[Chimera-users] chimera batch process

y.turgay at bioc.uzh.ch y.turgay at bioc.uzh.ch
Tue Aug 8 08:05:16 PDT 2017

Dear chimera users,
I was wondering if you could help me automate the following procedure in order to batch process all my tomograms.
What I want to do is to open a segmented tomogram, apply parameters like surface, the step size (1 of 8) to increase the connectivity of what has been segmented, to hide the dust (size: 50) and to threshold the tomogram to 0.5. Afterwards I would select all remaining objects and open a script to invert the surface and execute "mask #0 sel invert true" using the command line in chimera to substract the background from the tomogram. Finally I would save this as new map.
Can anyone help me with the commands I have to write in the Terminal to iterate through 200 tomogram folder and automate and batch process this.
Yagmur Turgay
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