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?

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.

Thanks for your time :-)

Rocco