[Chimera-users] change the center of a pdb model

[Elaine Meng]

Dear Jianhao Cao,
For atomic coordinates (PDB files) I don’t think it is as simple as saying “put the particle centers in the same place” — you would need to match or superimpose the structures somehow. The center of the particle is not necessarily the same as the origin coordinates (0,0,0). Methods to superimpose structures include manually translating and/or rotating one structure while the other one is frozen in place, but it can be difficult, especially if rotation is needed.  If it is only translation, the “move” command can be used.
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/superposition.html>
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/mouse.html#activedef>
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/move.html>

However, if you open the icosahedral capsid structures from the VIPER database instead of from PDB directly  (e.g. use Chimera menu: Fetch by ID and use database “VIPERdb” with the same IDs as PDB database) I believe those are already transformed into a common reference frame.  That should be the easiest, and includes structures that have been deposited in the PDB.

You can also go to the VIPERdb directly and check there: 
<http://viperdb.scripps.edu/main.php>

If your structures of interest are not deposited in the PDB or are not in VIPERdb for some other reason, however, you’d have to go to a more complicated approach.
I hope this helps,
Elaine
-----
Elaine C. Meng, Ph.D.                       
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco

> On Sep 18, 2018, at 5:48 AM, C.J. <biocjh at gmail.com> wrote:
> 
> Dear specialists,
> When I opened two pdb files of icosahedral model(two structures of the same virus), I found both center didn't overlap. My question is how to change the origin of a pdb model to overlap both. Thank you!
> -- 
> Best regards!
> Jianhao Cao