Dear chimeraX developers/users

Using version 1.9, I am trying to divide a very big mmcif model (230K + nonH atoms; >130 chains) and corresponding mrc map, into a number of smaller mmcif files (and corresponding cropped maps, covering just those parts).

What I’ve tried so far unsuccessfully:
I can create dummy atoms with build start atom, at desired x,y,z points, so that I can then use select zone to select a radius and keep parts near each dummy atom.
Yet, that is suboptimal: I would largely prefer to keep (build) boxes, and not spheres, ensuring complete recovery and no blind spots. 
So that each box slightly overlaps with the neighboring one, and systematically covers the whole original map volume.

1. How can I generate a script that will do this "systematic windowing” screening, making boxes of a defined side-length at each step, and keeping the model within?
2. How should I then crop the original map, so that it covers each box (with a small padding on the borders)?
3. How should I stitch back the models, so that I don’t loose any atomic coordinates information? (of course that stitching will be done after I do some refinement work on each boxed model vs map)

So sorry for the many questions! I’ve been trying hard to find this kind of strategy, and just can’t seem to succeed….

Thank you very much in advance
Alejandro


-- 
Alejandro Buschiazzo, PhD
Associate Professor
Laboratory of Molecular & Structural Microbiology
Institut Pasteur de Montevideo
Mataojo 2020
Montevideo 11400
URUGUAY
Phone: +598 25220910 ext. 120
Fax:  +598 25224185
https://pasteur.uy/en/laboratories/molecular-and-structural-microbiology/