Hi Paul and Jingjing,
I have the same issue. MacOS 14.7.1, and on both intel and Apple silicon macs.
The issue seems to be ModuleNotFoundError: No module named 'coot_gui_api'
though other errors are flagged. I have checked brew upgrades and rebuilt
several times but get the same issue. Full output is:
% coot
INFO:: built with GTK 4.16.3
pdd /usr/local/Cellar/coot/1.1.10/share/coot
There are 143 data in
/usr/local/Cellar/coot/1.1.10/share/coot/lib/data/monomers/list/mon_lib_list.cif
There are 2 data in
/usr/local/Cellar/coot/1.1.10/share/coot/lib/data/monomers/a/ALA.cif
There are 2 data in
/usr/local/Cellar/coot/1.1.10/share/coot/lib/data/monomers/a/ASP.cif
There are 2 data in
/usr/local/Cellar/coot/1.1.10/share/coot/lib/data/monomers/a/ASN.cif
There are 2 data in
/usr/local/Cellar/coot/1.1.10/share/coot/lib/data/monomers/c/CYS.cif
There are 2 data in
/usr/local/Cellar/coot/1.1.10/share/coot/lib/data/monomers/g/GLN.cif
There are 2 data in
/usr/local/Cellar/coot/1.1.10/share/coot/lib/data/monomers/g/GLY.cif
There are 2 data in
/usr/local/Cellar/coot/1.1.10/share/coot/lib/data/monomers/g/GLU.cif
There are 2 data in
/usr/local/Cellar/coot/1.1.10/share/coot/lib/data/monomers/p/PHE.cif
There are 2 data in
/usr/local/Cellar/coot/1.1.10/share/coot/lib/data/monomers/h/HIS.cif
There are 2 data in
/usr/local/Cellar/coot/1.1.10/share/coot/lib/data/monomers/i/ILE.cif
There are 2 data in
/usr/local/Cellar/coot/1.1.10/share/coot/lib/data/monomers/l/LYS.cif
There are 2 data in
/usr/local/Cellar/coot/1.1.10/share/coot/lib/data/monomers/l/LEU.cif
There are 2 data in
/usr/local/Cellar/coot/1.1.10/share/coot/lib/data/monomers/m/MET.cif
There are 2 data in
/usr/local/Cellar/coot/1.1.10/share/coot/lib/data/monomers/m/MSE.cif
There are 2 data in
/usr/local/Cellar/coot/1.1.10/share/coot/lib/data/monomers/p/PRO.cif
There are 2 data in
/usr/local/Cellar/coot/1.1.10/share/coot/lib/data/monomers/a/ARG.cif
There are 2 data in
/usr/local/Cellar/coot/1.1.10/share/coot/lib/data/monomers/s/SER.cif
There are 2 data in
/usr/local/Cellar/coot/1.1.10/share/coot/lib/data/monomers/t/THR.cif
There are 2 data in
/usr/local/Cellar/coot/1.1.10/share/coot/lib/data/monomers/v/VAL.cif
There are 2 data in
/usr/local/Cellar/coot/1.1.10/share/coot/lib/data/monomers/t/TRP.cif
There are 2 data in
/usr/local/Cellar/coot/1.1.10/share/coot/lib/data/monomers/t/TYR.cif
There are 2 data in
/usr/local/Cellar/coot/1.1.10/share/coot/lib/data/monomers/p/PO4.cif
There are 2 data in
/usr/local/Cellar/coot/1.1.10/share/coot/lib/data/monomers/s/SO4.cif
There are 2 data in
/usr/local/Cellar/coot/1.1.10/share/coot/lib/data/monomers/g/GOL.cif
There are 2 data in
/usr/local/Cellar/coot/1.1.10/share/coot/lib/data/monomers/c/CIT.cif
There are 2 data in
/usr/local/Cellar/coot/1.1.10/share/coot/lib/data/monomers/e/EDO.cif
There are 2 data in
/usr/local/Cellar/coot/1.1.10/share/coot/lib/data/monomers/a/A.cif
There are 2 data in
/usr/local/Cellar/coot/1.1.10/share/coot/lib/data/monomers/c/C.cif
There are 2 data in
/usr/local/Cellar/coot/1.1.10/share/coot/lib/data/monomers/g/G.cif
There are 2 data in
/usr/local/Cellar/coot/1.1.10/share/coot/lib/data/monomers/u/U.cif
There are 2 data in
/usr/local/Cellar/coot/1.1.10/share/coot/lib/data/monomers/d/DA.cif
There are 2 data in
/usr/local/Cellar/coot/1.1.10/share/coot/lib/data/monomers/d/DC.cif
There are 2 data in
/usr/local/Cellar/coot/1.1.10/share/coot/lib/data/monomers/d/DG.cif
There are 2 data in
/usr/local/Cellar/coot/1.1.10/share/coot/lib/data/monomers/d/DT.cif
There are 2 data in
/usr/local/Cellar/coot/1.1.10/share/coot/lib/data/monomers/h/HOH.cif
There are 2 data in
/usr/local/Cellar/coot/1.1.10/share/coot/lib/data/monomers/n/NA.cif
debug:: in setup_python() pydirectory is
/usr/local/Cellar/coot/1.1.10/share/coot/../../lib/python3.13/site-packages
debug:: in setup_python() pkgpydirectory is
/usr/local/Cellar/coot/1.1.10/share/coot/../../lib/python3.13/site-packages/coot
ERROR:: setup_python_coot_module() Null coot
INFO:: GL Version: 4.1 ATI-5.5.17
INFO:: GL Shading Language Version: 4.10
INFO:: GL Renderer: AMD Radeon Pro 5500M OpenGL Engine
INFO:: GL Vendor: ATI Technologies Inc.
WARNING:: validation failed: meshes-with-shadows.shader validation status 0
Shader compile meshes-with-shadows.shader validation-failed
WARNING:: validation failed: meshes-for-shadow-map.shader validation status 0
Shader compile meshes-for-shadow-map.shader validation-failed
WARNING:: validation failed: instanced-meshes-for-shadow-map.shader validation
status 0
Shader compile instanced-meshes-for-shadow-map.shader validation-failed
WARNING:: validation failed: meshes-for-ssao.shader validation status 0
Shader compile meshes-for-ssao.shader validation-failed
WARNING:: validation failed: instanced-meshes-for-ssao.shader validation status 0
Shader compile instanced-meshes-for-ssao.shader validation-failed
WARNING:: validation failed: texture-meshes-for-ssao.shader validation status 0
Shader compile texture-meshes-for-ssao.shader validation-failed
WARNING:: validation failed: texture-meshes-with-shadows.shader validation
status 0
Shader compile texture-meshes-with-shadows.shader validation-failed
WARNING:: validation failed: texture-meshes-shadow-map.shader validation status 0
Shader compile texture-meshes-shadow-map.shader validation-failed
WARNING:: validation failed: texture-meshes.shader validation status 0
Shader compile texture-meshes.shader validation-failed
WARNING:: validation failed: shadow-map-image-texture.shader validation status 0
Shader compile shadow-map-image-texture.shader validation-failed
WARNING:: validation failed: 9.ssao_geometry.shader validation status 0
Shader compile 9.ssao_geometry.shader validation-failed
WARNING:: validation failed: 9.ssao.shader validation status 0
Shader compile 9.ssao.shader validation-failed
WARNING:: validation failed: 9.ssao_blur.shader validation status 0
Shader compile 9.ssao_blur.shader validation-failed
WARNING:: validation failed: instanced-meshes-with-shadows.shader validation
status 0
Shader compile instanced-meshes-with-shadows.shader validation-failed
WARNING:: validation failed: outline-of-active-residue.shader validation status 0
Shader compile outline-of-active-residue.shader validation-failed
WARNING:: validation failed: map.shader validation status 0
Shader compile map.shader validation-failed
WARNING:: validation failed: draw-map-cap.shader validation status 0
Shader compile draw-map-cap.shader validation-failed
WARNING:: validation failed: model.shader validation status 0
Shader compile model.shader validation-failed
WARNING:: validation failed: central-cube.shader validation status 0
Shader compile central-cube.shader validation-failed
WARNING:: validation failed: central-cube.shader validation status 0
Shader compile central-cube.shader validation-failed
WARNING:: validation failed: hud-text.shader validation status 0
Shader compile hud-text.shader validation-failed
WARNING:: validation failed: hud-bars.shader validation status 0
Shader compile hud-bars.shader validation-failed
WARNING:: validation failed: hud-labels.shader validation status 0
Shader compile hud-labels.shader validation-failed
WARNING:: validation failed: hud-image-texture.shader validation status 0
Shader compile hud-image-texture.shader validation-failed
WARNING:: validation failed: atom-label.shader validation status 0
Shader compile atom-label.shader validation-failed
WARNING:: validation failed: moleculestotriangles.shader validation status 0
Shader compile moleculestotriangles.shader validation-failed
WARNING:: validation failed: lines.shader validation status 0
Shader compile lines.shader validation-failed
WARNING:: validation failed: lines-pulse.shader validation status 0
Shader compile lines-pulse.shader validation-failed
WARNING:: validation failed: rama-balls.shader validation status 0
Shader compile rama-balls.shader validation-failed
WARNING:: validation failed: particles.shader validation status 0
Shader compile particles.shader validation-failed
WARNING:: validation failed: instanced-objects.shader validation status 0
Shader compile instanced-objects.shader validation-failed
WARNING:: validation failed: extra-distance-restraints.shader validation status 0
Shader compile extra-distance-restraints.shader validation-failed
WARNING:: validation failed: hud-geometry-tooltip-text.shader validation status 0
Shader compile hud-geometry-tooltip-text.shader validation-failed
WARNING:: validation failed: residue-markers.shader validation status 0
Shader compile residue-markers.shader validation-failed
WARNING:: validation failed: residue-markers-for-ssao.shader validation status 0
Shader compile residue-markers-for-ssao.shader validation-failed
WARNING:: validation failed: ligand-view.shader validation status 0
Shader compile ligand-view.shader validation-failed
WARNING:: validation failed: model-as-mesh.shader validation status 0
Shader compile model-as-mesh.shader validation-failed
WARNING:: validation failed: symmetry-atoms-lines.shader validation status 0
Shader compile symmetry-atoms-lines.shader validation-failed
WARNING:: validation failed: hud-bars.shader validation status 0
Shader compile hud-bars.shader validation-failed
WARNING:: validation failed: rama-plot-axes-and-ticks.shader validation status 0
Shader compile rama-plot-axes-and-ticks.shader validation-failed
WARNING:: validation failed: rama-plot-phi-psi-markers.shader validation status 0
Shader compile rama-plot-phi-psi-markers.shader validation-failed
WARNING:: validation failed: hud-lines.shader validation status 0
Shader compile hud-lines.shader validation-failed
WARNING:: validation failed: background-image.shader validation status 0
Shader compile background-image.shader validation-failed
WARNING:: validation failed: meshes.shader validation status 0
Shader compile meshes.shader validation-failed
WARNING:: validation failed: texture-meshes.shader validation status 0
Shader compile texture-meshes.shader validation-failed
WARNING:: validation failed: effects.shader validation status 0
Shader compile effects.shader validation-failed
WARNING:: validation failed: blur-x.shader validation status 0
Shader compile blur-x.shader validation-failed
WARNING:: validation failed: blur-y.shader validation status 0
Shader compile blur-y.shader validation-failed
WARNING:: validation failed: depth-of-field.shader validation status 0
Shader compile depth-of-field.shader validation-failed
WARNING:: validation failed: rotation-centre-cross-hairs-for-ssao.shader
validation status 0
Shader compile rotation-centre-cross-hairs-for-ssao.shader validation-failed
GL ERROR:: Mesh::setup_buffers() --- start ---
ERROR:: setup_python() Null sys
ERROR:: setup_python() Null coot
SystemError: frame does not exist
######################################################
init_coot_as_python_module()
There are 143 data in
/usr/local/Cellar/coot/1.1.10/share/coot/lib/data/monomers/list/mon_lib_list.cif
There are 2 data in
/usr/local/Cellar/coot/1.1.10/share/coot/lib/data/monomers/a/ALA.cif
There are 2 data in
/usr/local/Cellar/coot/1.1.10/share/coot/lib/data/monomers/a/ASP.cif
There are 2 data in
/usr/local/Cellar/coot/1.1.10/share/coot/lib/data/monomers/a/ASN.cif
There are 2 data in
/usr/local/Cellar/coot/1.1.10/share/coot/lib/data/monomers/c/CYS.cif
There are 2 data in
/usr/local/Cellar/coot/1.1.10/share/coot/lib/data/monomers/g/GLN.cif
There are 2 data in
/usr/local/Cellar/coot/1.1.10/share/coot/lib/data/monomers/g/GLY.cif
There are 2 data in
/usr/local/Cellar/coot/1.1.10/share/coot/lib/data/monomers/g/GLU.cif
There are 2 data in
/usr/local/Cellar/coot/1.1.10/share/coot/lib/data/monomers/p/PHE.cif
There are 2 data in
/usr/local/Cellar/coot/1.1.10/share/coot/lib/data/monomers/h/HIS.cif
There are 2 data in
/usr/local/Cellar/coot/1.1.10/share/coot/lib/data/monomers/i/ILE.cif
There are 2 data in
/usr/local/Cellar/coot/1.1.10/share/coot/lib/data/monomers/l/LYS.cif
There are 2 data in
/usr/local/Cellar/coot/1.1.10/share/coot/lib/data/monomers/l/LEU.cif
There are 2 data in
/usr/local/Cellar/coot/1.1.10/share/coot/lib/data/monomers/m/MET.cif
There are 2 data in
/usr/local/Cellar/coot/1.1.10/share/coot/lib/data/monomers/m/MSE.cif
There are 2 data in
/usr/local/Cellar/coot/1.1.10/share/coot/lib/data/monomers/p/PRO.cif
There are 2 data in
/usr/local/Cellar/coot/1.1.10/share/coot/lib/data/monomers/a/ARG.cif
There are 2 data in
/usr/local/Cellar/coot/1.1.10/share/coot/lib/data/monomers/s/SER.cif
There are 2 data in
/usr/local/Cellar/coot/1.1.10/share/coot/lib/data/monomers/t/THR.cif
There are 2 data in
/usr/local/Cellar/coot/1.1.10/share/coot/lib/data/monomers/v/VAL.cif
There are 2 data in
/usr/local/Cellar/coot/1.1.10/share/coot/lib/data/monomers/t/TRP.cif
There are 2 data in
/usr/local/Cellar/coot/1.1.10/share/coot/lib/data/monomers/t/TYR.cif
There are 2 data in
/usr/local/Cellar/coot/1.1.10/share/coot/lib/data/monomers/p/PO4.cif
There are 2 data in
/usr/local/Cellar/coot/1.1.10/share/coot/lib/data/monomers/s/SO4.cif
There are 2 data in
/usr/local/Cellar/coot/1.1.10/share/coot/lib/data/monomers/g/GOL.cif
There are 2 data in
/usr/local/Cellar/coot/1.1.10/share/coot/lib/data/monomers/c/CIT.cif
There are 2 data in
/usr/local/Cellar/coot/1.1.10/share/coot/lib/data/monomers/e/EDO.cif
There are 2 data in
/usr/local/Cellar/coot/1.1.10/share/coot/lib/data/monomers/a/A.cif
There are 2 data in
/usr/local/Cellar/coot/1.1.10/share/coot/lib/data/monomers/c/C.cif
There are 2 data in
/usr/local/Cellar/coot/1.1.10/share/coot/lib/data/monomers/g/G.cif
There are 2 data in
/usr/local/Cellar/coot/1.1.10/share/coot/lib/data/monomers/u/U.cif
There are 2 data in
/usr/local/Cellar/coot/1.1.10/share/coot/lib/data/monomers/d/DA.cif
There are 2 data in
/usr/local/Cellar/coot/1.1.10/share/coot/lib/data/monomers/d/DC.cif
There are 2 data in
/usr/local/Cellar/coot/1.1.10/share/coot/lib/data/monomers/d/DG.cif
There are 2 data in
/usr/local/Cellar/coot/1.1.10/share/coot/lib/data/monomers/d/DT.cif
There are 2 data in
/usr/local/Cellar/coot/1.1.10/share/coot/lib/data/monomers/h/HOH.cif
There are 2 data in
/usr/local/Cellar/coot/1.1.10/share/coot/lib/data/monomers/n/NA.cif
** (MacCoot:87538): WARNING **: 15:45:48.829:
set_vertical_toolbar_internal_alignment: Toolbar item 0x7fcb45d1e2d0 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.
** (MacCoot:87538): WARNING **: 15:45:48.843:
set_vertical_toolbar_internal_alignment: Toolbar item 0x7fcb45d1e940 of type
GtkMenuButton: The parent widget that wraps GtkMenuButton::child is not a
GtkBox but a GtkGizmo. GtkMenuButton::child however is a GtkBox. Attempt will
be made to align it. It might not work.
** (MacCoot:87538): WARNING **: 15:45:48.843:
set_vertical_toolbar_internal_alignment: Toolbar item 0x7fcb45d1f7c0 of type
GtkMenuButton: The parent widget that wraps GtkMenuButton::child is not a
GtkBox but a GtkGizmo. GtkMenuButton::child however is a GtkBox. Attempt will
be made to align it. It might not work.
** (MacCoot:87538): WARNING **: 15:45:48.843:
set_vertical_toolbar_internal_alignment: Toolbar item 0x7fcb45d204d0 of type
GtkMenuButton: The parent widget that wraps GtkMenuButton::child is not a
GtkBox but a GtkGizmo. GtkMenuButton::child however is a GtkBox. Attempt will
be made to align it. It might not work.
** (MacCoot:87538): WARNING **: 15:45:48.843:
set_vertical_toolbar_internal_alignment: Toolbar item 0x7fcb45d211e0 of type
GtkMenuButton: The parent widget that wraps GtkMenuButton::child is not a
GtkBox but a GtkGizmo. GtkMenuButton::child however is a GtkBox. Attempt will
be made to align it. It might not work.
** (MacCoot:87538): WARNING **: 15:45:48.843:
set_vertical_toolbar_internal_alignment: Toolbar item 0x7fcb45d23fc0 of type
GtkMenuButton: The parent widget that wraps GtkMenuButton::child is not a
GtkBox but a GtkGizmo. GtkMenuButton::child however is a GtkBox. Attempt will
be made to align it. It might not work.
** (MacCoot:87538): WARNING **: 15:45:48.843:
set_vertical_toolbar_internal_alignment: Toolbar item 0x7fcb45d26080 of type
GtkMenuButton: The parent widget that wraps GtkMenuButton::child is not a
GtkBox but a GtkGizmo. GtkMenuButton::child however is a GtkBox. Attempt will
be made to align it. It might not work.
Traceback (most recent call last):
File "/Users/mgm/.local/state/Coot/0-coot.state.py", line 5, in <module>
import coot_gui
File
"/usr/local/Cellar/python@3.13/3.13.0_1/Frameworks/Python.framework/Versions/3.13/lib/python3.13/site-packages/coot/coot_gui.py",
line 44, in <module>
import coot_gui_api # this is imported on binary startup
^^^^^^^^^^^^^^^^^^^
ModuleNotFoundError: No module named 'coot_gui_api'
DEBUG:: --- new_startup_on_glarea_resize() 1100 1364
error draw_rotation_centre_crosshairs() A0 err 1286
render_3d_scene lambda B err 1286
error::draw_central_cube() F glDrawElements() err 1286
Regards
MGM
On 21/11/2024 08:46, Jingjing wrote:
[log in to unmask]">
Dear all,
I hope this email finds you well. I recently installed Coot using Homebrew
following the instructions provided by YoshitakaMo:
brew install brewsci/bio/coot --build-from-source
However, I am encountering a problem with the graphical user interface.
Specifically, after opening a map and a model, they do not appear in the GUI.
Additionally, the Display Manager does not show any information about the
opened map or model.
Could you please provide guidance on resolving this issue? Any help would be
greatly appreciated.
The output to the terminal/standard output should give you some useful
diagnostics.
Paul.
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