Hi Vid, The "clip hither -0.5 120" command in the Chimera script you mentioned moves the near clip plane away in 120 steps of 0.5 Angstroms. To do the same in ChimeraX which does not have the "frames" option for the clip command: perframe "clip near 0.5" frames 120 This isn't the same if the near clip plane is not yet enabled then the "clip near 0.5" sets the position 0.5 Angstroms behind the center of the displayed models, while if the near clip plane is enabled it moves it 0.5 Angstroms further away. So you could set the starting position 30 Angstroms in front of the center, then move 60 Angstroms back in 0.5 Angstrom steps use: clip near -30 perframe "clip near 0.5" frames 120 In the future we plane to add the frames option to the clip command. Tom
On Jun 26, 2020, at 3:50 PM, Vid Sustar <vid.sustar@abo.fi> wrote:
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 <clip2.cxc>_______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users