Frieda wrote: > Do these links start to get into the type of thing that would restrict > your development efforts, Miguel? Obviously I do not wish to do that. I > have little feel for it beyond your not using Chime and not having it > installed on your machine- which you have clearly stated. > > If it does get into a gray area, perhaps you could show us what solid > sphere rendering looks like in Jmol, so we can comment.
I am not sure exactly what you are asking ... but I will put some energy into this. > Previously, Miguel had said: > >> One of the problems I have had with slab is the various "slabbing >> modes". It is difficult for me to render a solid sphere that has had >> the front of it sliced off. I now have an idea of how to do this in a way that may not be difficult. >> And when it gets past the midpoint these >> turn into solid circles. Not difficult to implement, but rather ugly >> to my eye. > > Hmm, I don't think the Chime solid sphere slab is at all displeasing, The ugliness that I was referring to was specifically 'after it gets past the midpoint'. That is, when you are on the back side of the sphere and it starts shrinking. When that happens there is no shading ... everything is the same solid color. > so I imagine that the Jmol version looks rather different... I guess > the only point of showing it to us in Jmol would be if it could somehow > be modified using our suggestions, or implemented as an optional > slabbing mode. I'll put something together for you. >> It seems to me that perhaps one would want the slabbing mode to be >> different when working with large molecules as opposed to small >> molecules. That is, with large molecules it may be better for atoms to >> disappear completely rather than get sliced away. >> >> Q: What slabbing modes are useful when working with large molecules? >> >> Q: What slabbing modes are useful when working with small molecules >> (or zoomed in on a piece of a large molecule) ? > > For large molecule viewing, having atoms disappear would be superior to > having the empty circle (bubble) appearance that is the current > default. I understand that noone likes the current slab behavior. > But I would have to see it in action to say if it could really > live up to the clarity of a solid face rendering as I know it. > > I don't work much with small molecules so I can't really comment on > that. When working with a somewhat small section of a protein, such as > a beta sheet, or alpha helix (still a far cry from a typical "small > molecule" I think) I found that the solid face rendering continued to > be very useful. > > Are there any other choices for rendering slab besides the bubble, > solid sphere, and disappearing act? For sphere rendering, the bubble is dead ... or should I say 'burst' I will implement a solid hemisphere. Once you get past the center of the atom, it will disappear completely. We will defer further discussion until I implement that and people can take a look at it. Miguel ------------------------------------------------------- SF.Net email is sponsored by: Discover Easy Linux Migration Strategies from IBM. Find simple to follow Roadmaps, straightforward articles, informative Webcasts and more! Get everything you need to get up to speed, fast. http://ads.osdn.com/?ad_idt77&alloc_id492&op=click _______________________________________________ Jmol-users mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/jmol-users
