Dear Tom

thank you very much for your quick reply. 

I’m probably missing something silly, but what’d be the best way to save the model (mmcif) in “parts” (fragments), matching those exact volume boxes.

Perhaps important to add! : I already have a model that fits fairly well within the full map. (So, not in the situation of building model into each box separately)
What I need instead, is to split that large model (but not by chains, rather in “contiguous volume boxes”), so that I can refine smaller pieces, each with their proper neighboring chains environments

Again, this might be implied in your suggestion, but I tend to understand that your three steps only concern the cropping of the map

Thanx a bunch!
Ale


-- 
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/

On 10 Mar 2025, at 4:27 PM, Tom Goddard <goddard@sonic.net> wrote:

Hi Alejandro,

  I think the commands that will help you are "volume boxes" and "volume cover" and "combine".  The volume boxes command extracts a separate map centered on each marker atom.  The box can match the size of the marker atom which you could set by hand.  Then when when you have built a model for each piece you can make a cropped map that contains all the atoms in that box with the "volume cover" command.  Finally if you have a bunch of models built to these pieces of maps you can combine them into a single model with the "combine" command.

volume boxes #1 centers #2 userMarkerSize true

volume cover #1 atomBox #3 pad 20

combine #4-9

Here is documentation on these commands




  Tom


On Mar 10, 2025, at 9:02 AM, Alejandro Buschiazzo via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:

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/

_______________________________________________
ChimeraX-users mailing list -- chimerax-users@cgl.ucsf.edu
To unsubscribe send an email to chimerax-users-leave@cgl.ucsf.edu
Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/