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 <module> 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 <module> 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 <module> 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 <module> 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