Request to add Chimera1-like model "activity"

[bhargav.saligram@…]

The following bug report has been submitted:
Platform:        Darwin-18.0.0-x86_64-i386-64bit
ChimeraX Version: 0.8 (2018-11-10)
Description
Please add an option(checkbox) to select model in the model panel. This is to freeze the model which needs to be moved. Similar to what you have in chimera. 

Log:
UCSF ChimeraX version: 0.8 (2018-11-10)  
How to cite UCSF ChimeraX  

> open 5199 fromDatabase emdb

Opened emd_5199.map, grid size 500,500,500, pixel 1.23, shown at level 0.18,
step 2, values float32  

> lighting simple

> lighting shadows true

> lighting simple

> lighting shadows true

> open 4v7q

Summary of feedback from opening 4v7q fetched from pdb  
---  
notes | Fetching compressed mmCIF 4v7q from
http://files.rcsb.org/download/4v7q.cif  
Fetching CCD NAG from http://ligand-expo.rcsb.org/reports/N/NAG/NAG.cif  
  
4v7q title:  
Atomic model of an infectious rotavirus particle [more info...]  
  
Chain information for 4v7q #2  
---  
Chain | Description  
AA AB | Core scaffold protein  
AC AD AE AF AG AH AI AJ AK AL AM AN AO | Intermediate capsid protein VP6  
BA BF BG BH BI BJ BK BL BM BN BO BP BQ | Outer layer protein VP7  
BX BY BZ | Outer capsid protein VP4  
  
4v7q mmCIF Assemblies  
---  
1| complete icosahedral assembly  
  
  

> color zone #1 near #2 distance 5

> surface dust #1 size 5

> help help:user

Developer warnings in user commands index:

  * didn't expect href to be to tools/sequenceviewer.html on line 245

  

> sym #1 assembly 4 newModel false

No structures specified.  

> open 5mv5

Summary of feedback from opening 5mv5 fetched from pdb  
---  
note | Fetching compressed mmCIF 5mv5 from
http://files.rcsb.org/download/5mv5.cif  
  
5mv5 title:  
Structure of deformed wing virus, a honeybee pathogen [more info...]  
  
Chain information for 5mv5 #3  
---  
Chain | Description  
A | VP1  
B | VP2  
C | VP3  
  
5mv5 mmCIF Assemblies  
---  
1| complete icosahedral assembly  
2| icosahedral asymmetric unit  
3| icosahedral pentamer  
4| icosahedral 23 hexamer  
5| icosahedral asymmetric unit, std point frame  
  
  

> view

> open 5g52

Summary of feedback from opening 5g52 fetched from pdb  
---  
notes | Fetching compressed mmCIF 5g52 from
http://files.rcsb.org/download/5g52.cif  
Fetching CCD U5P from http://ligand-expo.rcsb.org/reports/U/U5P/U5P.cif  
  
5g52 title:  
Crystallographic structure of full particle of Deformed Wing Virus [more
info...]  
  
Chain information for 5g52 #4  
---  
Chain | Description  
A | VP1  
B | VP2  
C | VP3  
  
5g52 mmCIF Assemblies  
---  
1| complete icosahedral assembly  
2| icosahedral asymmetric unit  
3| icosahedral pentamer  
4| icosahedral 23 hexamer  
5| icosahedral asymmetric unit, std point frame  
  
  

> matchmaker #4 to #3

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 5mv5, chain C (#3) with 5g52, chain C (#4), sequence alignment
score = 1944.1  
RMSD between 250 pruned atom pairs is 0.693 angstroms; (across all 383 pairs:
24.058)  
  

> sym #1 assembly 4 newModel false

No structures specified.  

> sym #2 assembly 4 newModel false

Assembly "4" not found, have 1  

> morph #3,4

Computed 21 frame morph #5  

> coordset #5 1,21

> color #3 bychain

> coordset #3 1,21

> sym #2 assembly 8 newModel false

Assembly "8" not found, have 1  

> select #1

2 models selected  

> ~select #1

Nothing selected  

> hide #!1 models

> hide #!2 models

> view

> movie record

> coordset #5 1,21

> wait 25

> movie encode ~/Desktop/dwv.mp4

Movie saved to /Users/jfn624/Desktop/dwv.mp4  
  

> close all

> sym #3 i,222

No structures specified.  

> open 5199 fromDatabase emdb

Opened emd_5199.map, grid size 500,500,500, pixel 1.23, shown at level 0.18,
step 2, values float32  

> sym #3 i,222

No structures specified.  

> sym #1 i,222

No structures specified.  

> sym #1 i,222

No structures specified.  

> close

> open 5mv5

5mv5 title:  
Structure of deformed wing virus, a honeybee pathogen [more info...]  
  
Chain information for 5mv5 #1  
---  
Chain | Description  
A | VP1  
B | VP2  
C | VP3  
  
5mv5 mmCIF Assemblies  
---  
1| complete icosahedral assembly  
2| icosahedral asymmetric unit  
3| icosahedral pentamer  
4| icosahedral 23 hexamer  
5| icosahedral asymmetric unit, std point frame  
  
  

> open 3574 fromDatabase emdb

Summary of feedback from opening 3574 fetched from emdb  
---  
note | Fetching compressed map 3574 from
ftp://ftp.ebi.ac.uk/pub/databases/emdb/structures/EMD-3574/map/emd_3574.map.gz  
  
Opened emd_3574.map, grid size 546,546,546, pixel 1.05, shown at level 0.0749,
step 4, values float32  

> resfit #1/A map #2

> movie record

> movie encode ~/Desktop/resfit.mp4 framerate 25.0

Movie saved to /Users/jfn624/Desktop/resfit.mp4  
  

> ui mousemode rightMode bond rotation

> movie record

> movie encode ~/Desktop/resfit.mp4 framerate 25.0

Movie saved to /Users/jfn624/Desktop/resfit.mp4  
  

Unknown command: end  

> close




OpenGL version: 4.1 INTEL-12.0.34
OpenGL renderer: Intel Iris Pro OpenGL Engine
OpenGL vendor: Intel Inc.

[Tom Goddard]

ChimeraX moves individual models in a different way from Chimera. You select the model you want to move then use the move selected model mouse mode.

​https://www.cgl.ucsf.edu/chimerax/docs/user/tools/mousemodes.html

We don't currently plan to support the Chimera concept that only certain models are active = movable.