open 2xxx; light full - Bug or feature for PDB ID numbers starting with "2" ?

[jsgro@…]

Greetings,


Once in a while, for a few months now, I fetch and open the new ChimeraX software to get used to the new interface and also enjoy the beautiful renderings with ambient occlusion.


But something baffled me a lot (till today)  from the very first example on the ChimeraX Quick Start Guide<http://www.rbvi.ucsf.edu/chimerax/docs/quickstart/index.html>:


The first command open 2bbv; light full


It works great and looks great, just like on the tutorial page, with nicely rendered spheres.

It reminds me of my early days with visualizing Black Beetle Virus with Frodo on an Evans and Sutherland, long time ago!


Since I have worked a lot with virus structures I then called the easy rhinovirus 14 structure name that I remembered:

open 4rhv; light full

But then, every time, rather than the sphere, I get the ribbon diagram.


Then I tried others: 1opo, 4dpv, 1js9, 1aym all getting ribbon displays.


Then I wondered if the "2" in 2bbv was making a difference...


So I first called the old version of canine parvovirus "2dpv" (the new one,  4dpv had given the ribbon display) - and what do I get: a stick model !


Checking in PDBs for viruses that start with "2" I then find "2btv" for blue tongue...

And: I see the rendered spheres!


Another with 2:  2w0c (bacteriophage PM2) and ... rendered spheres!


SO it seems that IF the PDB code starts with 2, one gets spheres, otherwise ribbons (and some odd case stick model!)


Is this a "bug" or some odd feature ?


AHHHH BUT now I open poliovirus "2plv" and I get... ribbons !!!!


open 2e0z; light full : ribbons


And now, the first "non -2" to get spheres....West Nile Virus: open 3iyw; light full

and it starts with a "3" (First one showing sphere that did not start with a "2")


So now my theory of "2s" is debunct.... and I am still very confused... as to what the "default" view should be.


Thanks for any hint/feedback on this behavor!

Sincerely,

Jean-Yves Sgro


Jean-Yves Sgro, Ph.D.

Distinguished Scientist | Senior Scientist

Biotechnology Center<http://www.biotech.wisc.edu/services/brc/workshop>      | Biochemistry Department<https://biochem.wisc.edu/bcrf>

University of Wisconsin-Madison - USA

Email: jsgro@wisc.edu

Formerly at the Institute for Molecular Virology

- VirusWorld web site<http://www.virology.wisc.edu/virusworld/viruslist.php> -

[Eric Pettersen]

Hi Jean-Yves,

ChimeraX makes a best guess as to what depiction will be most informative and responsive for newly opened structures. The criteria is the number of chains, namely:

no chains: stick
1-4 chains: ribbon
5+ chains: space filling

Apparently ChimeraX finds no chains in the obsolete mmCIF version of 2dpv -- must have been a bad file. If you open the PDB version ("open 2dpv format pdb") then it shows as ribbons.

We intend to allow user control over the initial depiction, but haven't gotten there yet. To get from a ribbon depiction to the space-filling one, in the upper toolbar click on the ribbon outline to remove the ribbon, on the gray sphere to show atoms (in this case, sticks), on the red-gray-blue sphere molecule to show spheres, and on the purple+pink molecule to color by chain. Phwew! :-)

--Eric

Eric Pettersen
UCSF Computer Graphics Lab