id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 3530 setattr type conflict santiago.jus.are@… Eric Pettersen "{{{ The following bug report has been submitted: Platform: Windows-10-10.0.18362 ChimeraX Version: 1.0 (2020-06-04 23:15:07 UTC) Description Goog morning, setattr attribute is not able to recognize a value with fractional number?. I am trying to set an attribute with for instance: 0.999362813814197, but we obtain an error. 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 6y2g Summary of feedback from opening 6y2g fetched from pdb --- warning | Unable to infer polymer connectivity due to unspecified label_seq_id for residue ""GLY"" near line 6023 notes | Fetching compressed mmCIF 6y2g from http://files.rcsb.org/download/6y2g.cif Fetching CCD O6K from http://ligand-expo.rcsb.org/reports/O/O6K/O6K.cif 6y2g title: Crystal structure (orthorhombic form) of the complex resulting from the reaction between SARS-CoV-2 (2019-nCoV) main protease and tert-butyl (1-((S)-1-(((S)-4-(benzylamino)-3,4-dioxo-1-((S)-2-oxopyrrolidin-3-yl)butan-2-yl)amino)-3-cyclopropyl-1-oxopropan-2-yl)-2-oxo-1,2-dihydropyridin-3-yl)carbamate (alpha-ketoamide 13b) [more info...] Chain information for 6y2g #1 --- Chain | Description A B | Replicase polyprotein 1ab Non-standard residues in 6y2g #1 --- O6K — ~{tert}-butyl ~{N}-[1-[(2~{S})-3-cyclopropyl-1-oxidanylidene-1-[[(2~{S},3~{R})-3-oxidanyl-4-oxidanylidene-1-[(3~{S})-2-oxidanylidenepyrrolidin-3-yl]-4-[(phenylmethyl)amino]butan-2-yl]amino]propan-2-yl]-2-oxidanylidene- pyridin-3-yl]carbamate > ~show > select clear > select 1 Expected an objects specifier or a keyword > select :1 12 atoms, 10 bonds, 1 model selected > setattr :1 residues identity 1 create true Assigning identity attribute to 2 items > color byattribute identity /a palette 0,blue:1,red 2569 atoms, 496 residues, atom identity range 1 to 1 > select clear > color byattribute identity palette 0,blue:1,red 5072 atoms, 920 residues, atom identity range 1 to 1 > setattr :1,:2 residues identity 1,1 create true Expected a keyword > setattr :1-2 residues identity 1,1 create true Assigning identity attribute to 4 items Traceback (most recent call last): File ""C:\Program Files\ChimeraX 1.0\bin\lib\site- packages\chimerax\cmd_line\tool.py"", line 258, in execute cmd.run(cmd_text) File ""C:\Program Files\ChimeraX 1.0\bin\lib\site- packages\chimerax\core\commands\cli.py"", line 2805, in run result = ci.function(session, **kw_args) File ""C:\Program Files\ChimeraX 1.0\bin\lib\site- packages\chimerax\std_commands\setattr.py"", line 94, in set_attr register_attr(session, items.object_class, attr_name, type(value)) File ""C:\Program Files\ChimeraX 1.0\bin\lib\site- packages\chimerax\std_commands\setattr.py"", line 130, in register_attr class_obj.register_attr(session, attr_name, ""setattr command"", attr_type=attr_type) File ""C:\Program Files\ChimeraX 1.0\bin\lib\site- packages\chimerax\atomic\attr_registration.py"", line 50, in register_attr cls._attr_registration.register(session, attr_name, registerer, default_value, (attr_type, can_return_none)) File ""C:\Program Files\ChimeraX 1.0\bin\lib\site- packages\chimerax\atomic\attr_registration.py"", line 78, in register "" registration by %s"" % (attr_name, self.class_.__name__, registrant, prev_registrant)) ValueError: Registration of attr 'identity' with Residue by setattr command conflicts with previous registration by setattr command ValueError: Registration of attr 'identity' with Residue by setattr command conflicts with previous registration by setattr command File ""C:\Program Files\ChimeraX 1.0\bin\lib\site- packages\chimerax\atomic\attr_registration.py"", line 78, in register "" registration by %s"" % (attr_name, self.class_.__name__, registrant, prev_registrant)) See log for complete Python traceback. > setattr :1-2 residues identity 1 create true Assigning identity attribute to 4 items > color byattribute identity palette 0,blue:1,red 5072 atoms, 920 residues, atom identity range 1 to 1 > setattr :3 residues identity 1,1 create true Assigning identity attribute to 2 items Traceback (most recent call last): File ""C:\Program Files\ChimeraX 1.0\bin\lib\site- packages\chimerax\cmd_line\tool.py"", line 258, in execute cmd.run(cmd_text) File ""C:\Program Files\ChimeraX 1.0\bin\lib\site- packages\chimerax\core\commands\cli.py"", line 2805, in run result = ci.function(session, **kw_args) File ""C:\Program Files\ChimeraX 1.0\bin\lib\site- packages\chimerax\std_commands\setattr.py"", line 94, in set_attr register_attr(session, items.object_class, attr_name, type(value)) File ""C:\Program Files\ChimeraX 1.0\bin\lib\site- packages\chimerax\std_commands\setattr.py"", line 130, in register_attr class_obj.register_attr(session, attr_name, ""setattr command"", attr_type=attr_type) File ""C:\Program Files\ChimeraX 1.0\bin\lib\site- packages\chimerax\atomic\attr_registration.py"", line 50, in register_attr cls._attr_registration.register(session, attr_name, registerer, default_value, (attr_type, can_return_none)) File ""C:\Program Files\ChimeraX 1.0\bin\lib\site- packages\chimerax\atomic\attr_registration.py"", line 78, in register "" registration by %s"" % (attr_name, self.class_.__name__, registrant, prev_registrant)) ValueError: Registration of attr 'identity' with Residue by setattr command conflicts with previous registration by setattr command ValueError: Registration of attr 'identity' with Residue by setattr command conflicts with previous registration by setattr command File ""C:\Program Files\ChimeraX 1.0\bin\lib\site- packages\chimerax\atomic\attr_registration.py"", line 78, in register "" registration by %s"" % (attr_name, self.class_.__name__, registrant, prev_registrant)) See log for complete Python traceback. > setattr :3 residues identity 1 create true Assigning identity attribute to 2 items > color byattribute identity palette 0,blue:1,red 5072 atoms, 920 residues, atom identity range 1 to 1 > help help:devel > ui tool show Shell > close session > open 6y2g format mmcif fromDatabase pdb Summary of feedback from opening 6y2g fetched from pdb --- warning | Unable to infer polymer connectivity due to unspecified label_seq_id for residue ""GLY"" near line 6023 6y2g title: Crystal structure (orthorhombic form) of the complex resulting from the reaction between SARS-CoV-2 (2019-nCoV) main protease and tert-butyl (1-((S)-1-(((S)-4-(benzylamino)-3,4-dioxo-1-((S)-2-oxopyrrolidin-3-yl)butan-2-yl)amino)-3-cyclopropyl-1-oxopropan-2-yl)-2-oxo-1,2-dihydropyridin-3-yl)carbamate (alpha-ketoamide 13b) [more info...] Chain information for 6y2g #1 --- Chain | Description A B | Replicase polyprotein 1ab Non-standard residues in 6y2g #1 --- O6K — ~{tert}-butyl ~{N}-[1-[(2~{S})-3-cyclopropyl-1-oxidanylidene-1-[[(2~{S},3~{R})-3-oxidanyl-4-oxidanylidene-1-[(3~{S})-2-oxidanylidenepyrrolidin-3-yl]-4-[(phenylmethyl)amino]butan-2-yl]amino]propan-2-yl]-2-oxidanylidene- pyridin-3-yl]carbamate > open script.cxs No such file/path: script.cxs No such database 'C' > open C:\Users\Santiago\Escritorio\script.csx Unrecognized file suffix '.csx' > open C:\Users\Santiago\Escritorio\script.cxc > setattr :1 residues identity 1 create true Assigning identity attribute to 2 items > color byattribute identity /a palette 0,blue:1,red 2569 atoms, 496 residues, atom identity range 1 to 1 executed script.cxc > ~show > open C:\Users\Santiago\Escritorio\script.cxc > setattr :1 residues identity 1 create true Assigning identity attribute to 2 items > color byattribute identity /a palette 0,blue:1,red 2569 atoms, 496 residues, atom identity range 1 to 1 executed script.cxc > open C:\Users\Santiago\Escritorio\script.cxc > setattr :1 residues identity 1 create true Assigning identity attribute to 2 items > color byattribute identity /a palette 0,blue:1,red 2569 atoms, 496 residues, atom identity range 1 to 1 executed script.cxc > open C:\Users\Santiago\Escritorio\script.cxc > setattr :1 residues identity 1 create true Assigning identity attribute to 2 items > color byattribute identity /a palette 0,blue:1,red 2569 atoms, 496 residues, atom identity range 1 to 1 executed script.cxc > open C:\Users\Santiago\Escritorio\script.cxc > setattr :1 residues identity 1 create true Assigning identity attribute to 2 items > color byattribute identity palette 0,blue:1,red 5072 atoms, 920 residues, atom identity range 1 to 1 executed script.cxc No such database 'G' > open C:\Users\Santiago\Escritorio\nsp5_attribute_chimerax.cxc > setattr :1 identity_nsp5 1 create true Expected a keyword > open C:\Users\Santiago\Escritorio\nsp5_attribute_chimerax.cxc > setattr :1 residues identity_nsp5 1 create true Assigning identity_nsp5 attribute to 2 items > setattr :2 residues identity_nsp5 1 create true Assigning identity_nsp5 attribute to 2 items > setattr :3 residues identity_nsp5 1 create true Assigning identity_nsp5 attribute to 2 items > setattr :4 residues identity_nsp5 1 create true Assigning identity_nsp5 attribute to 2 items > setattr :5 residues identity_nsp5 1 create true Assigning identity_nsp5 attribute to 2 items > setattr :6 residues identity_nsp5 0.999362813814197 create true Assigning identity_nsp5 attribute to 2 items Traceback (most recent call last): File ""C:\Program Files\ChimeraX 1.0\bin\lib\site- packages\chimerax\cmd_line\tool.py"", line 258, in execute cmd.run(cmd_text) File ""C:\Program Files\ChimeraX 1.0\bin\lib\site- packages\chimerax\core\commands\cli.py"", line 2805, in run result = ci.function(session, **kw_args) File ""C:\Program Files\ChimeraX 1.0\bin\lib\site- packages\chimerax\open_command\cmd.py"", line 101, in cmd_open Command(session, registry=registry).run(provider_cmd_text, log=log) File ""C:\Program Files\ChimeraX 1.0\bin\lib\site- packages\chimerax\core\commands\cli.py"", line 2805, in run result = ci.function(session, **kw_args) File ""C:\Program Files\ChimeraX 1.0\bin\lib\site- packages\chimerax\open_command\cmd.py"", line 152, in provider_open name or model_name_from_path(fi.file_name)), provider_kw) File ""C:\Program Files\ChimeraX 1.0\bin\lib\site- packages\chimerax\open_command\cmd.py"", line 365, in collated_open return func(*func_args, **func_kw) File ""C:\Program Files\ChimeraX 1.0\bin\lib\site- packages\chimerax\core_formats\\__init__.py"", line 37, in open return open_command_script(session, data, file_name) File ""C:\Program Files\ChimeraX 1.0\bin\lib\site- packages\chimerax\core\scripting.py"", line 139, in open_command_script run(session, text) File ""C:\Program Files\ChimeraX 1.0\bin\lib\site- packages\chimerax\core\commands\run.py"", line 31, in run results = command.run(text, log=log) File ""C:\Program Files\ChimeraX 1.0\bin\lib\site- packages\chimerax\core\commands\cli.py"", line 2805, in run result = ci.function(session, **kw_args) File ""C:\Program Files\ChimeraX 1.0\bin\lib\site- packages\chimerax\std_commands\setattr.py"", line 94, in set_attr register_attr(session, items.object_class, attr_name, type(value)) File ""C:\Program Files\ChimeraX 1.0\bin\lib\site- packages\chimerax\std_commands\setattr.py"", line 130, in register_attr class_obj.register_attr(session, attr_name, ""setattr command"", attr_type=attr_type) File ""C:\Program Files\ChimeraX 1.0\bin\lib\site- packages\chimerax\atomic\attr_registration.py"", line 50, in register_attr cls._attr_registration.register(session, attr_name, registerer, default_value, (attr_type, can_return_none)) File ""C:\Program Files\ChimeraX 1.0\bin\lib\site- packages\chimerax\atomic\attr_registration.py"", line 78, in register "" registration by %s"" % (attr_name, self.class_.__name__, registrant, prev_registrant)) ValueError: Registration of attr 'identity_nsp5' with Residue by setattr command conflicts with previous registration by setattr command ValueError: Registration of attr 'identity_nsp5' with Residue by setattr command conflicts with previous registration by setattr command File ""C:\Program Files\ChimeraX 1.0\bin\lib\site- packages\chimerax\atomic\attr_registration.py"", line 78, in register "" registration by %s"" % (attr_name, self.class_.__name__, registrant, prev_registrant)) See log for complete Python traceback. > close session > open 6y2g format mmcif fromDatabase pdb Summary of feedback from opening 6y2g fetched from pdb --- warning | Unable to infer polymer connectivity due to unspecified label_seq_id for residue ""GLY"" near line 6023 6y2g title: Crystal structure (orthorhombic form) of the complex resulting from the reaction between SARS-CoV-2 (2019-nCoV) main protease and tert-butyl (1-((S)-1-(((S)-4-(benzylamino)-3,4-dioxo-1-((S)-2-oxopyrrolidin-3-yl)butan-2-yl)amino)-3-cyclopropyl-1-oxopropan-2-yl)-2-oxo-1,2-dihydropyridin-3-yl)carbamate (alpha-ketoamide 13b) [more info...] Chain information for 6y2g #1 --- Chain | Description A B | Replicase polyprotein 1ab Non-standard residues in 6y2g #1 --- O6K — ~{tert}-butyl ~{N}-[1-[(2~{S})-3-cyclopropyl-1-oxidanylidene-1-[[(2~{S},3~{R})-3-oxidanyl-4-oxidanylidene-1-[(3~{S})-2-oxidanylidenepyrrolidin-3-yl]-4-[(phenylmethyl)amino]butan-2-yl]amino]propan-2-yl]-2-oxidanylidene- pyridin-3-yl]carbamate > open C:\Users\Santiago\Escritorio\nsp5_attribute_chimerax.cxc > setattr :1 residues identity_nsp5 1 create true Assigning identity_nsp5 attribute to 2 items > setattr :2 residues identity_nsp5 1 create true Assigning identity_nsp5 attribute to 2 items > setattr :3 residues identity_nsp5 1 create true Assigning identity_nsp5 attribute to 2 items > setattr :4 residues identity_nsp5 1 create true Assigning identity_nsp5 attribute to 2 items > setattr :5 residues identity_nsp5 1 create true Assigning identity_nsp5 attribute to 2 items > setattr :6 residues identity_nsp5 0.999362813814197 create true Assigning identity_nsp5 attribute to 2 items Traceback (most recent call last): File ""C:\Program Files\ChimeraX 1.0\bin\lib\site- packages\chimerax\cmd_line\tool.py"", line 258, in execute cmd.run(cmd_text) File ""C:\Program Files\ChimeraX 1.0\bin\lib\site- packages\chimerax\core\commands\cli.py"", line 2805, in run result = ci.function(session, **kw_args) File ""C:\Program Files\ChimeraX 1.0\bin\lib\site- packages\chimerax\open_command\cmd.py"", line 101, in cmd_open Command(session, registry=registry).run(provider_cmd_text, log=log) File ""C:\Program Files\ChimeraX 1.0\bin\lib\site- packages\chimerax\core\commands\cli.py"", line 2805, in run result = ci.function(session, **kw_args) File ""C:\Program Files\ChimeraX 1.0\bin\lib\site- packages\chimerax\open_command\cmd.py"", line 152, in provider_open name or model_name_from_path(fi.file_name)), provider_kw) File ""C:\Program Files\ChimeraX 1.0\bin\lib\site- packages\chimerax\open_command\cmd.py"", line 365, in collated_open return func(*func_args, **func_kw) File ""C:\Program Files\ChimeraX 1.0\bin\lib\site- packages\chimerax\core_formats\\__init__.py"", line 37, in open return open_command_script(session, data, file_name) File ""C:\Program Files\ChimeraX 1.0\bin\lib\site- packages\chimerax\core\scripting.py"", line 139, in open_command_script run(session, text) File ""C:\Program Files\ChimeraX 1.0\bin\lib\site- packages\chimerax\core\commands\run.py"", line 31, in run results = command.run(text, log=log) File ""C:\Program Files\ChimeraX 1.0\bin\lib\site- packages\chimerax\core\commands\cli.py"", line 2805, in run result = ci.function(session, **kw_args) File ""C:\Program Files\ChimeraX 1.0\bin\lib\site- packages\chimerax\std_commands\setattr.py"", line 94, in set_attr register_attr(session, items.object_class, attr_name, type(value)) File ""C:\Program Files\ChimeraX 1.0\bin\lib\site- packages\chimerax\std_commands\setattr.py"", line 130, in register_attr class_obj.register_attr(session, attr_name, ""setattr command"", attr_type=attr_type) File ""C:\Program Files\ChimeraX 1.0\bin\lib\site- packages\chimerax\atomic\attr_registration.py"", line 50, in register_attr cls._attr_registration.register(session, attr_name, registerer, default_value, (attr_type, can_return_none)) File ""C:\Program Files\ChimeraX 1.0\bin\lib\site- packages\chimerax\atomic\attr_registration.py"", line 78, in register "" registration by %s"" % (attr_name, self.class_.__name__, registrant, prev_registrant)) ValueError: Registration of attr 'identity_nsp5' with Residue by setattr command conflicts with previous registration by setattr command ValueError: Registration of attr 'identity_nsp5' with Residue by setattr command conflicts with previous registration by setattr command File ""C:\Program Files\ChimeraX 1.0\bin\lib\site- packages\chimerax\atomic\attr_registration.py"", line 78, in register "" registration by %s"" % (attr_name, self.class_.__name__, registrant, prev_registrant)) See log for complete Python traceback. OpenGL version: 3.3.0 NVIDIA 388.16 OpenGL renderer: GeForce GTX 1060/PCIe/SSE2 OpenGL vendor: NVIDIA Corporation Manufacturer: Acer Model: Predator G3-572 OS: Microsoft Windows 10 Home Single Language (Build 18362) Memory: 17,057,812,480 MaxProcessMemory: 137,438,953,344 CPU: 8 Intel(R) Core(TM) i7-7700HQ CPU @ 2.80GHz"" PyQt version: 5.12.3 Compiled Qt version: 5.12.4 Runtime Qt version: 5.12.8 }}} " defect closed normal Structure Analysis not a bug all ChimeraX