I guess a lot of this "bond set" business is not documented....
On Sat, Sep 18, 2010 at 3:41 PM, Robert Hanson <[email protected]> wrote:
> 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
>
--
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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