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 https://www.cgl.ucsf.edu/chimerax/docs/user/commands/volume.html#boxes https://www.cgl.ucsf.edu/chimerax/docs/user/commands/volume.html#boxes https://www.cgl.ucsf.edu/chimerax/docs/user/commands/combine.html 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/
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