Wrong Clipper?

[chimerax-bug-report@…]

The following bug report has been submitted:
Platform:        Linux-4.15.0-54-generic-x86_64-with-debian-buster-sid
ChimeraX Version: 0.9 (2019-06-06)
Description
(Describe the actions that caused this problem to occur here)

Log:
Startup Messages  
---  
note | available bundle cache has not been initialized yet  
  
UCSF ChimeraX version: 0.9 (2019-06-06)  
© 2016-2019 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open
/net/rossmann/home/wang83/Desktop/cryosparc_VH7D_emptyNK/jspr1st/34all_shealth.mrc

Opened 34all_shealth.mrc, grid size 480,480,480, pixel 1.62, shown at level
0.98, step 2, values float32  

> hide #!1.1 models

> show #!1.1 models

> open
/net/rossmann/home/wang83/Desktop/cryosparc_VH7D_emptyNK/jspr1st/shlth_L2.pdb

Chain information for shlth_L2.pdb #2  
---  
Chain | Description  
A B C D E F G H I J K L | No description available  
  

> close #2

> open
/net/rossmann/home/wang83/Desktop/cryosparc_VH7D_emptyNK/shlth_1_rsr3-coot-3.pdb

Summary of feedback from opening
/net/rossmann/home/wang83/Desktop/cryosparc_VH7D_emptyNK/shlth_1_rsr3-coot-3.pdb  
---  
warnings | Ignored bad PDB record found on line 47  
GEOMETRY RESTRAINTS LIBRARY: CDL v1.2  
  
Ignored bad PDB record found on line 48  
DEVIATIONS FROM IDEAL VALUES.  
  
Ignored bad PDB record found on line 49  
BOND : 0.006 0.072 7064  
  
Ignored bad PDB record found on line 50  
ANGLE : 1.617 53.274 12727  
  
Ignored bad PDB record found on line 51  
CHIRALITY : 0.063 0.479 593  
  
16 messages similar to the above omitted  
Start residue of secondary structure not found: HELIX 1 1 ALA 83 PHE 90 1 8  
Start residue of secondary structure not found: HELIX 2 2 GLN 95 ASN 101 1 7  
Start residue of secondary structure not found: HELIX 3 3 PHE 103 PHE 104 1 2  
Start residue of secondary structure not found: HELIX 4 4 ILE 147 LEU 150 1 4  
Start residue of secondary structure not found: HELIX 6 6 ILE 260 VAL 267 1 8  
13 messages similar to the above omitted  
End residue of secondary structure not found: SHEET 1 D 2 ALA 152 ILE 160 0  
Start residue of secondary structure not found: SHEET 2 D 2 VAL 170 PHE 175 -1  
Start residue of secondary structure not found: SHEET 1 E 2 ALA 196 SER 199 0  
Start residue of secondary structure not found: SHEET 2 E 2 LYS 206 SER 209 -1  
Start residue of secondary structure not found: SHEET 1 F 2 TYR 298 PHE 301 0  
Start residue of secondary structure not found: SHEET 2 F 2 ARG 326 LEU 329 1  
6 messages similar to the above omitted  
End residue of secondary structure not found: HELIX 6 6 ILE 229 ALA 231 1 3  
Start residue of secondary structure not found: HELIX 7 7 LEU 257 VAL 267 1 11  
Start residue of secondary structure not found: HELIX 8 8 ASP 280 ALA 292 1 13  
Start residue of secondary structure not found: HELIX 9 9 THR 303 TYR 305 1 3  
Start residue of secondary structure not found: HELIX 10 10 PRO 313 LYS 318 1
6  
Start residue of secondary structure not found: HELIX 11 11 ARG 335 TYR 341 1
7  
14 messages similar to the above omitted  
  
Chain information for shlth_1_rsr3-coot-3.pdb #2  
---  
Chain | Description  
| No description available  
  

> hide #!1 models

> show #!1 models

> volume selMaps style mesh

> volume selMaps style surface

> rainbow selAtoms

> color selAtoms bychain

> toolshed show Registration

Thank you for registering your copy of ChimeraX. By providing the information
requested you will be helping us document the impact this software is having
in the scientific community. The information you supplied will only be used
for reporting summary usage statistics; no individual data will be released.  
Wang83@purdue.edu is subscribed to the ChimeraX discussion list  
Wang83@purdue.edu is subscribed to the ChimeraX announcements list  

> select #2

7159 atoms, 7170 bonds selected  

> toolshed show "Basic Actions"

> toolshed show ViewDockX

No suitable models found for ViewDockX  

> preset "initial styles" cartoon

Preset implemented in Python; no expansion to individual ChimeraX commands
available.  

> preset "initial styles" "space-filling (chain colors)"

Preset implemented in Python; no expansion to individual ChimeraX commands
available.  

> lighting shadows false

> lighting full

> lighting flat

> lighting simple

> lighting soft

> lighting shadows true intensity 0.5

> set silhouettes false

> set silhouettes true

> set silhouettes false

> color selAtoms bychain

> rainbow selAtoms

> color bfactor selAtoms

7159 atoms, 492 residues, atom bfactor range 30 to 114  

> style selAtoms sphere

Changed 7159 atom styles  

> style selAtoms stick

Changed 7159 atom styles  

> style selAtoms ball

Changed 7159 atom styles  

> show selAtoms ribbons

> style selAtoms ball

Changed 7159 atom styles  

> color selAtoms byhetero

> color selAtoms bychain

> rainbow selAtoms

> mlp selAtoms

Map values for surface "shlth_1_rsr3-coot-3.pdb_ SES surface": minimum -55.56,
mean -8.415, maximum 42.87  

> hide #!1.1 models

> hide #!1 models

> color bfactor selAtoms

7159 atoms, 492 residues, 1 surfaces, atom bfactor range 30 to 114  

> style selAtoms stick

Changed 7159 atom styles  

> color selAtoms byhetero

> color selAtoms bychain

> rainbow selAtoms

> color bfactor selAtoms

7159 atoms, 492 residues, 1 surfaces, atom bfactor range 30 to 114  

> show selAtoms ribbons

> hide selAtoms surfaces

> show selAtoms ribbons

> style selAtoms sphere

Changed 7159 atom styles  

> style selAtoms ball

Changed 7159 atom styles  

> style selAtoms stick

Changed 7159 atom styles  

> style selAtoms stick

Changed 7159 atom styles  

> hide selAtoms

> show selAtoms ribbons

> mlp selAtoms

Map values for surface "shlth_1_rsr3-coot-3.pdb_ SES surface": minimum -55.56,
mean -8.415, maximum 42.87  

> mlp selAtoms

Map values for surface "shlth_1_rsr3-coot-3.pdb_ SES surface": minimum -55.56,
mean -8.415, maximum 42.87  

> color bfactor selAtoms

7159 atoms, 492 residues, 1 surfaces, atom bfactor range 30 to 114  

> hide selAtoms surfaces

> show selAtoms ribbons

> ~select #2.1

7170 bonds selected  
Downloading bundle MolecularDynamicsViewer-1.1-py3-none-any.whl  
Bundle installation canceled  
Downloading bundle ChimeraX_ISOLDE-1.0b3-cp37-cp37m-linux_x86_64.whl  
Successfully installed ChimeraX-Clipper-0.9.7 ChimeraX-ISOLDE-1.0b3  
Installed ChimeraX-Clipper (0.9.7)  
Installed ChimeraX-ISOLDE (1.0b3)  
Downloading bundle ChimeraX_ISOLDE-1.0b3-cp37-cp37m-linux_x86_64.whl  
Successfully installed ChimeraX-ISOLDE-1.0b3  
Installed ChimeraX-ISOLDE (1.0b3)  

> toolshed show ISOLDE

> set selectionWidth 4

Chain information for shlth_1_rsr3-coot-3.pdb  
---  
Chain | Description  
2.3/  | No description available  
  
Done loading forcefield  
Traceback (most recent call last):  
File "/apps/chimerax/0.9/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 457, in _wheel_event  
f.wheel(MouseEvent(event))  
File "/apps/chimerax/0.9/lib/python3.7/site-
packages/chimerax/mouse_modes/std_modes.py", line 389, in wheel  
self.zoom(100*d*psize, stereo_scaling = not event.alt_down())  
File "/net/rossmann/home/wang83/.local/share/ChimeraX/0.9/site-
packages/chimerax/clipper/mousemodes.py", line 168, in zoom  
self.far_clip.plane_point = new_origin + distance*(1+self.far_clip_multiplier)  
File "/net/rossmann/home/wang83/.local/share/ChimeraX/0.9/site-
packages/chimerax/clipper/mousemodes.py", line 113, in far_clip  
from chimerax.core.graphics.clipping import CameraClipPlane  
ModuleNotFoundError: No module named 'chimerax.core.graphics.clipping'  
  
ModuleNotFoundError: No module named 'chimerax.core.graphics.clipping'  
  
File "/net/rossmann/home/wang83/.local/share/ChimeraX/0.9/site-
packages/chimerax/clipper/mousemodes.py", line 113, in far_clip  
from chimerax.core.graphics.clipping import CameraClipPlane  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/apps/chimerax/0.9/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 457, in _wheel_event  
f.wheel(MouseEvent(event))  
File "/apps/chimerax/0.9/lib/python3.7/site-
packages/chimerax/mouse_modes/std_modes.py", line 389, in wheel  
self.zoom(100*d*psize, stereo_scaling = not event.alt_down())  
File "/net/rossmann/home/wang83/.local/share/ChimeraX/0.9/site-
packages/chimerax/clipper/mousemodes.py", line 168, in zoom  
self.far_clip.plane_point = new_origin + distance*(1+self.far_clip_multiplier)  
File "/net/rossmann/home/wang83/.local/share/ChimeraX/0.9/site-
packages/chimerax/clipper/mousemodes.py", line 113, in far_clip  
from chimerax.core.graphics.clipping import CameraClipPlane  
ModuleNotFoundError: No module named 'chimerax.core.graphics.clipping'  
  
ModuleNotFoundError: No module named 'chimerax.core.graphics.clipping'  
  
File "/net/rossmann/home/wang83/.local/share/ChimeraX/0.9/site-
packages/chimerax/clipper/mousemodes.py", line 113, in far_clip  
from chimerax.core.graphics.clipping import CameraClipPlane  
  
See log for complete Python traceback.  
  




OpenGL version: 3.3.0 NVIDIA 390.77
OpenGL renderer: GeForce GTX 1060 6GB/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation

[Eric Pettersen]

Is this another case of the wrong Clipper version getting pulled in?

[Tristan Croll]

Yup. Same issue.