl_map_rendering() Pos A1 GL_INVALID_OPERATION
INFO:: making map from mtz filename
/usr/xtal/CCP4_9.0/ccp4-9/coot_py3/share/coot/data/rnasa-1.8-all_refmac1.mtz
INFO:: Number of observed reflections: 17554
INFO:: finding ASU unique map points with sampling rate 2.5
INFO:: grid sampling...Nuvw = ( 180, 216, 108)
Map extents: ..... 180 216 108
Map mean: ........ 8.79985e-06
Map sigma: ....... 0.173602
Map maximum: ..... 2.78252
Map minimum: ..... -1.78282
GL ERROR:: Mesh::setup_glsl_map_rendering() Pos A1 GL_INVALID_OPERATION
GL ERROR:: Mesh::setup_glsl_map_rendering() Pos A1 GL_INVALID_OPERATION
GL ERROR:: Mesh::setup_glsl_map_rendering() Pos A1 GL_INVALID_OPERATION
GL ERROR:: Mesh::setup_glsl_map_rendering() Pos A1 GL_INVALID_OPERATION
GL ERROR:: Mesh::setup_glsl_map_rendering() Pos A1 GL_INVALID_OPERATION
Kind regards / Vänliga hälsningar,
Lionel Trésaugues, PhD, Director
Structure-Based Drug Design
Sprint Bioscience
Main: +46 (0)8 411 44 55
Direct: +46(0)73 075 54 46
Email:
lionel.tresaug...@sprintbioscience.com<mailto:lionel.tresaug...@sprintbioscience.com>
www.sprintbioscience.com<http://www.sprintbioscience.com/>
Follow us on LinkedIn<https://se.linkedin.com/company/sprint-bioscience>
Follow us on Facebook<https://sv-se.facebook.com/SprintBioscience/>
[cid:image001.png@01DC223C.203C5800]
Confidentiality Note: This message is intended only for the use of the named
recipient(s) and may contain confidential, personal and/or privileged
information. If you are not the intended recipient, please delete this message.
Any unauthorized use of the information contained in this message is prohibited.
########################################################################
To unsubscribe from the COOT list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=COOT&A=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/
