[Chimera-users] How to modify a structure to put some atoms in a plane....

Elaine Meng meng at cgl.ucsf.edu
Thu Sep 12 09:00:15 PDT 2013

Hi Sergio,
I don't know what your starting point was, or what atom types are in your structure.   It is probably a matter of atom type, i.e. the carbon you want to be planar should be the Car type in Chimera.  You can check the atom types by showing them as labels, for example with commands:

labelopt info idatmType

If the carbon is not the Car type, you could specify that the carbon is trigonal with 3 bonds in the Modify Structure section of Build Structure (or change its atom type directly, for example with the setattr command) BEFORE adding the nitro group.  If you already had this whole structure with the nonplanar nitro group, it won't change it to planar.  You'd have to delete the nitro group, change the carbon atom type, then build it back on.

Actually I'd just fetch the structure (or something similar that you can later make small changes to) from Pub3D.  For example, I went to PubChem and searched for "nitroimidazole" and saw that 4-nitroimidazole is CID 18208, then used command:

open pubchem:18208

You could also use a SMILES string instead of PubChem CID, and either of these could be entered in the Start Structure section of Build Structure instead of in commands.

I should also mention Chimera minimization *is* appropriate for small organic molecules because it uses Antechamber to derive parameters for such molecules.  In fact, minimizing small molecules is often more effective than minimizing proteins because small molecules are less likely to get trapped in bad conformations that happen to be local minima.

I hope this helps,
Elaine C. Meng, Ph.D. 
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

On Sep 12, 2013, at 7:17 AM, Sergio Garay <sergio.alberto.garay at gmail.com> wrote:

> Hi all
> I'm trying to put a Nitrogen atoms of a Nitro group in the same plane that a imidazol ring, but until now with no success. I've tried using modify structure and changing the bond and geometry of the carbon to which the Nitrogen is joined, but it did not work. I attached an image with the problem. I've also tried to minimize the structure using AMBER ff (despite I know that this ff is not appropriate for small organic molecules) but it can fix the problem. May be I'm not clear enough so, I summarize: I want to put the Nitro group in the same plane of a imidazol ring (look at the picture, please). Any advice will be appreciated.

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