Hi Olivia, I made ChimeraX open .vdb files, in tomorrow's daily build. It opens the the vdb file and uses the sym #N i222 command to show the 60 fold symmetry. Tom
On Aug 24, 2021, at 9:34 AM, Tom Goddard <goddard@sonic.net> wrote:
Hi Olivia,
The Virus Particle Explorer .vdb files are just normal PDB files where the coordinates have been adjusted so the icosahedral virus capsid is centered at 0,0,0 and has a standard orientation. You can open it in ChimeraX with
open ~/Downloads/7rk8.vdb format pdb
and you can display the full capsid then with
sym #1 i222
That symmetry command applies icosahedral symmetry with 2-fold symmetry axes along x, y, z and just renders the asymmetric unit 60 times. If you really want 60 copies of the asymmetric unit so that you can select or color each copy individually you would instead use
sym #1 i222 copies true
As Elaine points out you can also open the structure directly from the PDB, and show the capsids, for example,
open 6mzx sym #1 assembly 1
Tom
On Aug 24, 2021, at 8:39 AM, Elaine Meng via ChimeraX-users <chimerax-users@cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu>> wrote:
Hi Olivia, You must be mixing up Chimera and ChimeraX ... they are two different programs!
For the others on the list: at the Virus Particle Explorer db, you can download crystal structures as "VIPER Coordinates" and that gives the file with the *.vdb file extension. E.g. from the Downloads menu on this page: <http://viperdb.scripps.edu/Info_Page.php?VDB=1rb8 <http://viperdb.scripps.edu/Info_Page.php?VDB=1rb8>>
In Chimera you can open a file ending in *.vdb directly. Although the file is actually PDB format (.pdb) it also contains information that Chimera uses to automatically generate the entire capsid from the single subunit coordinates in the file, using the Multiscale Models tool. Chimera documentation on this input file type: <https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/filetypes.html#object <https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/filetypes.html#object>>
If you want to stick with Chimera, there is a separate list for asking questions: chimera-users@cgl.ucsf.edu <mailto:chimera-users@cgl.ucsf.edu>
ChimeraX does not know the *.vdb suffix. You could change the filename to end in .pdb instead and just open it as a regular PDB file but that would just show the single subunit. Here are the file types ChimeraX knows: <https://rbvi.ucsf.edu/chimerax/docs/user/commands/open.html#formats <https://rbvi.ucsf.edu/chimerax/docs/user/commands/open.html#formats>>
If you want to use ChimeraX, rather than trying to figure out how to make the capsid from the file that was renamed from .vdb to .pdb, it would be simpler to just get that same entry from the PDB databank itself instead, e.g. command
open 1rb8
... that gets the structure in mmCIF format along with its symmetry information, and the Log will automatically show this table (see image attached below) in which you can click the "1" link to generate the whole capsid.
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Aug 24, 2021, at 7:44 AM, Olivia Leland via ChimeraX-users <chimerax-users@cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu>> wrote:
Hello,
I’m trying to upload a .vdb file from the Virus Particle Explorer databank. To my understanding, I should be able to upload a .vdb file for visualization. Every time I try to open said file, however, it returns the error:
<Screen Shot 2021-08-24 at 10.35.11 AM.png>
Is there a setting I haven’t activated in order to upload this file properly? Additionally, I’m unable to connect the software to the internet so I can’t use File>Fetch By ID... (it won’t show up for me) <Screen Shot 2021-08-24 at 10.36.41 AM.png>
Do you have any suggestions on how to fix this?
Best,
Olivia Leland (she/her)
Doctoral Student || Fraden Lab Martin A. Fisher School of Physics Brandeis University Waltham, MA 02453
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