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

Sergio Garay sergio.alberto.garay at gmail.com
Thu Sep 12 11:59:37 PDT 2013

Thank you very much, Elaine!!

I followed the 2nd option to get a first approach of my molecule (take a
similar molecule from PUBMED). Of course, your answer it also helps me to
understand some topics about Build Estructure. I have to apologize for
saying that Amber (or Chimera minimizer) is not appropriate for small
organic molecules, what I wanted to say instead was that: there are other
FFs which treat the atom's interactions with some more details, like MM2.


On Thu, Sep 12, 2013 at 1:00 PM, Elaine Meng <meng at cgl.ucsf.edu> wrote:

> 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
> label
> 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.
> <
> http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/editing/editing.html
> >
> <
> http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/editing/editing.html#modify
> >
> 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.
> <
> http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/editing/editing.html#start
> >
> 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.
> <
> http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/minimize/minimize.html
> >
> I hope this helps,
> Elaine
> ----------
> 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.
> >

Sergio Garay
Dr. en Ciencias Biológicas
Facultad de Bioquimica y Cs. Biológicas
Universidad Nacional del Litoral
Santa Fe - Argentina
C.C. 242 - Ciudad Universitaria - C.P. S3000ZAA
Ph. +54 (342) 4575-213
Fax. +54 (342) 4575-221
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