id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 2346 ViewDockX error if non-structures open Elaine Meng Conrad Huang "{{{ The following bug report has been submitted: Platform: Darwin-17.7.0-x86_64-i386-64bit ChimeraX Version: 0.91 (2019-08-21) Description using ""molmap"" after starting ViewDockX gives traceback open 121p open http://www.cgl.ucsf.edu/home/meng/chimerax/vdocs/user/formats/dock4.mol2 viewdockx molmap ligand 8 Log: Startup Messages --- warning | 'clip' is a prefix of an existing command 'clipper' UCSF ChimeraX version: 0.91 (2019-08-21) © 2016-2019 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open 121p format mmCIF fromDatabase pdb 121p title: Struktur und guanosintriphosphat-hydrolysemechanismus des C-terminal verkuerzten menschlichen krebsproteins P21-H-ras [more info...] Chain information for 121p #1 --- Chain | Description A | H-ras P21 protein Non-standard residues in 121p #1 --- GCP — phosphomethylphosphonic acid guanylate ester MG — magnesium ion 121p mmCIF Assemblies --- 1| author_defined_assembly > molmap ligand 8 > close session > open 121p 121p title: Struktur und guanosintriphosphat-hydrolysemechanismus des C-terminal verkuerzten menschlichen krebsproteins P21-H-ras [more info...] Chain information for 121p #1 --- Chain | Description A | H-ras P21 protein Non-standard residues in 121p #1 --- GCP — phosphomethylphosphonic acid guanylate ester MG — magnesium ion 121p mmCIF Assemblies --- 1| author_defined_assembly > open /Users/meng/Desktop/chidata/ras.mol2 Opened ras.mol2 containing 30 structures (744 atoms, 763 bonds) > viewdockx > molmap ligand 8 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/core/triggerset.py"", line 130, in invoke return self._func(self._name, data) File ""/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/viewdockx/tool.py"", line 165, in _update_display onoff = json.dumps(self._make_display(trigger_data)) File ""/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/viewdockx/tool.py"", line 175, in _make_display for s in structures] File ""/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/viewdockx/tool.py"", line 175, in for s in structures] AttributeError: 'VolumeSurface' object has no attribute 'atomspec' Error processing trigger ""model display changed"": AttributeError: 'VolumeSurface' 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/viewdockx/tool.py"", line 175, in for s in structures] 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 Surface/Binding Analysis fixed all ChimeraX