[Chimera-users] Editing mol2

Elaine Meng meng at cgl.ucsf.edu
Tue Nov 13 09:18:36 PST 2018

HI Francesco,
Chimera itself doesn’t use bond orders, and it has different atom types than the mol2 atom types which are traditionally from Tripos SYBYL.  However, as explained here, if you read in the structure as mol2 it will remember the bond orders and the Sybyl atom types and use them again when you write out the file:

Any added atoms and partial charges are also included.

However, for the parts that you modify or add after reading in the mol2, the Sybyl atom types and bond orders will be guessed when writing out a new mol2 file, so you may want to check in a text editor to see if you agree with those parts.

> On Nov 12, 2018, at 11:28 AM, Francesco Pietra <chiendarret at gmail.com> wrote:
> Hi Elaine:
> What I want to do is changing atom types and bond orders in a .mol2 file, to set that in order. So far, I did that, after workout with chimera modifying structure, by opening the .mol2 file with Jmol, which shows both the bond order and the atom type, and then editing manually the .mol2 file. However, I wonder whether this is a safe procedure.
> cheers
> francesco
> On Mon, Nov 12, 2018 at 5:37 PM Elaine Meng <meng at cgl.ucsf.edu> wrote:
> Hi Francesco,
> You can open a mol2 file and edit the structure (delete atoms, add atoms or functional groups, add hydrogens and charges, etc.) and then save another mol2 file.  I”m not sure that’s what you mean, though.
> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/savemodel.html>
> I hope this helps,
> Elaine
> -----
> Elaine C. Meng, Ph.D.                       
> UCSF Chimera(X) team
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
> > On Nov 11, 2018, at 12:44 PM, Francesco Pietra <chiendarret at gmail.com> wrote:
> > 
> > Hi all:
> > Is it possible editing .mol2 files with chimera?
> > thanks
> > francesco pietrta
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