[Chimera-users] How to generate submodels in a mol2 file in Chimera?

Eric Pettersen pett at cgl.ucsf.edu
Mon Dec 1 10:23:19 PST 2008

To supplement Elaine's answer:  you can have model numbers higher than  
9.  The command line interface only shows buttons for models 0-9, but  
you can have models 10+, there just aren't buttons for them.  They can  
still be referenced in commands (e.g. #13) and will show up in the  
Model Panel.


                         Eric Pettersen
                         UCSF Computer Graphics Lab

On Dec 1, 2008, at 10:16 AM, Elaine Meng wrote:

> 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 at 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
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> Chimera-users at cgl.ucsf.edu
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