Hello, I would like to add HAEM group to a protein reconstructed from pdb data. I am working on Windows platform. Could you please help me how can I do that? many thanks Tamas
Hi Tomas, There is no reasonable way to do this using only Chimera. Here is one idea that includes Chimera but also text-editing PDB files: (a) go to the PDB web site find another PDB that already has HEM in it, if possible a protein related to yours, and open that in Chimera too. For example, your protein is open as model #0, and you open the other protein that includes a HEM residue as model #1. RCSB PDB web site: <http://www.rcsb.org/pdb/home/home.do> (b) superimpose the two structures so that the HEM is in the place you want to put it in your protein. Here is some discussion of different ways to superimpose structures in Chimera: <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/superposition.html> (c) choose "File... Save PDB" from the Chimera menu and save model #1 as a PDB file "relative to" model #0. Be sure to save it somewhere you can find it for the next step. <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/savemodel.html#pdb> (d) text-edit to create a new PDB file that has the HEM residue from the PDB file of model #1 that you just wrote, plus all the atoms (at least the atoms you want) from the original PDB file of model #0. This would give a fairly crude model of your protein plus HEM. 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 Feb 28, 2011, at 12:33 PM, ImRyLiBS9XN6ZXIgVGFt4XMi wrote:
Hello,
I would like to add HAEM group to a protein reconstructed from pdb data. I am working on Windows platform. Could you please help me how can I do that? many thanks Tamas
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On Feb 28, 2011, at 5:57 PM, Elaine Meng wrote:
Hi Tomas, There is no reasonable way to do this using only Chimera. Here is one idea that includes Chimera but also text-editing PDB files:
I think there is a Chimera-only way also. The first two steps would be the same:
(a) go to the PDB web site find another PDB that already has HEM in it, if possible a protein related to yours, and open that in Chimera too. For example, your protein is open as model #0, and you open the other protein that includes a HEM residue as model #1. RCSB PDB web site: <http://www.rcsb.org/pdb/home/home.do>
(b) superimpose the two structures so that the HEM is in the place you want to put it in your protein. Here is some discussion of different ways to superimpose structures in Chimera: <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/superposition.html>
At this point delete away the non-HEM atoms in model #1 with this command (show the command line with Favorites->Command Line): del #1 & ~:hem You may want to fine-tune your positioning by moving the HEM relative to your model (the "Active" check buttons in the Model Panel and at the bottom of the command line control which models move in response to the mouse). Also, you may want to adjust the torsion angles of the carboxylic acid groups by control-double clicking on a bond you want to rotate and choosing "Adjust Torsion". Then use Copy/Combine in the Model Panel to combine model 0 and model 1 into a single new model. You can then use File->Save PDB to save the combined model to a file. --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu
(c) choose "File... Save PDB" from the Chimera menu and save model #1 as a PDB file "relative to" model #0. Be sure to save it somewhere you can find it for the next step. <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/savemodel.html#pdb>
(d) text-edit to create a new PDB file that has the HEM residue from the PDB file of model #1 that you just wrote, plus all the atoms (at least the atoms you want) from the original PDB file of model #0.
This would give a fairly crude model of your protein plus HEM. 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 Feb 28, 2011, at 12:33 PM, ImRyLiBS9XN6ZXIgVGFt4XMi wrote:
Hello,
I would like to add HAEM group to a protein reconstructed from pdb data. I am working on Windows platform. Could you please help me how can I do that? many thanks Tamas
_______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
_______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
participants (3)
-
"dr. R�szer Tam�s" -
Elaine Meng -
Eric Pettersen