Hi Francisca, What you want to do is pretty much covered in Chimera’s “basic programming primer”: Very Basic Chimera Programming Primer <https://www.cgl.ucsf.edu/chimera/docs/ProgrammersGuide/basicPrimer.html> The only thing I would add is that depending on your needs you might benefit from using the “--script” argument (follow the “--nogui” link in the primer to see other possible command line args, such as “--script”). You save Python sessions with the “save” command and WebGL HTML with the “export” command. —Eric Eric Pettersen UCSF Computer Graphics Lab

On Mar 27, 2018, at 10:46 AM, Wood Ortiz, Francisca (NIH/NEI) [F] <francisca.woodortiz@nih.gov> wrote:

Hello, I am a post-bac fellow at the NEI/NIH working with protein modeling. We are hoping to automate a procedure which requires the protein structure to be colored using an attribute file and exported as an .html and .py session. We would like this to be completed from the command line without the need to open the Chimera graphics window. Could this be done? Thank you for your help.

Best, Francisca Wood Ortiz Postbaccalaureate Fellow, Ophthalmic Genetics and Visual Function Branch, NIH/NEI

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