It would be useful to be able set separate surface properties for the interior of opaque closed surfaces that have been made visible by the clipping planes set in Per-Model-Clipping. These are normally backface polygons.

This could be complicated to implement in a general way. In my opinion, that's probably not necessary. The only feature that I really pine for is the ability to make the interior surface darker/lighter than the exterior surface. Perhaps a slider could be added to Per-Model-Clipping tool that allows the user to make the backface polygons darker or lighter than the regular polygons. (Perhaps the default should be about 25% darker. That would look pretty and I hope it would be easy to add.)

Another feature that would be useful is the ability to make the closed surfaces look solid so that when you cut into them, instead of seeing the interior, a polygon face is added to close the surface and make it look like a solid object. (For example, lighter-colored surfaces in the cartoon: http://www.biochem.mpg.de/hartl/mhartl/index.html

I realize these features should be low on the priority list. Maybee a quicky feature to implement when you get board working on the slow, difficult, useful stuff. Cheers!

Andrew

On Fri, 25 Feb 2005, Andrew Jewett wrote:

Hi. Please forgive me for sending this message twice. In the first version, I forgot to include a subject line, so I'm sending it again.

---

On Fri, 25 Feb 2005, Thomas Goddard wrote:

...

chimera-users@cgl.ucsf.edu

When using the Per-Model-Clipping tool and selecting which model to apply the clipping to, there should be an option "All Models", and it should be the default option.

Without this feature, some unintended results can happen. Suppose the user generates a surface either with MSMS or multiscale. If the user then uses the menu to select Tools->Graphics->Per-Model-Clipping The default model is the one with the atoms and bonds, not the surface model. When the user moves the clipping plane it will seem like nothing is hapenning.

The user has to be quite attentive to realize that they have to select the surface model from the list. It would be better to have an "all models" option that is the default.

Thanks Cheers!

Andrew

Hi Andrew, I want to supplement Tom's answer a little bit. He didn't really emphasize that the capping stuff he wrote works interactively -- as you move the clip plane around the cap adjusts, maintaining the illusion of cutting through a solid. Having the interior of a surface look different from the exterior has been on Greg's "to do" list for a while now. It still seems worthwhile despite the capping extension since there are times you might want to "cut through" a surface to expose the underlying structure. At any rate, there are a lot of things on Greg's to-do list, so I don't know when he'll have time to get to this.

--Eric

On Mar 1, 2005, at 9:38 AM, Thomas Goddard wrote:

Hi Andrew,

We have already implemented capping of clipped surfaces. When you cut the surface with a clip plane it appears solid. The cap can be made a different color, or you can colormap volume data onto it. This is not yet released, but we plan to make a snapshot within 2 to 3 weeks that will include it. It only works for molecular, volume and multiscale surfaces, not ribbons, spheres or other molecular model representations.

The phage T4 slab in the Chimera image gallery illustrates the capping. Also the semliki forest virus images shows it.

http://www.cgl.ucsf.edu/chimera/ImageGallery/

If you have the above capping is it still important to have different interior and exterior surface colors? We added the capping because views of the interior of a surface don't seem very useful.

Tom _______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users