Hi Ben, Your command is exactly right - I just tried it - but you must be using an old version of Chimera. The advantage of using the documentation included with your download (opened from the Chimera Help menu or with the "help" command) is that it should be fairly synchronized with the software and will not confuse you with options that do not exist in what you have! In this case, however, you can just get a newer version of Chimera (see below) and it will work. The pages under http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/ are "development documentation," which I am constantly changing as Chimera changes. It will generally have newer things than your downloaded software. The pages under http://www.cgl.ucsf.edu/chimera/current/docs/ UsersGuide/ are documentation for the most recent production release (currently Nov 2007) and I see the format option to "write" was present at that time. Thus if you get the Nov 2007 production release: http://www.cgl.ucsf.edu/chimera/download.html#production you should be all set to write mol2 files from the command line. There are also much newer "daily builds" although they are essentially untested and exist mainly to provide access to the very latest developments. Best, Elaine ----- Elaine C. Meng, Ph.D. meng@cgl.ucsf.edu UCSF Computer Graphics Lab and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco http://www.cgl.ucsf.edu/home/meng/index.html On Feb 7, 2008, at 11:32 AM, Ben Keshet wrote:
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