[Chimera-users] hem group

Eric Pettersen pett at cgl.ucsf.edu
Mon Feb 28 18:08:35 PST 2011

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 Pettersen
                         UCSF Computer Graphics Lab

> (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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