[chimera-dev] suggestion for feature addition to chimera

Eric Pettersen pett at cgl.ucsf.edu
Wed Sep 9 13:53:14 PDT 2009

On Sep 4, 2009, at 5:09 PM, Rocco Varela wrote:

> Hello,
> I have a small suggestion for an additional feature for Chimera that  
> I think would be useful.  I often look at structures of multiple  
> small molecules, some artificial and some real, and I noticed  
> something interesting with the way Chimera writes mol2 files.
> Here is Scenario 1:
> 1) I open a mol2 file that contains multiple molecules flagged as  
> "separate" MOLECULEs.
> 2) I save the loaded file as mol2 and select "a single file  
> [combined @MOLECULE section]" for the "Save multiple models in"  
> option.
> 3) After saving and reloading this new mol2 file that now has a  
> single MOLECULE section, all the "names" of the previous molecules  
> have been lost. (ex. s-030, s-048, s-055, etc...) Instead in the  
> SUBSTRUCTURE section "UNK0" is used.
> It would useful if Chimera could name the components of the new  
> single molecule with the proper names.  I could easily write a  
> script to fix this after the fact but I thought it might be a useful  
> option for other people too?

Okay, I changed the Mol2 writer to use the model name instead of the  
residue type under the following conditions (only):

1) Combining models into a single @MOLECULE
2) All models are a single residue
3) Model names are unique and residue types are not

This change will be in tonight's build.

> Scenario 2:
> 1) Same as 1 above.
> 2) Now I want to save all the MOLECULEs in the file as separate mol2  
> files but with the proper "names" that are listed in the original  
> file loaded.  Currently the only option is to provide a common name  
> and to append the "model number".  It would be nice if we were  
> allowed to NOT provide a common name and allow it to name all the  
> files according to the molecule "names" not model numbers.

This seems like a reasonable enough request.  I will open a ticket in  
our Trac database for it, with you on the recipient list so you'll  
know when it gets done.  It's a tad more work than the preceding  
change because aside from adding code to support it, the interface has  
to be changed to allow for the option and the documentation has to be  
updated to describe it -- whereas the other change can sneak in under  
the radar. :-)


                         Eric Pettersen
                         UCSF Computer Graphics Lab

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