Hi Vincent,
How to put the filename prefix in output files is explained in the "forEach" help:

<https://rbvi.ucsf.edu/chimerax/docs/user/commands/open.html#forEachFile>

Namely, you have to use "$file" in the image save command in your cxc file.

Less important, I don't think you need the #* in your script (although I guess it doesn't hurt if it works) -- simply using the chain spec (e.g. /B) will get that chain in all models.

I hope this helps,
Elaine
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Elaine C. Meng, Ph.D.                       
UCSF Chimera(X) team
Resource for Biocomputing, Visualization, and Informatics
Department of Pharmaceutical Chemistry
University of California, San Francisco

On Jan 20, 2025, at 3:12 AM, Vincent CHAPTAL via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:

Hi, 

I would like to open multiple alphafold results that are stored in several folders, make an image, and save the image in those orignial folders. 

I'm using the forEach command to open all the results and run the script to create an image, and it works very well: 

open script.cxc forEach /PATH*/ranked_*.pdb

script.cxc: 
open reference-structure.pdb
match #1 to #2
color #*/B green
color #*/C red
color #*/D blue
view matrix camera 0.87509,0.019021,-0.48356,-124.35,0.48393,-0.035333,0.87439,694.49,-0.00044561,-0.99919,-0.040123,163.41



I'm only stuck at the saving process where I'd like to save an image ranked_*.png matching the original name and folder location:
save /PATH*/$file.png     doesn't work because the /PATH*/ is not recognized as an existing directory. 
save /$PATH*/$file.png   gives the same error. 

If I remove the /PATH/ it saves all the images on top of each other and it defeats the purpose. 


Could you let me know how to save in the folder where the .pdb was read from? 

Thank you
Vincent