id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 3217 Saving mmCIF: citation is None goddard@… Greg Couch "{{{ The following bug report has been submitted: Platform: Darwin-19.4.0-x86_64-i386-64bit ChimeraX Version: 1.0rc202005121634 (2020-05-12 16:34:48 UTC) Description Saving a few selected RNA residues of 7bv2 with selectedOnly true. Log: UCSF ChimeraX version: 1.0rc202005121634 (2020-05-12) © 2016-2020 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open 7bv2 format mmcif fromDatabase pdb 7bv2 title: The nsp12-nsp7-nsp8 complex bound to the template-primer RNA and triphosphate form of Remdesivir(RTP) [more info...] Chain information for 7bv2 #1 --- Chain | Description A | SARS-CoV-2 Nsp12 B | SARS-CoV-2 nsp8 C | SARS-CoV-2 nsp7 P | Primer T | Templete Non-standard residues in 7bv2 #1 --- F86 — [(2~{R},3~{S},4~{R},5~{R})-5-(4-azanylpyrrolo[2,1-f][1,2,4]triazin-7-yl)-5-cyano-3,4-bis(oxidanyl)oxolan-2-yl]methyl dihydrogen phosphate MG — magnesium ion POP — pyrophosphate 2- ZN — zinc ion > style stick Changed 8555 atom styles > style ball Changed 8555 atom styles > surface /a-c > color byhetero > surface close > hide /a-c > surface /a-c > open A.cif Chain information for A.cif #2 --- Chain | Description T | Templete > hide #!1 models Drag select of 22 atoms, 24 bonds > show #!1 models > ui mousemode right ""translate selected models"" > style sel ball Changed 22 atom styles > open U.cif Chain information for U.cif #3 --- Chain | Description T | Templete > ~select #2 Nothing selected > select #3 20 atoms, 21 bonds, 1 model selected > style sel ball Changed 20 atom styles > Unknown command: sequence #1/T > usage seq sequence associate chains [target] — associate chain(s) with sequence target: alignment-id or [alignment-id:]sequence-name-or-number sequence chain chains — show structure chain sequence sequence disassociate chains [alignment] — disassociate chain(s) from alignment alignment: alignment-id sequence dissociate [optional] — alias of ""sequence disassociate $*"" optional: the rest of line sequence viewer [alignmentS] subcommandText — send subcommand to viewer 'viewer' alignmentS: alignment-id, some alignment-id, or nothing subcommandText: the rest of line > select #1/T 290 atoms, 322 bonds, 1 model selected Alignment identifier is 1.T > sequence chain #1/T Destroying pre-existing alignment with identifier 1.T Alignment identifier is 1.T > hide /a-c surfaces > sequence chain #/P Missing or invalid ""chains"" argument: invalid chains specifier > sequence chain #1/P Alignment identifier is 1.P > help save > save auaac.cif selectedOnly true Traceback (most recent call last): File ""/Users/goddard/ucsf/cx-1.0/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/cmd_line/tool.py"", line 258, in execute cmd.run(cmd_text) File ""/Users/goddard/ucsf/cx-1.0/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/commands/cli.py"", line 2849, in run result = ci.function(session, **kw_args) File ""/Users/goddard/ucsf/cx-1.0/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/save_command/cmd.py"", line 60, in cmd_save Command(session, registry=registry).run(provider_cmd_text, log=log) File ""/Users/goddard/ucsf/cx-1.0/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/commands/cli.py"", line 2849, in run result = ci.function(session, **kw_args) File ""/Users/goddard/ucsf/cx-1.0/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/save_command/cmd.py"", line 73, in provider_save mgr).save(session, path, **provider_kw) File ""/Users/goddard/ucsf/cx-1.0/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/atomic/mmcif/__init__.py"", line 124, in save mmcif_write.write_mmcif(session, path, **kw) File ""/Users/goddard/ucsf/cx-1.0/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/atomic/mmcif/mmcif_write.py"", line 139, in write_mmcif save_structure(session, f, [m], [xforms[m]], used_data_names, selected_only, displayed_only) File ""/Users/goddard/ucsf/cx-1.0/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/atomic/mmcif/mmcif_write.py"", line 303, in save_structure citation.print(file, fixed_width=True) AttributeError: 'NoneType' object has no attribute 'print' AttributeError: 'NoneType' object has no attribute 'print' File ""/Users/goddard/ucsf/cx-1.0/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/atomic/mmcif/mmcif_write.py"", line 303, in save_structure citation.print(file, fixed_width=True) See log for complete Python traceback. OpenGL version: 4.1 ATI-3.8.24 OpenGL renderer: AMD Radeon Pro Vega 20 OpenGL Engine OpenGL vendor: ATI Technologies Inc.Hardware: Hardware Overview: Model Name: MacBook Pro Model Identifier: MacBookPro15,3 Processor Name: 8-Core Intel Core i9 Processor Speed: 2.4 GHz Number of Processors: 1 Total Number of Cores: 8 L2 Cache (per Core): 256 KB L3 Cache: 16 MB Hyper-Threading Technology: Enabled Memory: 32 GB Boot ROM Version: 1037.100.362.0.0 (iBridge: 17.16.14281.0.0,0) Software: System Software Overview: System Version: macOS 10.15.4 (19E287) Kernel Version: Darwin 19.4.0 Time since boot: 5 days 23:58 Graphics/Displays: Intel UHD Graphics 630: Chipset Model: Intel UHD Graphics 630 Type: GPU Bus: Built-In VRAM (Dynamic, Max): 1536 MB Vendor: Intel Device ID: 0x3e9b Revision ID: 0x0002 Automatic Graphics Switching: Supported gMux Version: 5.0.0 Metal: Supported, feature set macOS GPUFamily2 v1 Radeon Pro Vega 20: Chipset Model: Radeon Pro Vega 20 Type: GPU Bus: PCIe PCIe Lane Width: x8 VRAM (Total): 4 GB Vendor: AMD (0x1002) Device ID: 0x69af Revision ID: 0x00c0 ROM Revision: 113-D2060I-087 VBIOS Version: 113-D20601MA0T-016 Option ROM Version: 113-D20601MA0T-016 EFI Driver Version: 01.01.087 Automatic Graphics Switching: Supported gMux Version: 5.0.0 Metal: Supported, feature set macOS GPUFamily2 v1 Displays: Color LCD: Display Type: Built-In Retina LCD Resolution: 2880 x 1800 Retina Framebuffer Depth: 24-Bit Color (ARGB8888) Main Display: Yes Mirror: Off Online: Yes Automatically Adjust Brightness: No Connection Type: Internal PyQt version: 5.12.3 Compiled Qt version: 5.12.4 Runtime Qt version: 5.12.8 }}} " defect closed normal 1.0 Input/Output duplicate all ChimeraX