[chimerax-users] How to do repetitive task using Python or command line in ChimeraX?

[Joel Meyerson]

Hi Seowon,
You can create a cxc file in a text editor and then execute it at the ChimeraX command line using the "open script-name.cxc" command. Just be sure to provide the full path to the script, or change your working directory. There are some nice example scripts on the ChimeraX page which can help migrate from Chimera to ChimeraX.

https://www.cgl.ucsf.edu/chimerax/gallery.html

I hope that answers your question.
Best,
Joel
On 4/9/20, 1:26 AM, "ChimeraX-users on behalf of 이서원" <chimerax-users-bounces at cgl.ucsf.edu on behalf of selcia20 at snu.ac.kr> wrote:

    Hello,
    
    I think I'm good at dealing with the previous Chimera command line,
    and I'm learning Python coding and ChimeraX little by little.
    
    In Chimera, I was able to apply the Chimera command to a Python script
    using runCommand.
    So, I wrote some python scripts for Chimera, such as automatically
    coloring or cropping maps and/or models based on the target
    specification list in plain text.
    
    However, I think there's no python modules like runCommand, and I
    don't know how to repetitively input specifications by .cxc files.
    (Do I have to make as many .cxc files as many as the number of the variables?)
    Also I tried to understand the ChimeraX developer tutorial, but I
    failed to import color functions on chimeraX Python Shell.
    (I didn't understand how to import experimental API)
    
    Is there any fancy way to create a .cxc file that executes by
    sequentially inputting variables in the list?
    Or, How to import python modules such as color functions?
    (https://urldefense.proofpoint.com/v2/url?u=https-3A__www.cgl.ucsf.edu_chimerax_docs_devel_core_commands_user-5Fcommands.html&d=DwIGaQ&c=lb62iw4YL4RFalcE2hQUQealT9-RXrryqt9KZX2qu2s&r=JnYzuUa3E5p4u7qrfPzeZV8LIgMpwauz4WIvX7NJIi8&m=j7Tpmyo5XDVqMjqkGEuzR9uY2VhT76OIZl-yNu45ox0&s=kEjKLfMWQpeflIuqRONfyOB_NGRIqwqyxp73rpxs77c&e= )
    
    Best regards, Seowon
    ______________________________________________________________________________________
    이 서 원        | Selcia Seowon Lee
    selcia20 at snu.ac.kr
    Laboratory of Molecular Imaging , Ph.D. Candidate
    Department of Biological Sciences, College of Natural Sciences
    Seoul National University, Gwanak-gu Gwanak-ro 1, Bldg105 Rm109, Seoul
    08826, Korea
    
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