Hi Yeung,
You can save as many models/submodels as you want into one mol2 file.   
Choose File.... Save Mol2.  In that dialog there is an option to "Save  
multiple models in":
  a single file [individual @MOLECULE sections]
  multiple files [appending model number]
  a single file [combined @MOLECULE section]

If you choose "individual @MOLECULE sections", that means that when  
you read the file back into Chimera, all the models/submodels that you  
have now will be submodels in that newly opened model.  If you choose  
"combined @MOLECULE sections" that means when you read the file back  
into Chimera, all the models you have now will be one giant model.  It  
sounds like you want "individual".
<http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/savemodel.html#mol2>

Best,
Elaine
-----
Elaine C. Meng, Ph.D.                          meng@cgl.ucsf.edu
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco
                     http://www.cgl.ucsf.edu/home/meng/index.html



On Dec 1, 2008, at 4:34 AM, CHIU,YEUNG wrote:

Dear friends,

Hello! I'm wondering how many models and submodels in all can

Chimera save into one single mol2 file? Right now I can have

models only 0-9 into one single mol2 file. I think I'm going to

use submodels, but how can I generate them? For instance, if I

have a brunch of pdb files which contain one molecule each, I'd

like to combine them into one mol2 file, which has a submodel

corresponding to each molecule. (If this statement of the problem

is not clear enough, please let me know).

Thank you for your help and sorry to bother the others. Best

wishes.

Sincerely yours

CHIU,YEUNG

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