[Chimera-users] How to place a metal ion in protein model

Suneel N.A. leptolysin at gmail.com
Thu Jan 5 14:00:40 PST 2012

Hi Elaine
Thank you very much for the timely reply. I am glad to see it. The
information you sent was really helpful. Here are some of the details for
your suggestions/queries
(a) I used 1ZWX for homology modelling. The other closest models are 2DDR
and 3I5V. They are crystallised with bound metal ions.As you suggested I
will try to superimpose with the metal ion (though I am not that good in
using chimera).

I have  another query: I am trying to model a protein based on homology
modelling strategy. I came to know that Chimera can model the protein based
on the same strategy. When I attempted modelling using the Modeller tool of
chimera it gives me an error "Running modeller for  query via web service
failed; see reply log for more information. When I see the reply log :
Import modeller, Import error:No module named modeller".
Infact I even got the licence key from the modeller website and used it in
the dialogue box but still this error message is shown.

Another query is, for modelling a protein (whose structure is unknown) ,
how do we import the sequences into  chimera? In one of the chimera videos
on modelling, they show that the protein sequence is  imported/fetched from
Uniport. But in my  chimera software under the Fetch tab I don't see an
Uniprot option. In this regard please tell me how to import sequences.

Please do the needful. Will be looking for the reply.
Thanking you in anticipation
Yours Sincerely

On Wed, Jan 4, 2012 at 10:21 AM, Elaine Meng <meng at cgl.ucsf.edu> wrote:

> Hi Suneel,
> Chimera doesn't have a tool to predict metal binding sites from a
> structure.  There is a tool called "Add Ions" which will roughly place ions
> around a structure, but it is meant for adding counterions for simulation
> purposes and is ineffective for binding site prediction.
> First, I would consider the following:
> (a) what protein was used as the template for the homology model?  Does it
> bind metal? If so, the site is probably in the same place.  You could just
> superimpose the template (with metal ion included) and model structures to
> see the binding site.
> <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/superposition.html>
> (b) do you have any other data about which residues bind the metal?  You
> may be able to create a metal ion with Build Structure (under Tools...
> Structure Editing) and place the metal near the protein yourself,
> interactively, with the mouse.
> <
> http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/editing/editing.html
> >
> <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/mouse.html#activedef>
> (c) I believe there are several web servers that will try to identify
> metal-binding sites and other active sites from your uploaded protein
> structure.  I would recommend doing some literature or web searching to
> find these.  I have used some in the past, but it was a few years ago.
>  Here are some web server names to search for and try: PAR-3D, PDBSiteScan,
> PINTS, ProFunc, Protemot, SuMo
> Chimera has a Metal Geometry tool (under Tools... Structure Analysis), but
> it is meant to analyze the binding geometry of structures that already
> contain the metal ion, or to analyze the possibilities after you have
> manually placed the metal ion.
> <
> http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/metalgeom/metalgeom.html
> >
> Best,
> 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 Jan 2, 2012, at 1:36 AM, Suneel N.A. wrote:
> > Hi
> > Its my pleasure to introduce myself, I am  Suneel, graduate student from
> India. I am not a bioinformatician by profession but a eager aspirant of
> learning bioinformatics. I am new to Chimera, but as I started using it,
>  the desire for leraning Bioinformatics increased more and more. Chimera is
> such an awesome tool packed with so many options. I love it . I have small
> question for you.
> > I have a predicted the structure of protein using in silico tools (based
> on homology modeling). Literature sates that this protein binds to
> Magnesium. Now I would like to know if I can use chimera to place the metal
> in the modeled structure and prove/validate it based on metal geometry.
> > Please do the needful.
> > Thanking you in anticipation
> > yours sincerely
> > suneel
> >

*Suneel Narayanavari. A*
Graduate Student
Prof. Manjula Sritharan's Laboratory of Infection Biology
Department of Animal Sciences
School of  Life Sciences
University of Hyderabad
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