[Chimera-users] command line writing PDB files

Thomas Goddard goddard at cgl.ucsf.edu
Thu Feb 18 17:57:31 PST 2010

Hi Matt,

   The Chimera "write" command writes PDB files and I see from the 
User's Guide


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.



> 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

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