Hi Bruno, Here's how to replace proteins A,B,C of virus capsid PDB 8b38 and write a new mmCIF files that includes the symmetry information to make the full capsid. First off PDB 8b38 is an unfortunate example where the icosahedral symmetry does not have its center at 0,0,0. It is convenient if the center of symmetry is at 0,0,0 so I'll show you how to make a model that has that. open 8b38 open 15823 from emdb The PDB 8b38 comes from cryoEM and the map is EMDB entry 15823. Using menu Tools / Volume Data / Map Coordinates I see the origin grid index is 0,0,0, in other words the the coordinate origin x=y=z=0 is at grid point 0,0,0 at the corner of the volume. I want it near the middle of the volume. To figure out the center of symmetry of the map I use measure sym #2 > Symmetry emdb 15823: Icosahedral 222, center 175 175 174 I set the map origin index to 175 175 174 in the Map Coordinates dialog and press the Enter key. That moves the map and now the atomic model 8b38 does not align with the map. So I want to move the atomic model to the same position. Do this using command move -192.5,-192.5,-191.4 model #1 The amount I moved use that the map grid spacing is 1.1 Angstroms so 192.5, 192.5, 191.4 = 1.1*175, 1.1*175, 1.1*174. Now we have the 8b38 capsid centered at 0,0,0. Next dock the 3 homolog proteins to the 3 chains of 8b38. Since there are no homologs in the PDB for these virus capsid proteins I use 3 AlphaFold predictions in my example open alphafold_a.cif open alphafold_b.cif open alphafold_c.cif mm #3 to #1/A mm #4 to #1/B mm #5 to #1/C Now combine those 3 docked models into a single model combine #3-5 Then show the icosahedral symmetry and have it add the mmCIF assembly info to the combined model sym #6 i,222 addmmcifassembly true Then save the new model save virus.cif model #6 This will save just the asymmetric unit with assembly info to reconstruct the full capsid. Here's how to open the saved model and show the capsid open virus.cif sym #7 assembly 1 Tom

On Feb 20, 2025, at 1:56 AM, Bruno Hay Mele via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:

Hi everyone,

I am trying to build the capsid for a homolog of Chaetoceros socialis forma radians RNA virus 1 (PDB: 8b38). My approach was to work by homology, transferring the assembly/symmetry information from the PDB entry to my model, which I built by assembling homologs of the three subunits of 8b38. Unfortunately, this has not been as straightforward as I hoped.

Ib€m a complete newbie in this area, and my attempts to copy the relevant parts of the assembly information or use the ChimeraX b€symb€ tool have led nowhere. Could someone please point me to the right solution? Ib€d really appreciate both:

A practical solution: How to correctly transfer the symmetry information and generate the full capsid assembly in ChimeraX. Some references or explanations: Resources that explain why the solution works this way, so I can understand the underlying principles.

Any help or pointers would be very much appreciated.

Thank you very much for your time and assistance.

Cheers, -- Bruno Hay Mele, PhD 2D-20, Biology Dept., University of Naples Federico II https://github.com/bhym/ | +39 081 67 9118

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