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

[Elaine Meng]

Hi CJ,
By default, when the VIPERdb file is opened and the capsid is generated using icosahedral symmetry, only the first copy of the protein is loaded as atoms, and the others are just drawn with lower-resolution surfaces.  

The Multiscale Models dialog also appears automatically.  In that tool you can 
- Select chains “All”
and then do a bunch of other things to them, for example
- to show high-resolution surfaces, change Resolution to 0 and click “Resurface”

The first copy is still shown as ribbons.  If you want to show that first copy as surface too, (while everything is still selected), choose Style “Show… Surface”  in the Multiscale Models dialog.

Although you can use scolor on the model (it makes a separate model, see the Model Panel), you probably don’t want to do that since it colors the entire capsid, even if you select just one subunit and use “scolor sel [etc.]”  Instead you would use the Multiscale Models dialog to select and color the subunits.  If you Ctrl-click to select one subunit, you can use Extend “Copies” in that dialog to increase the selection to all of its symmetry copies.

Many other things can be done with the Multiscale Models tool, just click Help on that dialog to see its manual page, or view the copy at our website here:
<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/multiscale/framemulti.html>

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 8:03 PM, C.J. <biocjh at gmail.com> wrote:
> 
> 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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