June 2024 - ChimeraX-users - RBVI Mailing Lists

Fetch many pdbs/maps from the pdb-redo?
by Francisco Murphy Pérez 05 Jun '24

05 Jun '24

Dear all I thought this was going to work, `open "1iee, 2blx, 2bly" fromDatabase redo format mmcif`... but it does not. I have many more ids that I want to open... Can I fetch them all with a single command? Thanks

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Morph command for protein-ligand complexes
by Enrico Martinez 05 Jun '24

05 Jun '24

Dear ChimeraX users! I have a question about recording movie with the transitions between different conformations using morph command. Having five conformations for the same protein, after its supermpostiion using mm #2-5 to #1 I generated a trajectory with the transition using: morph #2,3,4,5,6 core 0.1 frames 100 wrap f rate linear And then recorded movie using: # start recording movie record size 3840,2160 supersample 1 coordset #7 1,400,1 computeSs true wait 400 My question is about morph command. Assuming that all 5 models are very well superimposed and the difference is only the bound ligand (which is different in every model!), would it be possible to include these different ligands in the final morphed trajectory, thus making a smooth transition between different binding poses ? Many thanks in advance ! Enrico

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How to reproduce the output of "info" in python script?
by Artie Kushner 04 Jun '24

04 Jun '24

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: image.png]

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Question/ GPCR complex
by Ranti Dev Shukla 03 Jun '24

03 Jun '24

Hello, Greetings from NIH, Maryland. I am trying to make FRET for G-proteins. I put CFP protein within G.alfa2 on a loop between two nearby helixes and YFP protein on the N-terminal of G-beta. I made the complex using Alphafold but how to see this complex along with the membrane? Is there some command for it please? I would appreciate your kind help. Thanks Ranti Best wishes, Ranti Dev Shukla Visiting Fellow, NIH, Rockville, MD Email: rantibio2(a)gmail.com *rantibio3(a)gmail.com <rantibio3(a)gmail.com>* Phone: +1 865-910-2985 *Teachers* make a lasting impact in the lives of their students

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Rotation of the multi-model object using the symmetric axis
by Enrico Martinez 03 Jun '24

03 Jun '24

Dear Chimera-X users! I am dealing with the visualisation of a complex dimer where each monomer is defined as a separate model like #1 and #2. For visualisation purposes I need to rotate the input construct by 180 degrees with the axis of rotation in the middle between the two monomers to avoid the shift of the complex in the x-plane at the end. That's what I have tried: # turn on 180 deg during 10 sec roll y 0.72 250 center #1,2 protein wait 250 but the construct still shifted a bit towards one of the monomers. How could I do ii using the rotation axis, which would be in the center between them ? Many thanks in advance Enrico

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Conversion of multiple files into PDB
by Enrico Martinez 03 Jun '24

03 Jun '24

Dear ChimeraX Users ! I am dealing with the analysis of multiple structural coordinates generated by AlphaFold for a target protein in *.cif extension. My goal is superimpose all the coordinates to the first model and save them in .pdb as separate files. So my script could be: open ./*.cif match #2-6 to #1 # probably there is a better solution # and some command for save What could be the solution to save all the coordinates in automatic way in separate pdb with the name patterns corresponded to the ID of these models ? Many thanks in advance Enrico

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