Generically, from looking at paper methods sections, the typical workflow components seem to be:

1. get protein coordinates: use previously solved structure, or make homology model (Modeller, Swissmodel), or use AI method (Alphafold; haven't seen ESMfold)
   
   
2. fit protein(s) into cryoEM map: Chimera, ChimeraX, other; map segmentation could be done first, followed by segment-specific fitting
   
   
3. dealing with het groups (could be interleaved with other steps): covalent modifications like glycosylations and phosphorylations, noncovalently bound small-molecule ligands: building in isolation, building into the structure along with macromolecule, could involve docking, minimization, MD, etc.
   
   
4. refinement: most often coot+phenix, sometimes ISOLDE and/or specialized loop modeling (Modloop, Modeller), Rosetta (via StarMap); iterative with the above

Example recent publications:

1. Structure of the Saccharolobus solfataricus type III-D CRISPR effector. Cannone G, Kompaniiets D, Graham S, White MF, Spagnolo L. Curr Res Struct Biol. 2023 Feb 10;5:100098. doi: 10.1016/j.crstbi.2023.100098. PMID: 36843655 open access
   – Chimera fit to segments, combining maps (presumably both could be done in ChimeraX), ChimeraX alphafold predict; phenix, coot
   
   
2. Structure of the Newcastle Disease Virus L protein in complex with tetrameric phosphoprotein. Cong J, Feng X, Kang H, Fu W, Wang L, Wang C, Li X, Chen Y, Rao Z. Nat Commun. 2023 Mar 10;14(1):1324. doi: 10.1038/s41467-023-37012-y. PMID: 36898997 open access
   – Chimera fitting alphafold model (could be done in ChimeraX), figures along with Pymol; coot, phenix
   
   
3. CD19 CAR antigen engagement mechanisms and affinity tuning. He C, Mansilla-Soto J, Khanra N, Hamieh M, Bustos V, Paquette AJ, Garcia Angus A, Shore DM, Rice WJ, Khelashvili G, Sadelain M, Meyerson JR. Sci Immunol. 2023 Mar 10;8(81):eadf1426. doi: 10.1126/sciimmunol.adf1426. PMID: 36867678 link
   – Chimera fitting Swissmodel homology model (presumably could use Modeller and ChimeraX); phenix, coot; ChimeraX figures
   
   
4. The intestinal MUC2 mucin C-terminus is stabilized by an extra disulfide bond in comparison to von Willebrand factor and other gel-forming mucins. Gallego P, Garcia-Bonete MJ, Trillo-Muyo S, Recktenwald CV, Johansson MEV, Hansson GC. Nat Commun. 2023 Apr 8;14(1):1969. doi: 10.1038/s41467-023-37666-8. PMID: 37031240 open access
   – Chimera fitting and figures along with Pymol; coot, phenix; ChimeraX fitting; alphafold, CHARMM-GUI to add glycosylations, Modloop to fill in "the non-assigned loops from the Cryo-EM/AlphaFold model," whatever that means
   
   
5. Delivering a toxic metal to the active site of urease. Nim YS, Fong IYH, Deme J, Tsang KL, Caesar J, Johnson S, Pang LTH, Yuen NMH, Ng TLC, Choi T, Wong YYH, Lea SM, Wong KB. Sci Adv. 2023 Apr 21;9(16):eadf7790. doi: 10.1126/sciadv.adf7790. PMID: 37083535 open access
   – Chimera Modeller interface, fitting (both could be done via ChimeraX); phenix, coot; figures ChimeraX and pymol
   
   
6. Structural basis of membrane skeleton organization in red blood cells. Li N, Chen S, Xu K, He MT, Dong MQ, Zhang QC, Gao N. Cell. 2023 Apr 27;186(9):1912-1929.e18. doi: 10.1016/j.cell.2023.03.017. PMID: 37044097 link
   – ChimeraX fitting alphafold model; coot, pymol
   
   
7. Structure of the endosomal Commander complex linked to Ritscher-Schinzel syndrome. Healy MD, McNally KE, Butkovič R, Chilton M, Kato K, Sacharz J, McConville C, Moody ERR, Shaw S, Planelles-Herrero VJ, Yadav SKN, Ross J, Borucu U, Palmer CS, Chen KE, Croll TI, Hall RJ, Caruana NJ, Ghai R, Nguyen THD, Heesom KJ, Saitoh S, Berger I, Schaffitzel C, Williams TA, Stroud DA, Derivery E, Collins BM, Cullen PJ. Cell. 2023 May 11;186(10):2219-2237.e29. doi: 10.1016/j.cell.2023.04.003. PMID: 37172566 open access
   – Chimera map viz, ChimeraX fitting alphafold model, ISOLDE; phenix, coot, pymol
   
   
8. Cryo-EM structure of the Saccharomyces cerevisiae Rpd3L histone deacetylase complex. Patel AB, Qing J, Tam KH, Zaman S, Luiso M, Radhakrishnan I, He Y. Nat Commun. 2023 May 27;14(1):3061. doi: 10.1038/s41467-023-38687-z. PMID: 37244892 open access
   – de novo building and alphafold multimer predictions for various chain combinations; phenix, coot; ChimeraX figures
   
   
9. Structure and transport mechanism of the human calcium pump SPCA1. Wu M, Wu C, Song T, Pan K, Wang Y, Liu Z. Cell Res. 2023 May 31. doi: 10.1038/s41422-023-00827-x. Online ahead of print. PMID: 37258749 open access
   – ChimeraX fitting alphafold model; coot, phenix
   
   
10. A multi-enzyme machine polymerizes the Haemophilus influenzae type b capsule. Cifuente JO, Schulze J, Bethe A, Di Domenico V, Litschko C, Budde I, Eidenberger L, Thiesler H, Ramón Roth I, Berger M, Claus H, D'Angelo C, Marina A, Gerardy-Schahn R, Schubert M, Guerin ME, Fiebig T. Nat Chem Biol. 2023 Jun 5. doi: 10.1038/s41589-023-01324-3. Online ahead of print. PMID: 37277468 open access
    – example of crystallography + alphafold, coot, phenix; vina docking; Chimera sequence-structure analysis, small-molecule editing (could be done in ChimeraX), minimization
11. Structural basis of NINJ1-mediated plasma membrane rupture in cell death. Degen M, Santos JC, Pluhackova K, Cebrero G, Ramos S, Jankevicius G, Hartenian E, Guillerm U, Mari SA, Kohl B, Müller DJ, Schanda P, Maier T, Perez C, Sieben C, Broz P, Hiller S. Nature. 2023 Jun 29;618(7967):1065-1071. doi: 10.1038/s41586-023-05991-z. PMID: 37198476 open access
    – ChimeraX map processing, fitting alphafold model, zone; phenix refinement, molprobity assessment, coot

Previous ChimeraX papers in Protein Science:

UCSF ChimeraX: Structure visualization for researchers, educators, and developers. Pettersen EF, Goddard TD, Huang CC, Meng EC, Couch GS, Croll TI, Morris JH, Ferrin TE. Protein Sci. 2021 Jan;30(1):70-82.

UCSF ChimeraX: Meeting modern challenges in visualization and analysis. Goddard TD, Huang CC, Meng EC, Pettersen EF, Couch GS, Morris JH, Ferrin TE. Protein Sci. 2018 Jan;27(1):14-25.