[Chimera-users] How can one create a sculpted view of a cellular assembly?

Tom Goddard goddard at sonic.net
Wed Jan 21 12:15:56 PST 2015


Hi Kenward,

  As Elaine points out you can do some fancy cut open views in Chimera now, although the user interface is difficult — requires that you know a lot about Chimera.  I’ve attached 3 images of the cellPACK HIV model cut open and here are the commands I used to do it.

  First I used menu File / Fetch by Id and entered cellPACK identifier HIV-1_0.1.6_6 to load an HIV virus model.  Then I held the ctrl key and drag selected a box having one corner at the center of the virus to select one octant.  This takes a long time — with my 2 year old Mac graphics it took 10 seconds for that selection to happen, older graphics will be slower still.  Then I hid all the selected molecules with command

	sop hidePieces sel

That command is "surface operation” hide the selected pieces.  That gave the first image I’ve attached.  In the second image I add back all molecules within 40 nm of the virus center.  First I place a marker at the virus center with command

	ac mz

This runs keyboard accelerator “mz” which puts a marker at 0,0,0 which happens to be the center of the virus.  Then I select everything within 400 Angstroms:

 	zonesel #1 400 #

Here the marker is model #1 (you can see this in Model Panel) — it says select everything in # (that is notation for all models) within 400 Angstroms of #1.  Then show those molecule surfaces:

	sop showPieces sel

This gives the second image.  Now I wanted to show the full HIV capsid core in the third image so I used:

	sop showPieces #0.23

because model #0.23 is the core capsid according to Model Panel.

  I have long thought we need simpler user interface to do these kinds of things.  I even think I added a feature request to our Chimera database for the fancy clipping mode you suggested where all surfaces that intercept the clip plane are shown in their entirety to give a bumpy clip surface.  We have been working on Chimera 2 a year and these kinds of features are more likely to bei put into Chimera 2 than in Chimera 1.

	Tom



> On Jan 21, 2015, at 8:51 AM, Elaine Meng  wrote:
> 
> Hi Kenward,
> Those suggestions all make sense for exploring and displaying a multicomponent structure.  In fact, the cellpack.org “use” page shows an HIV model depicted in other software that shows some of your suggested features:
> <http://www.cellpack.org/use>
> 
> This page also lists the available Cellpack models that you can open with Fetch by ID in Chimera 1.10.1 or daily build. Currently just HIV-1_0.1.6_6 but we expect additional ones soon.
> 
> Chimera does have some capabilities along the lines of your suggestions, but not fully.  Here’s what it has now (others, please chime in if I forgot anything):
> 
> (1) The Per-Model Clipping tool (in menu under Tools… Depiction) allows single-plane or slab clipping that only applies to a single model and also rotates with that model.  If you fetch the Cellpack model mentioned above, then in Model Panel choose to “ungroup,” you will see that all the different components of that HIV overall model are different models in Chimera that could be shown/hidden or per-model clipped separately.  The Cellpack component models are surface models in Chimera.
> <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/per-model/per-model.html>
> 
> (2) Although clipping will show parts of individual components, you can avoid that by instead selecting and hiding some subset of the surfaces, since each surface piece is selected as a whole. You can drag out selection areas with Ctrl-drag, then hide all the surfaces that were in that area with menu: Actions… Surface… hide.  The trick is to select only the surfaces that you really wanted to hide, as the drag will select all the stuff in the area.  I could first drag out a selection area, then subtract specific models from that selection, e.g. command: ~select #0.17
> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/selection.html#pickselect>
> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/select.html#newer>
> 
> (3) There is a Volume Eraser tool (under Tools… Volume Data) that lets you erase volume data (grid data, density maps mainly) within a spherical bubble that you can move around manually.  However, as the name suggests, it is for volume data, not surface models.  Similarly there are “vop” commands for chopping out octants of volume data.  
> <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/voleraser/voleraser.html>
> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/vop.html#cutoctant>
> 
> (4) Multiscale Models does allow selecting all like components (copies of the same molecule) so that they can all be shown/hidden at the same time.
> <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/multiscale/framemulti.html>
> 
> What you might need instead to implement your suggestions is a selection tool that selects surface pieces within a sphere, wedge, or other more complicated shape, or fancier set of controls specifically meant for working with Cellpack models.  
> 
> I hope this helps somewhat!  Good ideas, thanks!
> Elaine
> -----
> Elaine C. Meng, Ph.D.                       
> UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
> 
> 
> 
> On Jan 20, 2015, at 11:32 PM, Kenward Vaughan wrote:
> 
>> As I slowly approach the operational realization of my computational/visualization lab, I received your lovely holiday card. This seriously elevated my dreams of larger scale possibilities for chemistry and biology students through the cellPack resources.
>> 
>> In playing with it, I found myself wanting a more robust version of a clipping plane which would have several characteristics:
>> 
>> 3 dimensional - take a cell and hack out 1 or 2 adjoining octants relative to its center to give a sliced view similar to what is found in some texts (also often used in geology books to depict the earth's internal structure--see http://www.the-science-site.com/earths-interior.html for an example).
>> 
>> Being able to leave the nucleus alone while the surface strips away the cytoplasm would be cool, much like the referenced image above showing the core of the earth.  Likely a difficult one to actually implement?
>> 
>> Have the clipped surface not be flat, but rather allow a component to stay visible as the surface is moved past it until some determined relationship at which point it vanishes (perhaps when it has passed entirely through the clipping surface?). The clipped surface would thus show structure of a sort.
>> 
>> Have the choice of the clipping surface being static with the assembly (it could rotate with the assembly, keeping the same internal view), or separately static (how a clipping plane behaves now--as I know it--where rotating the structure causes things to move through the unmoving plane.
>> 
>> 
>> One approach I can imagine would be the use of a spherical or ellipsoidal (?) surface of specific size at a specific distance from the center of the cellular assembly.
>> 
>> 
>> Is this already implemented in a way that can be manipulated to achieve at least the major aspects of this effect (e.g. logical ANDing of clipping by 3 intersecting planes)?
>> 
>> Sorry for the long question... ;-/
>> 
>> 
>> Kenward
>> -- 
>> In a completely rational society, the best of us would aspire to be
>> _teachers_ and the rest of us would have to settle for something less,
>> because passing civilization along from one generation to the next
>> ought to be the highest honor and the highest responsibility anyone
>> could have.     - Lee Iacocca
>> 
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