Thank you kindly, Eric. That does it. I borrow pages from the "recipes" frequently, but must have missed this bit. Thanks a lot again! Best, Artem On Tue, Jun 4, 2024 at 11:48 AM Eric Pettersen <pett@cgl.ucsf.edu> wrote:
Hi Artie, Here's some code to compute a dictionary mapping chain IDs to model identifiers:
cid_to_spec = {} from chimerax.atomic import all_atomic_structures for s in all_atomic_structures(session): for chain in s.chains: cid_to_spec[chain.chain_id] = s.atomspec
There is documentation for the chimerax.atomic module (along with several other modules) here: Python Modules — ChimeraX 1.9 documentation <https://www.cgl.ucsf.edu/chimerax/docs/devel/modules.html>. Also, aside from looking at the Python code that ships with ChimeraX (which is frequently a good learning approach), there are some ChimeraX "recipes" that provide example scripts for performing various tasks here: ChimeraX Recipes <https://rbvi.github.io/chimerax-recipes/>, which sometimes are useful for discovering how to code something similar. And don't hesitate to ask questions on this list either. :-)
--Eric
Eric Pettersen UCSF Computer Graphics Lab
On Jun 4, 2024, at 10:45 AM, Artie Kushner via ChimeraX-users < chimerax-users@cgl.ucsf.edu> wrote:
Hi there, hope you are all doing well
I'm wondering if anyone has a good idea of how to reproduce the output of the *info* command in the GUI inside a python script. Precisely the *info* command without any specifiers s.t. that all models and submodels are listed with minimal info. Like the following:
*...#1.87, 4v6x Cu, shown419 atoms, 421 bonds, 56 residues, 1 chains (Cu)#1.88, 4v6x Cv, shown419 atoms, 421 bonds, 56 residues, 1 chains (Cv)#1.89, 4v6x Cz, shown1741 atoms, 1769 bonds, 217 residues, 1 chains (Cz)*
Perhaps there is a better way to do this, but my use case is splitting a bigger structure into multiple chains (as you can tell from above there are 89 chains in 4V6X). I'd like to be able to correlate chain IDs (ex. *Cz*) with the model identifiers (ex. *#1.89*) programmatically from within python to script against individual chains further. I'm sure there is more than one way to do it, but i haven't been able to find either so far.
Most that i found is the model_info command:
*from chimerax.list_info.util import spec, model_info...def test_func(session, structure: AtomicStructure): print(model_info(structure))**<<<Missing or invalid "structure" argument: must specify 1 atomic structure, got 89 for "#1".*
*def register_ribrepr_command(logger): from chimerax.core.commands import CmdDesc, register from chimerax.atomic import AtomicStructureArg, Chain, Residue, Atom desc = CmdDesc( required = [("structure", AtomicStructureArg)], required_arguments = ["structure"], synopsis = "representation ", ) register("test_func", desc, test_func, logger=logger)*
but it presupposes that I pass the model by spec I pass the "top-level" structure. It throws error saying that it contains 89 instead of 1 structures: *Missing or invalid "structure" argument: must specify 1 atomic structure, got 89 for "#1".*
Any other way of getting at the correspondence dict between chains/"submodels" created with i.e. *`split chains`* and their chain_id's (aka *auth_asym_id* 's) in Python space would work for me. Perhaps there is a way to list all objects in the "Models" section (picture below)?
Thanks in advance Artie
<image.png>
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