Tiling not handling surfaces

[Elaine Meng]

The following bug report has been submitted:
Platform:        Darwin-17.7.0-x86_64-i386-64bit
ChimeraX Version: 0.91 (2019-06-14)
Description
"tile" command unhappy if molecular surfaces present

e.g. 
open 1g1p
surf
tile


Log:
UCSF ChimeraX version: 0.91 (2019-06-14)  
© 2016-2019 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open 1pho format mmCIF fromDatabase pdb

1pho title:  
Crystal structures explain functional properties of two E. Coli porins [more
info...]  
  
Chain information for 1pho #1  
---  
Chain | Description  
A | phosphoporin  
  
1pho mmCIF Assemblies  
---  
1| author_and_software_defined_assembly  
  
  

> preset custom "kyte doolittle hydrophobicity"

Assigning kdh attribute to 31 items  
Assigning kdh attribute to 14 items  
Assigning kdh attribute to 27 items  
Assigning kdh attribute to 16 items  
Assigning kdh attribute to 23 items  
Assigning kdh attribute to 12 items  
Assigning kdh attribute to 1 item  
Assigning kdh attribute to 36 items  
Assigning kdh attribute to 3 items  
Assigning kdh attribute to 18 items  
Assigning kdh attribute to 23 items  
Assigning kdh attribute to 0 items  
Assigning kdh attribute to 7 items  
Assigning kdh attribute to 0 items  
Assigning kdh attribute to 27 items  
Assigning kdh attribute to 12 items  
Assigning kdh attribute to 13 items  
Assigning kdh attribute to 21 items  
Assigning kdh attribute to 21 items  
Assigning kdh attribute to 3 items  
Assigning kdh attribute to 22 items  
1 surfaces, atom kdh range -4.5 to 4.5  
Preset expands to these ChimeraX commands:

    
    
    # Kyte-Doolittle hydrophobicity + make MSE same as MET
    setattr :asp res kdh -3.5 create t
    setattr :glu res kdh -3.5 create t
    setattr :asn res kdh -3.5 create t
    setattr :gln res kdh -3.5 create t
    setattr :lys res kdh -3.9 create t
    setattr :arg res kdh -4.5 create t
    setattr :his res kdh -3.2 create t
    setattr :gly res kdh -0.4 create t
    setattr :pro res kdh -1.6 create t
    setattr :ser res kdh -0.8 create t
    setattr :thr res kdh -0.7 create t
    setattr :cys res kdh 2.5 create t
    setattr :met res kdh 1.9 create t
    setattr :mse res kdh 1.9 create t
    setattr :ala res kdh 1.8 create t
    setattr :val res kdh 4.2 create t
    setattr :ile res kdh 4.5 create t
    setattr :leu res kdh 3.8 create t
    setattr :phe res kdh 2.8 create t
    setattr :trp res kdh -0.9 create t
    setattr :tyr res kdh -1.3 create t
    surf protein
    color byattribute kdh target s palette dodgerblue:white:orangered
    

  

> lighting soft

> lighting full

> lighting simple

> lighting full

> sym #1 assembly 1

> view

> preset custom "kyte doolittle hydrophobicity"

Assigning kdh attribute to 62 items  
Assigning kdh attribute to 28 items  
Assigning kdh attribute to 54 items  
Assigning kdh attribute to 32 items  
Assigning kdh attribute to 46 items  
Assigning kdh attribute to 24 items  
Assigning kdh attribute to 2 items  
Assigning kdh attribute to 72 items  
Assigning kdh attribute to 6 items  
Assigning kdh attribute to 36 items  
Assigning kdh attribute to 46 items  
Assigning kdh attribute to 0 items  
Assigning kdh attribute to 14 items  
Assigning kdh attribute to 0 items  
Assigning kdh attribute to 54 items  
Assigning kdh attribute to 24 items  
Assigning kdh attribute to 26 items  
Assigning kdh attribute to 42 items  
Assigning kdh attribute to 42 items  
Assigning kdh attribute to 6 items  
Assigning kdh attribute to 44 items  
2 surfaces, atom kdh range -4.5 to 4.5  
Preset expands to these ChimeraX commands:

    
    
    # Kyte-Doolittle hydrophobicity + make MSE same as MET
    setattr :asp res kdh -3.5 create t
    setattr :glu res kdh -3.5 create t
    setattr :asn res kdh -3.5 create t
    setattr :gln res kdh -3.5 create t
    setattr :lys res kdh -3.9 create t
    setattr :arg res kdh -4.5 create t
    setattr :his res kdh -3.2 create t
    setattr :gly res kdh -0.4 create t
    setattr :pro res kdh -1.6 create t
    setattr :ser res kdh -0.8 create t
    setattr :thr res kdh -0.7 create t
    setattr :cys res kdh 2.5 create t
    setattr :met res kdh 1.9 create t
    setattr :mse res kdh 1.9 create t
    setattr :ala res kdh 1.8 create t
    setattr :val res kdh 4.2 create t
    setattr :ile res kdh 4.5 create t
    setattr :leu res kdh 3.8 create t
    setattr :phe res kdh 2.8 create t
    setattr :trp res kdh -0.9 create t
    setattr :tyr res kdh -1.3 create t
    surf protein
    color byattribute kdh target s palette dodgerblue:white:orangered
    

  

> tile

Traceback (most recent call last):  
File
"/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/cmd_line/tool.py", line 254, in execute  
cmd.run(cmd_text)  
File
"/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/commands/cli.py", line 2641, in run  
result = ci.function(session, **kw_args)  
File
"/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/std_commands/tile.py", line 21, in tile  
anchor_spec = models[0].atomspec  
AttributeError: 'MolecularSurface' object has no attribute 'atomspec'  
  
AttributeError: 'MolecularSurface' object has no attribute 'atomspec'  
  
File
"/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/std_commands/tile.py", line 21, in tile  
anchor_spec = models[0].atomspec  
  
See log for complete Python traceback.  
  

> close

> open 1g1p format mmCIF fromDatabase pdb

Summary of feedback from opening 1g1p fetched from pdb  
---  
warning | Atom H1 is not in the residue template for ASP #1 in chain A  
  
1g1p title:  
NMR Solution Structures of delta-Conotoxin EVIA from Conus ermineus that
Selectively Acts on Vertebrate Neuronal Na+ Channels [more info...]  
  
Chain information for 1g1p  
---  
Chain | Description  
1.1/A 1.2/A 1.3/A 1.4/A 1.5/A 1.6/A 1.7/A 1.8/A 1.9/A 1.10/A 1.11/A 1.12/A
1.13/A 1.14/A 1.15/A 1.16/A 1.17/A 1.18/A | conotoxin evia  
  
  

> surface

> tile

Traceback (most recent call last):  
File
"/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/cmd_line/tool.py", line 254, in execute  
cmd.run(cmd_text)  
File
"/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/commands/cli.py", line 2641, in run  
result = ci.function(session, **kw_args)  
File
"/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/std_commands/tile.py", line 21, in tile  
anchor_spec = models[0].atomspec  
AttributeError: 'MolecularSurface' object has no attribute 'atomspec'  
  
AttributeError: 'MolecularSurface' object has no attribute 'atomspec'  
  
File
"/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/std_commands/tile.py", line 21, in tile  
anchor_spec = models[0].atomspec  
  
See log for complete Python traceback.  
  




OpenGL version: 4.1 NVIDIA-10.32.0 355.11.10.10.40.102
OpenGL renderer: NVIDIA GeForce GTX 675MX OpenGL Engine
OpenGL vendor: NVIDIA Corporation

[Elaine Meng]

I guess I was expecting the atomic models to be tiled and their respective surfaces to stay with their atomic models.

[Conrad Huang]

Fixed in c6eba37af.

Only atomic structures are tiled now, and their surfaces follow them.