Eric, an interesting challenge with an amazingly simple solution.
Option 1: using CONNECTED(), select BONDS and color BONDS
load c6h6.smol
select bonds @{connected({_C},{_C},"aromaticDouble")}; color bonds yellow
select bonds @{connected({_C},{_C},"aromaticSingle")}; color bonds red
select bonds @{connected({_H},{_C},"single")}; color bonds blue
1) the CONNECTED function returns a bond set
2) the SELECT command can select bonds
3) the COLOR command can color selected bonds
Option 2: actually, you don't need the select business
load c6h6.smol
color @{connected({_C},{_C},"aromaticDouble")} yellow
color @{connected({_C},{_C},"aromaticSingle")} red
color @{connected({_H},{_C},"single")} blue
1) the CONNECTED function returns a bond set
2) the COLOR command can color bond sets
Note that you can create a bond set yourself. They are designated using
[{...}]
Var a = [{2 4 6}] # three bonds
color @a red
Bob
On Sat, Sep 18, 2010 at 1:17 PM, Eric Martz <[email protected]>wrote:
> 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
>
>
>
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--
Robert M. Hanson
Professor of Chemistry
St. Olaf College
1520 St. Olaf Ave.
Northfield, MN 55057
http://www.stolaf.edu/people/hansonr
phone: 507-786-3107
If nature does not answer first what we want,
it is better to take what answer we get.
-- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900
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