[Chimera-users] placement of metal ion in the protein model

si yang siyang13 at gmail.com
Thu Jan 24 20:45:42 PST 2013

Thank you for your advice...

On Thu, Jan 24, 2013 at 7:25 AM, Elaine Meng <meng at cgl.ucsf.edu> wrote:

> Hi Zhao Yang,
> If the predicted structure was based on a related protein structure that
> does contain the metal, you could superimpose your protein and the related
> protein, then save one of them as PDB "relative to" the other one, then
> text-edit to copy the metal ion from the related protein PDB file and add
> it to your protein's PDB file.  Here is more information on superimposing
> and saving structures:
> <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/superposition.html>
> <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/savemodel.html#pdb>
> Or, you could use Build Structure (in menu under Tools... Structure
> Editing):
> <
> http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/editing/editing.html
> >
> ...to add an atom (Start Structure section) and then change its element
> type to Zn (using the Modify Structure section).  When adding the atom, if
> you knew the desired X,Y,Z coordinates you could add it directly to the
> same model as your protein.  If not, you could add the atom as a new model
> and use the mouse to put it where you want it,
> <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/mouse.html#activedef>
> ...then combine the protein model and ion model into one model, for
> example with the "combine" command:
> <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/combine.html>
> See also this earlier answer to a similar question:
> <
> http://plato.cgl.ucsf.edu/pipermail/chimera-users/2012-January/007053.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 Jan 19, 2013, at 8:18 AM, si yang wrote:
> > Good day to you, currently i am using Chimera to do some bioinformatics
> analysis, i want to put zinc ion into my predicted protein structure at the
> known binding sites, but i try to insert :Tools/structure editing/add ion/,
> but the option did not consists of zinc ion, hence may i know what are the
> alternative ways to introduce the zinc ion in order to facilitate the
> downstream application such as docking??
> >
> > Hopefully can hear from you as soon as possible.... thank you
> > --
> > Zhao Yang

Tan Soo Huei
Department of Cell and Molecular Biology
Faculty of Biotechnology and Biomolecular Science
Universiti Putra Malaysia
43400, Serdang
Selangor, Malaysia
Tel: +6019-9155603
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