id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 2088 Tiling not handling surfaces Elaine Meng Conrad Huang "{{{ 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 }}} " defect closed normal Structure Comparison fixed all ChimeraX