Hi Trent, Unfortunately many Chimera capabilities do not have equivalent commands, though we are working on adding more commands. The multiscale tool and scene export as vrml cannot be done with Chimera commands. But all the capabilities are available with Python scripts. Attached is a Python script to export a batch of PDB files in a directory as VRML or OBJ. For OBJ format you'll need to download the Export OBJ plug-in that I just added to the Chimera experimental features web page: http://www.cgl.ucsf.edu/chimera/experimental/experimental.html To use the script, edit the line near the bottom to set directory for the PDB files. Then use Chimera File / Open... to open it. It will create the vrml or obj files in the same directory. I tried in with the latest Chimera production release 1.2470. Tom # ----------------------------------------------------------------------------- # Open PDB file, make multiscale model, and export 3d scene. # # Allowed export formats are POV-Ray, RenderMan, X3D, VRML, and OBJ. # OBJ format requires installing the separate ExportOBJ Chimera plug-in # from the Chimera experimental features web page. # def export_pdb_as_multiscale(pdb_path, resolution, export_format, export_path): # Open PDB from chimera import openModels as om mlist = om.open(pdb_path) # Create multiscale model from MultiScale import multiscale_model_dialog d = multiscale_model_dialog(create = True) d.surface_resolution.set('%g' % resolution) # For copies of molecule: d.multimer_none, d.multimer_unitcell d.multimer_type.set(d.multimer_biounit) d.make_multimers(mlist) # Export scene. if export_format == 'OBJ': import ExportOBJ ExportOBJ.write_surfaces_as_wavefront_obj(export_path) else: from chimera import exports exports.doExportCommand(export_format, export_path) # Close files from chimera import closeSession closeSession() # ----------------------------------------------------------------------------- # Export multiscale surface models for all PDB files in a directory. # def export_pdbs(dir, resolution, export_format, export_suffix): from os import listdir filenames = [n for n in listdir(dir) if n.endswith('.pdb')] from os.path import join for f in filenames: pdb_path = join(dir, f) export_path = join(dir, f.rstrip('.pdb') + export_suffix) export_pdb_as_multiscale(pdb_path, resolution, export_format, export_path) # ----------------------------------------------------------------------------- # Formats: 'VRML', 'OBJ', 'POV-Ray', 'RenderMan', 'X3D' # export_pdbs(dir = '/tmp/pdbfiles', # location of PDB files resolution = 3, export_format = 'VRML', export_suffix = '.vrml')