[Chimera-users] merging 2 pdb files

Adrian Javaherian aajavaherian at gmail.com
Wed May 28 16:04:14 PDT 2014


Thank you so much!!


On Thu, May 29, 2014 at 2:02 AM, Elaine Meng <meng at cgl.ucsf.edu> wrote:

> 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).
> <
> http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/editing/editing.html
> >
>
> 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).
> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/savemodel.html#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.
> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/modelpanel.html#combine>
>
> There is also a "combine" command with the same options, but it may be
> easier to use the graphical interface mentioned above.
> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/combine.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 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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