SELECTING HBONDS I would like to be able to color hbonds according to what they connect. I would like to be able to distinguish, for example, these categores of hydrogen bonds:
protein sidechain TO protein sidechain protein sidechain TO protein backbone protein backbone TO protein backbone protein TO water water TO water water TO DNA protein sidechain TO DNA sidechain protein backbone TO DNA backbone protein backbone TO DNA sidechain protein sidechain TO DNA backbone DNA sidechain TO DNA sidechain (Watson-Crick) DNA sidechain TO DNA backbone Conveniently, the hbonds command accepts two atom expressions. Thus, each of the above categories can be calculated separately. Yay! The problem arises in coloring what has just been calculated. I have not discovered any way to select the above subsets of atom pairs without selecting unwanted hbonds. For example, if I "select (protein and sidechain), (DNA and backbone)", the "color hbonds yellow", I am not only coloring the hbonds from protein-sidechain to DNA-backbone, but also the hbonds from protein-sidechain to protein-sidechain, and from DNA-backbone to DNA-backbone. I am aware of "set bondmode or" vs. "set bondmode and" but I don't see how these could help. Possible solutions: 1. IF "CALCULATE HBONDS" LEFT THE ATOMS IT CONNECTS SELECTED, THIS WOULD BE EASY. A slight complication arises when you want to color a subset of hbonds after selecting something else. When you repeat the "calculate hbonds (protein and sidechain) (DNA and backbone)" command, it adds no new hbonds if they are already in existence. IT COULD NEVERTHELESS SELECT THEM. Alternatively (and I think I would prefer this) the "calculate hbonds" command could delete, then recalculate hbonds. Currently, it appears to me that one must "hbonds delete" before "calculate hbonds" in order to re-calculate a set. 2. A "select hbonded (atom expression 1) (atom expression 2)" command would solve the problem in a more direct manner. At the same time, for similar purposes, a "select connected (...) (...)" would be useful for covalent bonds. Like "calculate hbonds", "connect" also accepts two atom expressions. There is already "select connected" and "select connected (atom expression)", but no option for a second atom expression. --------------- HIDING/DISPLAYING HBONDS I would like to have e.g. checkboxes that show and hide each of the above categories of hydrogen bonds. "hide hbonds" does nothing. "hbonds hide" is illegal. Am I missing the syntax here? Or do we need new code in Jmol to hide/display hbonds? If hiding and displaying is not available, I can do "hbonds delete" and start over from the beginning, recalculating for all the currently checked categories and colorings, but this is a bit cumbersome. Thanks, -Eric ------------------------------------------------------------------------------ Start uncovering the many advantages of virtual appliances and start using them to simplify application deployment and accelerate your shift to cloud computing. http://p.sf.net/sfu/novell-sfdev2dev _______________________________________________ Jmol-users mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/jmol-users
