Glad you figured out what you needed.  The ChimeraX Recipes web page has many example Python scripts for working with atomic models and maps.

https://rbvi.github.io/chimerax-recipes/

  Tom

On Aug 11, 2025, at 3:18 PM, Nikhil Rajan <nrajan53045@utexas.edu> wrote:

Hi,

I was hoping to create a Volume object from a pre-existing map on emdb. Then I would fit my AtomicStructure into that Volume object via fitmap.

I ended up figuring out how to create the Volume object (via the ArrayGridData class and volume_from_grid_data method). Thank you for your help though!

Nikhil

On Mon, Aug 11, 2025 at 1:30 PM Tom Goddard <goddard@sonic.net> wrote:
If you mean you want to create a map using the atomic model the ChimeraX command to do it is "molmap" and the ChimeraX Programming Guide documents the equivalent Python function


To import that function in Python you would use

from chimerax.map.molmap import molmap

  Tom


On Aug 10, 2025, at 5:54 PM, Nikhil Rajan via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:

Hey Eric, 

The struct_edit.add_atom() method worked like a charm, thank you so much!

Just to confirm, for maps, is there any method you'd recommend when creating its corresponding Volume object?

Best,
Nikhil 

On Fri, Aug 8, 2025 at 12:46 PM Eric Pettersen <pett@cgl.ucsf.edu> wrote:
Hi Nikhil,
You absolutely can create structures completely in the Python layer, though the flow is kind of in the opposite direction: you create an AtomicStructure, use it's new_residue() method to create residues as needed and then add atoms to those residues.  For creating atoms I recommend using the chimerax.atomic.struct_edit.add_atom() method, which handles a lot of bookkeeping that you might otherwise forget or not know about (rather than the low-level new_atom() method of AtomicStructure).
Once you create a structure, you add it to the ChimeraX session with session.models.add([structure]).

--Eric

Eric Pettersen
UCSF Computer Graphics Lab


On Aug 8, 2025, at 9:38 AM, nrajan53045--- via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:

Hi there,

I am new to ChimeraX and its python API. As I was looking through the documentation, I noticed there were some atomic data classes (AtomicStructure, Atom, Atoms, Residue). Say I have a PDB file with information about all the atoms in the model, am I able to simply create Atom objects from reading the PDB file and, consequently, add these Atom objects to an AtomicStructure object?

The reason I want to do this is because I want to use the fitmap function while limiting any disk IO. So, opening the file in ChimeraX (even if using the no gui offscreen functionality) would not work. I thought of simply creating objects from scratch, but I am running into errors when instantiating them.

Sorry if this is an obscure problem or if I was unclear. Thanks for your help!

Best,
Nikhil
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