id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 3633 """save xxx.cif sel true"" causes a traceback when nothing is selected" Tristan Croll Greg Couch "{{{ The following bug report has been submitted: Platform: Linux-3.10.0-1127.13.1.el7.x86_64-x86_64-with-centos-7.8.2003-Core ChimeraX Version: 1.0 (2020-06-04 23:15:07 UTC) Description ""save xxx.cif sel true"" causes a traceback when nothing is selected. Log: UCSF ChimeraX version: 1.0 (2020-06-04) © 2016-2020 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open 6nnr format mmcif fromDatabase pdb 6nnr title: high-resolution structure of wild-type E. coli thymidylate synthase [more info...] Chain information for 6nnr #1 --- Chain | Description A B | Thymidylate synthase Non-standard residues in 6nnr #1 --- CB3 — 10-propargyl-5,8-dideazafolic acid EPE — 4-(2-hydroxyethyl)-1-piperazine ethanesulfonic acid (HEPES) NA — sodium ion UMC — 2'-deoxy-5'-uridylic acid > save test.cif selectedOnly true Traceback (most recent call last): File ""/opt/UCSF/ChimeraX/lib/python3.7/site- packages/chimerax/cmd_line/tool.py"", line 258, in execute cmd.run(cmd_text) File ""/opt/UCSF/ChimeraX/lib/python3.7/site- packages/chimerax/core/commands/cli.py"", line 2805, in run result = ci.function(session, **kw_args) File ""/opt/UCSF/ChimeraX/lib/python3.7/site- packages/chimerax/save_command/cmd.py"", line 66, in cmd_save Command(session, registry=registry).run(provider_cmd_text, log=log) File ""/opt/UCSF/ChimeraX/lib/python3.7/site- packages/chimerax/core/commands/cli.py"", line 2805, in run result = ci.function(session, **kw_args) File ""/opt/UCSF/ChimeraX/lib/python3.7/site- packages/chimerax/save_command/cmd.py"", line 79, in provider_save mgr).save(session, path, **provider_kw) File ""/opt/UCSF/ChimeraX/lib/python3.7/site- packages/chimerax/atomic/mmcif/__init__.py"", line 87, in save mmcif_write.write_mmcif(session, path, **kw) File ""/opt/UCSF/ChimeraX/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 ""/opt/UCSF/ChimeraX/lib/python3.7/site- packages/chimerax/atomic/mmcif/mmcif_write.py"", line 270, in save_structure restrict = concatenate(session.selection.items(""atoms"")) File ""/opt/UCSF/ChimeraX/lib/python3.7/site- packages/chimerax/atomic/molarray.py"", line 343, in concatenate c = object_class(None) TypeError: 'NoneType' object is not callable TypeError: 'NoneType' object is not callable File ""/opt/UCSF/ChimeraX/lib/python3.7/site- packages/chimerax/atomic/molarray.py"", line 343, in concatenate c = object_class(None) See log for complete Python traceback. > save test.pdb selectedOnly true > select clear OpenGL version: 3.3.0 NVIDIA 450.51.05 OpenGL renderer: TITAN Xp/PCIe/SSE2 OpenGL vendor: NVIDIA Corporation Manufacturer: Dell Inc. Model: Precision T5600 OS: CentOS Linux 7 Core Architecture: 64bit ELF CPU: 32 Intel(R) Xeon(R) CPU E5-2687W 0 @ 3.10GHz Cache Size: 20480 KB Memory: total used free shared buff/cache available Mem: 62G 6.8G 42G 241M 13G 55G Swap: 4.9G 0B 4.9G Graphics: 03:00.0 VGA compatible controller [0300]: NVIDIA Corporation GP102 [TITAN Xp] [10de:1b02] (rev a1) Subsystem: NVIDIA Corporation Device [10de:11df] Kernel driver in use: nvidia PyQt version: 5.12.3 Compiled Qt version: 5.12.4 Runtime Qt version: 5.12.8 }}} " defect closed normal Input/Output fixed all ChimeraX