id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 3636 mmcif_write fails with temporary/unopened structure 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 Saving to mmcif via provider_save() does not work for a model that isn't part of the session, since `model.id` is None. 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 map_with_ligand.ccp4 Opened map_with_ligand.ccp4, grid size 250,250,96, pixel 0.464,0.464,0.46, shown at level 3.62, step 1, values float32 > open model_noligand.pdb Chain information for model_noligand.pdb #2 --- Chain | Description A | No description available > open ligand_answer.pdb > view :ATP > phenix fit ligand #2 ATP A #1 Connected to Phenix server on localhost:15010 Restraints written to /run/media/tic20/storage/Downloads/ligand_fit/ATP_restraints.cif 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 ""/home/tic20/.local/share/ChimeraX/1.0/site- packages/chimerax/phenix/cmd.py"", line 146, in phenix_fit_ligand provider_save(session, model_file, models=[temp_model]) 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 118, in write_mmcif grouped.setdefault(m.id[:-1], []).append(m) TypeError: 'NoneType' object is not subscriptable TypeError: 'NoneType' object is not subscriptable File ""/opt/UCSF/ChimeraX/lib/python3.7/site- packages/chimerax/atomic/mmcif/mmcif_write.py"", line 118, in write_mmcif grouped.setdefault(m.id[:-1], []).append(m) See log for complete Python traceback. 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 5.7G 45G 220M 11G 56G 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