Hi again... Thanks for getting back so quickly, and sorry to bother you again. I tried to use the format mol2 before but I get an error. I think that I am missing something very basic - I saw the man page (http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/write.html) And I tried the command: "write format mol2 selected 0 his.mol2" and different variations of that, and I always get an error: "format is not a model number". What am I doing wrong? Could you please write the command to save a selection as mol2? Thanks, -ben -----Original Message----- From: Elaine Meng [mailto:meng@cgl.ucsf.edu] Sent: Thursday, February 07, 2008 1:30 PM To: Ben Keshet Cc: chimera BB Subject: Re: [Chimera-users] using IDLE Me again! Just noticed you also omitted "format mol2" from the "write" command. The default format is PDB (even if you name it *.mol2). In my experiments I was concentrating on what atoms were there rather than the output format. Anyway, each command has a man page that describes its options and defaults. If you type the command "help [full-command-name]" it will show that command's man page, for example: help write and each individual command page links back to the index of all commands. Hopefully no more postscripts on this message... Elaine