Hi Ben, reading more carefully what you wanted to do, it sounds like you don't want the alias to include "open" if you are just going to write out several different parts of the same input file. It sounds like you want something more like open input.mol2 alias ^getparts sel $1; write selected 0 $2.mol2 getparts :2-4 out1 getparts :4,8-10 out2 getparts :his,arg out3 ... there are a lot of different ways to do just about everything, however, and that is just one variant! For example, the alias could open the input file if it also closed it at the end (otherwise you'd get a lot of copies of the same thing opened in Chimera). Elaine On Feb 7, 2008, at 9:32 AM, Ben Keshet wrote:
Hi Eric,
Thanks for the detailed answer. I think the .cmd script will be sufficient for my purpose, however I was unable to write it correctly. What I want to do is slightly more complex than I outlined – I need to: open a mol2 structure, select certain residues (say select: 69-70), save the selected residues as a mol2 file, and select different residues and save them several more times. The .cmd looks something like that:
alias ^process open $1.mol2; sel : 69-70; write selected 0 $1.his_CEGI.mol2;
process p2