[Chimera-users] merging 2 pdb files

Elaine Meng meng at cgl.ucsf.edu
Wed May 28 16:02:40 PDT 2014

Hi Adrian,
Yes, but how to do it depends on what exactly you are trying to do. Each file you open becomes a "model" in Chimera, so when you open 2 PDB files, you will have 2 models.  

If you want to make a covalent bond between the models so that their relative positions change, then you would need to use the "Join Models" tab in the Build Structure tool (in menu under Tools... Structure Editing). 

Otherwise if you just want to put all the atoms in one PDB file without bonding between the two structures or changing their relative positions:

(A) You can just write both models to one PDB file without making them into a single model.  It is an option in the Save PDB dialog (menu: File... Save PDB).

(B) You can merge the 2 models into one model (before saving PDB) using the "copy/combine" function in the Model Panel.  Open the two PDB files in Chimera, then show Model Panel (in menu under Favorites).  In the Model Panel, on the left side click-drag to choose both structures, then click the "copy/combine" button on the right.  There will be a dialog with some options.

There is also a "combine" command with the same options, but it may be easier to use the graphical interface mentioned above.

I hope this helps,
Elaine C. Meng, Ph.D.                       
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

On May 28, 2014, at 3:37 PM, Adrian Javaherian wrote:

> Hi,
> My name is Adrian. I am a graduate student at Bar Ilan University in Israel.  I have 2 pdb files, each containing rRNA sequences and I would like to combine the 2 to make 1 pdb file displaying all of the rRNA subunits.  I download the Chimera program.  Is it possible to do this on your program and if so, can you please tell me how?
> Thank you so much,
> Adrian

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