id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 2302 mmCIF write: citation_author is None tetterst@… Greg Couch "{{{ The following bug report has been submitted: Platform: Linux-4.15.0-54-generic-x86_64-with-debian-stretch-sid ChimeraX Version: 0.91 (2019-08-07) Description Tried to save chains in mmcif format, because pdb names multiple chains the same way, e.g. /T and /TA will both be called /T after saving in pdb Log: UCSF ChimeraX version: 0.91 (2019-08-07) © 2016-2019 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open /home/hilvertg/Desktop/RSR41_QRST_andSurroundings.pdb Chain information for RSR41_QRST_andSurroundings.pdb #1 --- Chain | Description A | No description available B D J Q S X | No description available E R | No description available F | No description available G | No description available H V | No description available I | No description available M | No description available T | No description available U | No description available > save help Missing filename suffix help > close > open /home/hilvertg/tetterst/NCL12_phenix_2/RealSpaceRefine_41/NCL12_smallermap_apply_ncs_40_real_space_refined.cif Summary of feedback from opening /home/hilvertg/tetterst/NCL12_phenix_2/RealSpaceRefine_41/NCL12_smallermap_apply_ncs_40_real_space_refined.cif --- warnings | skipping chem_comp category: Missing column 'type' near line 3469 Missing entity information. Treating each chain as a separate entity. Bad residue range for secondary structure ""4"" near line 335 Bad residue range for secondary structure ""8"" near line 339 Bad residue range for secondary structure ""12"" near line 343 Bad residue range for secondary structure ""16"" near line 347 Bad residue range for secondary structure ""20"" near line 351 235 messages similar to the above omitted Invalid sheet range for strand ""1 1"" near line 2253 Invalid sheet range for strand ""1 3"" near line 2255 Invalid sheet range for strand ""2 1"" near line 2256 Invalid sheet range for strand ""2 3"" near line 2258 Invalid sheet range for strand ""3 1"" near line 2259 475 messages similar to the above omitted Missing or incomplete entity_poly_seq table. Inferred polymer connectivity. Chain information for NCL12_smallermap_apply_ncs_40_real_space_refined.cif #1 --- Chain | Description A BA BB BC BD BE BF BG BH BI C DA DB DC DD DE DF DG DH DI E FA FB FC FD FE FF FG FH FI G HA HB HC HD HE HF HG HH I JA JB JC JD JE JF JG JH K LA LB LC LD LE LF LG LH M NA NB NC ND NE NF NG NH O PA PB PC PD PE PF PG PH Q RA RB RC RD RE RF RG RH S TA TB TC TD TE TF TG TH V VA VB VC VD VE VF VG VH X XA XB XC XD XE XF XG XH Z ZA ZB ZC ZD ZE ZF ZG ZH | No description available AA AC AE AG AI B CB CD CF CH EA EC EE EG EI F GB GD GF GH IA IC IE IG J KB KD KF KH MA MC ME MG N OB OD OF OH QA QC QE QG R SB SD SF SH UA UC UE UG W WB WD WF WH YA YC YE YG | No description available AB AD AF AH CA CC CE CG CI D EB ED EF EH GA GC GE GG GI H IB ID IF IH KA KC KE KG L MB MD MF MH OA OC OE OG P QB QD QF QH SA SC SE SG T UB UD UF UH WA WC WE WG Y YB YD YF YH | No description available > select zone /Q,R,S,T 15 Selected 6950 atoms > select up 7748 atoms, 7801 bonds, 1 model selected > select up 21478 atoms, 21847 bonds, 1 model selected > select up 286320 atoms, 291240 bonds, 1 model selected > select down 21478 atoms, 21847 bonds, 1 model selected > select add /Q,R,S,T 26250 atoms, 26701 bonds, 1 model selected > save /home/hilvertg/Desktop/RSR41_QRST_andSurroundings.cif selectedOnly true format mmcif Traceback (most recent call last): File ""/usr/lib/ucsf-chimerax-daily/lib/python3.7/site- packages/chimerax/cmd_line/tool.py"", line 254, in execute cmd.run(cmd_text) File ""/usr/lib/ucsf-chimerax-daily/lib/python3.7/site- packages/chimerax/core/commands/cli.py"", line 2655, in run result = ci.function(session, **kw_args) File ""/usr/lib/ucsf-chimerax-daily/lib/python3.7/site- packages/chimerax/core/commands/save.py"", line 61, in save fmt.export(session, filename, fmt.nicknames[0], **kw) File ""/usr/lib/ucsf-chimerax-daily/lib/python3.7/site- packages/chimerax/core/io.py"", line 213, in export result = self.export_func(session, path, **kw) File ""/usr/lib/ucsf-chimerax-daily/lib/python3.7/site- packages/chimerax/atomic/mmcif/__init__.py"", line 62, in save_file return mmcif_write.write_mmcif(session, path, models=models, rel_model=rel_model, selected_only=selected_only, displayed_only=displayed_only) File ""/usr/lib/ucsf-chimerax-daily/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 ""/usr/lib/ucsf-chimerax-daily/lib/python3.7/site- packages/chimerax/atomic/mmcif/mmcif_write.py"", line 325, in save_structure citation_author.extend(ChimeraX_authors) AttributeError: 'NoneType' object has no attribute 'extend' AttributeError: 'NoneType' object has no attribute 'extend' File ""/usr/lib/ucsf-chimerax-daily/lib/python3.7/site- packages/chimerax/atomic/mmcif/mmcif_write.py"", line 325, in save_structure citation_author.extend(ChimeraX_authors) See log for complete Python traceback. > save /home/hilvertg/Desktop/RSR41_QRST_andSurroundings.cif selectedOnly true Traceback (most recent call last): File ""/usr/lib/ucsf-chimerax-daily/lib/python3.7/site- packages/chimerax/cmd_line/tool.py"", line 254, in execute cmd.run(cmd_text) File ""/usr/lib/ucsf-chimerax-daily/lib/python3.7/site- packages/chimerax/core/commands/cli.py"", line 2655, in run result = ci.function(session, **kw_args) File ""/usr/lib/ucsf-chimerax-daily/lib/python3.7/site- packages/chimerax/core/commands/save.py"", line 61, in save fmt.export(session, filename, fmt.nicknames[0], **kw) File ""/usr/lib/ucsf-chimerax-daily/lib/python3.7/site- packages/chimerax/core/io.py"", line 213, in export result = self.export_func(session, path, **kw) File ""/usr/lib/ucsf-chimerax-daily/lib/python3.7/site- packages/chimerax/atomic/mmcif/__init__.py"", line 62, in save_file return mmcif_write.write_mmcif(session, path, models=models, rel_model=rel_model, selected_only=selected_only, displayed_only=displayed_only) File ""/usr/lib/ucsf-chimerax-daily/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 ""/usr/lib/ucsf-chimerax-daily/lib/python3.7/site- packages/chimerax/atomic/mmcif/mmcif_write.py"", line 325, in save_structure citation_author.extend(ChimeraX_authors) AttributeError: 'NoneType' object has no attribute 'extend' AttributeError: 'NoneType' object has no attribute 'extend' File ""/usr/lib/ucsf-chimerax-daily/lib/python3.7/site- packages/chimerax/atomic/mmcif/mmcif_write.py"", line 325, in save_structure citation_author.extend(ChimeraX_authors) See log for complete Python traceback. OpenGL version: 3.3.0 NVIDIA 396.54 OpenGL renderer: GeForce GTX 1060 6GB/PCIe/SSE2 OpenGL vendor: NVIDIA Corporation }}} " defect closed normal 1.0 Input/Output fixed all ChimeraX