On 01/21/2015 12:15 PM, Tom Goddard wrote:
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. ...
Thank you both for the pointers and examples of approaches for doing this. I had not paid attention to the information about the objects being surfaces for Chimera. After assimilating Tom's suggested commands and playing a bit, what was created fits what I am looking for, and I'm ready to play further to expand on it. Some of the selection methods Elaine suggested will help with that. Thank you so much with this! I expect I may have a few more questions down the line, and appreciate knowing the tremendous resource you folks represent to me and others using this wonderful software. Kenward
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 <http://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): ...
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 ...
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