id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 3425 RFE: command to add C-terminal oxygens Tristan Croll Eric Pettersen "{{{ The following bug report has been submitted: Platform: Linux-3.10.0-1062.9.1.el7.x86_64-x86_64-with-centos-7.7.1908-Core ChimeraX Version: 1.0 (2020-06-04 23:15:07 UTC) Description I just put this together as a script to go in the ChimeraX presets directory, to help Dirk Fahrenkamp who was asking about how to add C-terminal OXT atoms to chains in his (very large) model. I know AddH will do this when it knows from the provided sequence that a residue is actually C-terminal, but as far as I'm aware there's no existing tool to do it manually. Anyway, it might be nice to implement something like this as a command? 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 3io0 format mmcif fromDatabase pdb 3io0 title: Crystal structure of EtuB from Clostridium kluyveri [more info...] Chain information for 3io0 #1 --- Chain | Description A | EtuB protein 3io0 mmCIF Assemblies --- 1| author_and_software_defined_assembly > preset custom ""add oxt"" > open /home/tic20/chimerax_presets/add_oxt.py No atoms selected! > show > hide cartoons > select /A:303@CA 1 atom, 1 model selected > preset custom ""add oxt"" > open /home/tic20/chimerax_presets/add_oxt.py Selection must be from a single model! > preset custom ""add oxt"" > open /home/tic20/chimerax_presets/add_oxt.py Traceback (most recent call last): File ""/opt/UCSF/ChimeraX/lib/python3.7/site-packages/chimerax/ui/gui.py"", line 1027, in run(ses, ""preset %s%s"" % (cat, StringArg.unparse(name.lower())))) File ""/opt/UCSF/ChimeraX/lib/python3.7/site- packages/chimerax/core/commands/run.py"", line 31, in run results = command.run(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/preset_mgr/cmd.py"", line 49, in preset_cmd session.presets.preset_function(cat, matches[0])() File ""/opt/UCSF/ChimeraX/lib/python3.7/site- packages/chimerax/preset_mgr/manager.py"", line 89, in name: lambda p=preset: self.execute(p) File ""/opt/UCSF/ChimeraX/lib/python3.7/site- packages/chimerax/preset_mgr/manager.py"", line 68, in execute preset() File ""/opt/UCSF/ChimeraX/lib/python3.7/site- packages/chimerax/preset_mgr/manager.py"", line 109, in run=run, ses=self.session: run(ses, ""open "" + p, log=False) File ""/opt/UCSF/ChimeraX/lib/python3.7/site- packages/chimerax/core/commands/run.py"", line 31, in run results = command.run(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/open_command/cmd.py"", line 101, in cmd_open 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/open_command/cmd.py"", line 152, in provider_open name or model_name_from_path(fi.file_name)), provider_kw) File ""/opt/UCSF/ChimeraX/lib/python3.7/site- packages/chimerax/open_command/cmd.py"", line 365, in collated_open return func(*func_args, **func_kw) File ""/opt/UCSF/ChimeraX/lib/python3.7/site- packages/chimerax/core_formats/__init__.py"", line 48, in open return open_python_script(session, data, file_name) File ""/opt/UCSF/ChimeraX/lib/python3.7/site- packages/chimerax/core/scripting.py"", line 82, in open_python_script _exec_python(session, code, argv) File ""/opt/UCSF/ChimeraX/lib/python3.7/site- packages/chimerax/core/scripting.py"", line 59, in _exec_python exec(code, sandbox.__dict__) File ""add_oxt.py"", line 25, in NameError: name 'add_oxt' is not defined NameError: name 'add_oxt' is not defined File ""add_oxt.py"", line 25, in See log for complete Python traceback. > preset custom ""add oxt"" > open /home/tic20/chimerax_presets/add_oxt.py Traceback (most recent call last): File ""/opt/UCSF/ChimeraX/lib/python3.7/site-packages/chimerax/ui/gui.py"", line 1027, in run(ses, ""preset %s%s"" % (cat, StringArg.unparse(name.lower())))) File ""/opt/UCSF/ChimeraX/lib/python3.7/site- packages/chimerax/core/commands/run.py"", line 31, in run results = command.run(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/preset_mgr/cmd.py"", line 49, in preset_cmd session.presets.preset_function(cat, matches[0])() File ""/opt/UCSF/ChimeraX/lib/python3.7/site- packages/chimerax/preset_mgr/manager.py"", line 89, in name: lambda p=preset: self.execute(p) File ""/opt/UCSF/ChimeraX/lib/python3.7/site- packages/chimerax/preset_mgr/manager.py"", line 68, in execute preset() File ""/opt/UCSF/ChimeraX/lib/python3.7/site- packages/chimerax/preset_mgr/manager.py"", line 109, in run=run, ses=self.session: run(ses, ""open "" + p, log=False) File ""/opt/UCSF/ChimeraX/lib/python3.7/site- packages/chimerax/core/commands/run.py"", line 31, in run results = command.run(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/open_command/cmd.py"", line 101, in cmd_open 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/open_command/cmd.py"", line 152, in provider_open name or model_name_from_path(fi.file_name)), provider_kw) File ""/opt/UCSF/ChimeraX/lib/python3.7/site- packages/chimerax/open_command/cmd.py"", line 365, in collated_open return func(*func_args, **func_kw) File ""/opt/UCSF/ChimeraX/lib/python3.7/site- packages/chimerax/core_formats/__init__.py"", line 48, in open return open_python_script(session, data, file_name) File ""/opt/UCSF/ChimeraX/lib/python3.7/site- packages/chimerax/core/scripting.py"", line 82, in open_python_script _exec_python(session, code, argv) File ""/opt/UCSF/ChimeraX/lib/python3.7/site- packages/chimerax/core/scripting.py"", line 59, in _exec_python exec(code, sandbox.__dict__) File ""add_oxt.py"", line 49, in File ""add_oxt.py"", line 24, in add_oxt AttributeError: 'str' object has no attribute 'chain_id' AttributeError: 'str' object has no attribute 'chain_id' File ""add_oxt.py"", line 24, in add_oxt See log for complete Python traceback. > preset custom ""add oxt"" > open /home/tic20/chimerax_presets/add_oxt.py Added a C-terminal OXT to chain A executed add_oxt.py Preset implemented in Python; no expansion to individual ChimeraX commands available. > close > open 3io0 format mmcif fromDatabase pdb 3io0 title: Crystal structure of EtuB from Clostridium kluyveri [more info...] Chain information for 3io0 #1 --- Chain | Description A | EtuB protein 3io0 mmCIF Assemblies --- 1| author_and_software_defined_assembly > show atoms > hide cartoons > select /A:304@N 1 atom, 1 model selected > preset custom ""add oxt"" > open /home/tic20/chimerax_presets/add_oxt.py Added a C-terminal OXT to chain A executed add_oxt.py Preset implemented in Python; no expansion to individual ChimeraX commands available. > select /A:304@OXT 1 atom, 1 model selected > delete sel > show cartoons > hide cartoons > cofr centerOfView showPivot true > select /A:303@C 1 atom, 1 model selected > show sel cartoons > select clear > show cartoons > hide cartoons > select /A:304@C 1 atom, 1 model selected > preset custom ""add oxt"" > open /home/tic20/chimerax_presets/add_oxt.py Added a C-terminal OXT to chain A executed add_oxt.py Preset implemented in Python; no expansion to individual ChimeraX commands available. OpenGL version: 3.3.0 NVIDIA 440.33.01 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 3.5G 50G 99M 8.9G 58G 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 File attachment: add_oxt.py }}} [attachment:""add_oxt.py""] " defect closed normal Structure Editing duplicate Elaine Meng all ChimeraX