id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 3448 ChimeraX bug report submission vid.sustar@… Tom Goddard "{{{ The following bug report has been submitted: Platform: Linux-5.3.0-61-generic-x86_64-with-debian-buster-sid ChimeraX Version: 1.0 (2020-06-04 23:15:07 UTC) Description Hello! I have tried to adapt the cliping script from http://www.rbvi.ucsf.edu/chimera/data/movie-howto-mar2012/scripts/clip.cmd to work in ChimeraX (because my structure is too big, to be loaded properly in earlier Chimera) I tried to convert the old commands to the ChimeraX, but I get an error in the line ""clip front -0.5 120"": Expected a keyword Please advise me how to change the code to work with ChimeraX to create a movie or to simply save a series of images of cliped planes Best regards, Vid Sustar 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 /home/user/MASTERS/Chimera_files/PythonScripts/clip2.py Traceback (most recent call last): File ""/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/open_command/dialog.py"", line 150, in _qt_safe if data_format is None else "" format "" + StringArg.unparse(data_format.nicknames[0]))) File ""/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/core/commands/run.py"", line 31, in run results = command.run(text, log=log) File ""/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/core/commands/cli.py"", line 2805, in run result = ci.function(session, **kw_args) File ""/usr/lib/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 ""/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/core/commands/cli.py"", line 2805, in run result = ci.function(session, **kw_args) File ""/usr/lib/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 ""/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/open_command/cmd.py"", line 365, in collated_open return func(*func_args, **func_kw) File ""/usr/lib/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 ""/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/core/scripting.py"", line 82, in open_python_script _exec_python(session, code, argv) File ""/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/core/scripting.py"", line 59, in _exec_python exec(code, sandbox.__dict__) File ""clip2.py"", line 3, in ModuleNotFoundError: No module named 'chimera' ModuleNotFoundError: No module named 'chimera' File ""clip2.py"", line 3, in See log for complete Python traceback. > ui tool show Shell /usr/lib/ucsf-chimerax/lib/python3.7/site- packages/IPython/core/history.py:226: UserWarning: IPython History requires SQLite, your history will not be saved warn(""IPython History requires SQLite, your history will not be saved"") > select up Nothing selected > open /home/user/MASTERS/Chimera_files/PythonScripts/clip2.py Traceback (most recent call last): File ""/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/open_command/dialog.py"", line 150, in _qt_safe if data_format is None else "" format "" + StringArg.unparse(data_format.nicknames[0]))) File ""/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/core/commands/run.py"", line 31, in run results = command.run(text, log=log) File ""/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/core/commands/cli.py"", line 2805, in run result = ci.function(session, **kw_args) File ""/usr/lib/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 ""/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/core/commands/cli.py"", line 2805, in run result = ci.function(session, **kw_args) File ""/usr/lib/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 ""/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/open_command/cmd.py"", line 365, in collated_open return func(*func_args, **func_kw) File ""/usr/lib/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 ""/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/core/scripting.py"", line 82, in open_python_script _exec_python(session, code, argv) File ""/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/core/scripting.py"", line 59, in _exec_python exec(code, sandbox.__dict__) File ""clip2.py"", line 3, in ModuleNotFoundError: No module named 'chimera' ModuleNotFoundError: No module named 'chimera' File ""clip2.py"", line 3, in See log for complete Python traceback. > open /home/user/MASTERS/Chimera_files/PythonScripts/writeMol2.py Traceback (most recent call last): File ""/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/open_command/dialog.py"", line 150, in _qt_safe if data_format is None else "" format "" + StringArg.unparse(data_format.nicknames[0]))) File ""/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/core/commands/run.py"", line 31, in run results = command.run(text, log=log) File ""/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/core/commands/cli.py"", line 2805, in run result = ci.function(session, **kw_args) File ""/usr/lib/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 ""/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/core/commands/cli.py"", line 2805, in run result = ci.function(session, **kw_args) File ""/usr/lib/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 ""/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/open_command/cmd.py"", line 365, in collated_open return func(*func_args, **func_kw) File ""/usr/lib/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 ""/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/core/scripting.py"", line 82, in open_python_script _exec_python(session, code, argv) File ""/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/core/scripting.py"", line 59, in _exec_python exec(code, sandbox.__dict__) File ""writeMol2.py"", line 2, in ModuleNotFoundError: No module named 'chimera' ModuleNotFoundError: No module named 'chimera' File ""writeMol2.py"", line 2, in See log for complete Python traceback. > help help:user > open /home/user/MASTERS/Chimera_files/PythonScripts/clip2.py Traceback (most recent call last): File ""/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/open_command/dialog.py"", line 150, in _qt_safe if data_format is None else "" format "" + StringArg.unparse(data_format.nicknames[0]))) File ""/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/core/commands/run.py"", line 31, in run results = command.run(text, log=log) File ""/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/core/commands/cli.py"", line 2805, in run result = ci.function(session, **kw_args) File ""/usr/lib/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 ""/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/core/commands/cli.py"", line 2805, in run result = ci.function(session, **kw_args) File ""/usr/lib/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 ""/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/open_command/cmd.py"", line 365, in collated_open return func(*func_args, **func_kw) File ""/usr/lib/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 ""/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/core/scripting.py"", line 82, in open_python_script _exec_python(session, code, argv) File ""/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/core/scripting.py"", line 59, in _exec_python exec(code, sandbox.__dict__) File ""clip2.py"", line 4, in ImportError: cannot import name 'runCommand' from 'chimerax' (unknown location) ImportError: cannot import name 'runCommand' from 'chimerax' (unknown location) File ""clip2.py"", line 4, in See log for complete Python traceback. > open /home/user/MASTERS/Chimera_files/PythonScripts/clip2.cxc > open /home/user/MASTERS/Chimera_files/testPDBfiles/Sys1nanopart.pdb > select :wat 157584 atoms, 157584 bonds, 1 model selected > hide sel target a > select ~sel 37869 atoms, 34860 bonds, 1 model selected > surface sel > color (#!1 & sel) white > select ::name=""OQL"" 2380 atoms, 2520 bonds, 1 model selected > color (#!1 & sel) red > select ::name=""ONC"" 4200 atoms, 3920 bonds, 1 model selected > color (#!1 & sel) blue > select ::name=""NP"" 2869 atoms, 1 model selected > color (#!1 & sel) yellow > lighting flat > lighting shadows false > graphics silhouettes false > movie record supersample 3 > clip front -0.5 > wait wait requires a frame count argument unless motion is in progress > movie encode clip.mp4 bitrate 200 Movie encoding failed because no images were recorded. > close session > open /home/user/MASTERS/Chimera_files/PythonScripts/clip2.cxc > open /home/user/MASTERS/Chimera_files/testPDBfiles/Sys1nanopart.pdb > select :wat 157584 atoms, 157584 bonds, 1 model selected > hide sel target a > select ~sel 37869 atoms, 34860 bonds, 1 model selected > surface sel > color (#!1 & sel) white > select ::name=""OQL"" 2380 atoms, 2520 bonds, 1 model selected > color (#!1 & sel) red > select ::name=""ONC"" 4200 atoms, 3920 bonds, 1 model selected > color (#!1 & sel) blue > select ::name=""NP"" 2869 atoms, 1 model selected > color (#!1 & sel) yellow > lighting flat > lighting shadows false > graphics silhouettes false > movie record supersample 3 > clip front -0.5 120 Expected a keyword > close session > open /home/user/MASTERS/Chimera_files/PythonScripts/clip2.cxc > open /home/user/MASTERS/Chimera_files/testPDBfiles/Sys1nanopart.pdb > select :wat 157584 atoms, 157584 bonds, 1 model selected > hide sel target a > select ~sel 37869 atoms, 34860 bonds, 1 model selected > surface sel > color (#!1 & sel) white > select ::name=""OQL"" 2380 atoms, 2520 bonds, 1 model selected > color (#!1 & sel) red > select ::name=""ONC"" 4200 atoms, 3920 bonds, 1 model selected > color (#!1 & sel) blue > select ::name=""NP"" 2869 atoms, 1 model selected > color (#!1 & sel) yellow > lighting flat > lighting shadows false > graphics silhouettes false > windowsize 200 150 > copy file clip.jpg Unknown command: copy file clip.jpg > copy Unknown command: copy > save /home/user/Desktop/image1.png supersample 3 > movie record Already recording a movie > open /home/user/Desktop/gbpmovie.cxc No such file/path: /home/user/Desktop/gbpmovie.cxc > close session > open /home/user/MASTERS/Chimera_files/PythonScripts/clip2.cxc > open /home/user/MASTERS/Chimera_files/testPDBfiles/Sys1nanopart.pdb > select :wat 157584 atoms, 157584 bonds, 1 model selected > hide sel target a > select ~sel 37869 atoms, 34860 bonds, 1 model selected > surface sel > color (#!1 & sel) white > select ::name=""OQL"" 2380 atoms, 2520 bonds, 1 model selected > color (#!1 & sel) red > select ::name=""ONC"" 4200 atoms, 3920 bonds, 1 model selected > color (#!1 & sel) blue > select ::name=""NP"" 2869 atoms, 1 model selected > color (#!1 & sel) yellow > lighting flat > lighting shadows false > graphics silhouettes false > movie record supersample 3 Already recording a movie > movie stop > movie record supersample 3 > movie stop > movie stop Not currently recording > close session > open /home/user/MASTERS/Chimera_files/PythonScripts/clip2.cxc > open /home/user/MASTERS/Chimera_files/testPDBfiles/Sys1nanopart.pdb > select :wat 157584 atoms, 157584 bonds, 1 model selected > hide sel target a > select ~sel 37869 atoms, 34860 bonds, 1 model selected > surface sel > color (#!1 & sel) white > select ::name=""OQL"" 2380 atoms, 2520 bonds, 1 model selected > color (#!1 & sel) red > select ::name=""ONC"" 4200 atoms, 3920 bonds, 1 model selected > color (#!1 & sel) blue > select ::name=""NP"" 2869 atoms, 1 model selected > color (#!1 & sel) yellow > lighting flat > lighting shadows false > graphics silhouettes false > movie record supersample 3 > clip front -0.5 120 ; wait 120 ; movie encode clip.mp4 bitrate 200 Expected a keyword > help help:contact.html OpenGL version: 3.3.0 NVIDIA 440.100 OpenGL renderer: GeForce RTX 2060/PCIe/SSE2 OpenGL vendor: NVIDIA Corporation Manufacturer: Micro-Star International Co., Ltd. Model: GL63 8SE OS: Ubuntu 18.04 bionic Architecture: 64bit ELF CPU: 12 Intel(R) Core(TM) i7-8750H CPU @ 2.20GHz Cache Size: 9216 KB Memory: total used free shared buff/cache available Mem: 31G 6.1G 18G 662M 6.6G 24G Swap: 2.0G 0B 2.0G Graphics: 00:02.0 VGA compatible controller [0300]: Intel Corporation Device [8086:3e9b] Subsystem: Micro-Star International Co., Ltd. [MSI] Device [1462:126a] Kernel driver in use: i915 PyQt version: 5.12.3 Compiled Qt version: 5.12.4 Runtime Qt version: 5.12.8 File attachment: clip2.cxc }}} [attachment:""clip2.cxc""] " defect closed normal Depiction not a bug all ChimeraX