placement of metal ion in the protein model
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
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
Thank you for your advice... On Thu, Jan 24, 2013 at 7:25 AM, Elaine Meng <meng@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.htm...
...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
participants (2)
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Elaine Meng -
si yang