[chimerax-users] ChimeraX command line iterate through models for individual file export

[Tom Goddard]

Hi Austin,

  Of course I remember you, it was a great trip to Rocky Mountain Laboratories.  Thanks for your hospitality!  And I see your SARS-Cov-2 images in the media -- very nice.

  Here's the ChimeraX voodoo to save all your objs in one command

	perframe "save ~/Desktop/objs/model$1.obj model #1.$1" frames 23

It uses the perframe command that runs another command once each frame (usually used for recording an animation video).  The $1 gets the frame number substituted in 1, 2, 3 and the frames tells it how many frames, in your case use 100 to get the 100 models.  Here are the perframe docs

	https://www.cgl.ucsf.edu/chimerax/docs/user/commands/perframe.html <https://www.cgl.ucsf.edu/chimerax/docs/user/commands/perframe.html>

if you need more info.

	Tom


> On Jul 29, 2020, at 10:19 PM, Athman, Austin (NIH/NIAID) [E] <austin.athman at nih.gov> wrote:
> 
> Tom,
>  
> I’m Austin Athman, from the NIAID Rocky Mountain Laboratories Visual Arts Department. I took some of your sessions on ChimeraX when you were out to Hamilton MT in the past, and I believe you assisted my colleague Ryan Kissinger on some ChimeraX questions he had. I have one for you I hope you can help.
>  
> I have received a morphing model of the spike protein on RSV for an animation project we are working on for Barney Graham and Jason McLellan. The morph is in 100 steps, and I have 2 different morphs (one for attachment, and another for fusion), making 200 steps total. I am exporting the surface model of each step to an OBJ file for use in our animation software. I have managed to write a single command line that I copy/paste in over and over, changing just the id and file number for export to get the files I need. 
>  
> Is there a way I can automate this further, so that ChimeraX will iterate through each id and export to individual files for me without copy/pasting the command each time and modifying it? It would save me hours of time.
>  
> Unfortunately, I am very new to ChimeraX, and know only enough to get me into trouble, specifically, how to show/hide surfaces, and export!
>  
> Here is a screenshot of my model, and also the Excel doc I use to keep track and build my command for each file export, just so you can see what I am doing at the moment. It takes some time for each to save as well, so I don’t know if that delay will make it difficult for the command line to wait and continue each time for each export. There may be some additional commands I can just add between each line in the excel, and I can just copy and past the entire thing and let it run, but that is where I hope you might be able to tell me what I am missing.
>  
> Hope you are well in these times. Also, thank you for your work and videos on coronavirus. Good informative stuff.
>  
> -Austin Athman
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> Rocky Mountain Laboratories NIH/NIAID
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>  
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