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

[C.J.]

Dear Dr. Meng,

Thank you for your help, the vdb format is good.
However, there is still some problem. When I opened vdb file and display
the surface, the resolution of vdb surface was lower than the one of pdb
surface.
Anther question is that I couldn't select the chain and color it using
command like "surface #0.1; scolor #0.1 color blue".
Am I missing something? Thank you!

Regards!
Jianhao Cao

Elaine Meng <meng at cgl.ucsf.edu> 于2018年9月19日周三 上午12:59写道：

> 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
>
>

-- 
Best regards!
C.J.
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