[Chimera-users] using IDLE

Elaine Meng meng at cgl.ucsf.edu
Thu Feb 7 12:09:08 PST 2008

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/ 

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:


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.
Elaine C. Meng, Ph.D.                          meng at cgl.ucsf.edu
UCSF Computer Graphics Lab and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

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

More information about the Chimera-users mailing list