view matrix camera: No module named 'chimerax.core.geometry'

[Greg Couch]

The following bug report has been submitted:
Platform:        Windows-10-10.0.18362
ChimeraX Version: 1.1.dev202006190400 (2020-06-19 04:00:14 UTC)
Description
Tried the "view matrix camera ...." command.

Log:
UCSF ChimeraX version: 1.1.dev202006190400 (2020-06-19)  
© 2016-2020 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open switch.cxc

> windowsize 600 800

> set bgColor white

> set silhouettes true

> open 1tag

Summary of feedback from opening 1tag fetched from pdb  
---  
warning | Unable to infer polymer connectivity due to unspecified label_seq_id
for residue "GDP" near line 3513  
  
1tag title:  
Structural determinants for activation of the α-subunit of A heterotrimeric G
protein [more info...]  
  
Chain information for 1tag #1  
---  
Chain | Description  
A | transducin-α  
  
Non-standard residues in 1tag #1  
---  
MG — magnesium ion  
  

> open 1tnd

1tnd title:  
The 2.2 angstroms crystal structure of transducin-α complexed with GTP γ S
[more info...]  
  
Chain information for 1tnd #2  
---  
Chain | Description  
A B C | transducin  
  
Non-standard residues in 1tnd #2  
---  
CAC — cacodylate ion (dimethylarsinate)  
GSP — 5'-guanosine-diphosphate-monothiophosphate  
MG — magnesium ion  
  
1tnd mmCIF Assemblies  
---  
1| author_defined_assembly  
2| author_defined_assembly  
3| author_defined_assembly  
  

> delete ~ /a

> hide

> mmaker #2 to #1 compute f

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker 1tag, chain A (#1) with 1tnd, chain A (#2), sequence alignment
score = 1667.6  
RMSD between 290 pruned atom pairs is 0.544 angstroms; (across all 314 pairs:
1.253)  
  

> cartoon style modeHelix tube sides 24

> transparency (protein & ~ :173-182,196-211,228-237) 100 target c

> hide (#1 & protein & ~ :173-182,196-211,228-237) cartoons

> show #2 & ligand

> style ligand sphere

Changed 60 atom styles  

> turn x 180

> 2dlabels text "Switch 1" xpos .05 ypos .38

> 2dlabels text "Switch 2" xpos .22 ypos .07

> 2dlabels text "Switch 3" xpos .65 ypos .48

> 2dlabels text GDP-bound color tan xpos .73 ypos .08

> 2dlabels text GTP-bound color deep sky blue xpos .73 ypos .04

> 2dlabels text "Transducin α-Subunit" xpos .04 ypos .93 size 30

> turn x -50

> turn y -50

> turn z -50

> move x 10

> move y 15

> move z 30

executed switch.cxc  

> usage view

view [objects [frames]] [clip true or false] [cofr true or false] [orient]
[pad a number]  
— adjust camera so everything is visible  
objects: an objects specifier or a view name  
frames: an integer ≥ 1  
Subcommands are:

  * view delete
  * view initial
  * view list
  * view matrix
  * view name
  * view position

  

> view matrix

camera position:
0.41318,-0.4924,0.76604,132.81,-0.86961,0.036357,0.4924,72.133,-0.27031,-0.86961,-0.41318,-21.344  
model positions:
#1,1,0,0,0,0,1,0,0,0,0,1,0,#1.1,1,0,0,0,0,1,0,0,0,0,1,0,#2,0.1263,0.77723,0.61641,-41.17,-0.60462,-0.43232,0.66899,33.747,0.78644,-0.45718,0.41533,48.76,#2.1,1,0,0,0,0,1,0,0,0,0,1,0,#3,1,0,0,0,0,1,0,0,0,0,1,0,#3.1,1,0,0,0,0,1,0,0,0,0,1,0,#3.2,1,0,0,0,0,1,0,0,0,0,1,0,#3.3,1,0,0,0,0,1,0,0,0,0,1,0,#3.4,1,0,0,0,0,1,0,0,0,0,1,0,#3.5,1,0,0,0,0,1,0,0,0,0,1,0,#3.6,1,0,0,0,0,1,0,0,0,0,1,0  
  

> usage view matrix

view matrix [camera a position] [models model positions] [coordinateSystem a
coordinate-system]  
— set camera and model positions  
Traceback (most recent call last):  
File "A:\cygwin64\home\gregc\src\chimerax\ChimeraX.app\bin\lib\site-
packages\chimerax\cmd_line\tool.py", line 263, in execute  
cmd.run(cmd_text)  
File "A:\cygwin64\home\gregc\src\chimerax\ChimeraX.app\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2772, in run  
self._process_keyword_arguments(final, prev_annos)  
File "A:\cygwin64\home\gregc\src\chimerax\ChimeraX.app\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2698, in
_process_keyword_arguments  
value, text = self._parse_arg(anno, text, session, final)  
File "A:\cygwin64\home\gregc\src\chimerax\ChimeraX.app\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2413, in _parse_arg  
value, replacement, rest = annotation.parse(text, session)  
File "A:\cygwin64\home\gregc\src\chimerax\ChimeraX.app\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 1488, in parse  
p = PlaceArg.parse_place(token.split(','))  
File "A:\cygwin64\home\gregc\src\chimerax\ChimeraX.app\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 1499, in parse_place  
from ..geometry import Place  
ModuleNotFoundError: No module named 'chimerax.core.geometry'  
  
ModuleNotFoundError: No module named 'chimerax.core.geometry'  
  
File "A:\cygwin64\home\gregc\src\chimerax\ChimeraX.app\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 1499, in parse_place  
from ..geometry import Place  
  
See log for complete Python traceback.  
  




OpenGL version: 3.3.0 NVIDIA 445.87
OpenGL renderer: GeForce GTX 970/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
Manufacturer: MSI
Model: MS-7885
OS: Microsoft Windows 10 Home (Build 18363)
Memory: 34,258,157,568
MaxProcessMemory: 137,438,953,344
CPU: 12 Intel(R) Core(TM) i7-5820K CPU @ 3.30GHz"
PyQt version: 5.12.3
Compiled Qt version: 5.12.4
Runtime Qt version: 5.12.8

[Greg Couch]

In particular:

view matrix camera 0.41318,-0.4924,0.76604,132.81,-0.86961,0.036357,0.4924,72.133,-0.27031,-0.86961,-0.41318,-21.344

Needs to be added to test suite.

[Tom Goddard]

Fixed.

Missed a relative import of geometry module.