Hi Matt, The Chimera "write" command writes PDB files and I see from the User's Guide http://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/midas/write.html that it takes a "selected" option to write only the selected atoms of a specified model. The command would look like write selected 2 someatoms.pdb Here 2 is the model number and it can only write the selected atoms from one model. If the selected atoms are in more than one model it gets trickier because they could have overlapping residue numbers and chain identifiers. You could then use the "combine" command to merge the different molecules while renaming chains or renumbering to avoid clashes. http://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/midas/combine.html Tom

Is there a command line string for writing out selected atoms as a PDB file?

thanks, matt

Matthew Dougherty National Center for Macromolecular Imaging Baylor College of Medicine