[Chimera-users] using IDLE

Elaine Meng meng at cgl.ucsf.edu
Thu Feb 7 10:03:14 PST 2008

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).

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

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