ps - I forgot to mention that this bond set syntax [{...}] makes it
unnecessary to use BOND in the select command:
select [{2}]
selects the third bond in the model.
On Tue, Jan 17, 2017 at 7:32 PM, Robert Hanson <hans...@stolaf.edu> wrote:
> If you know the ordering in the file, you can select them using the
> select BOND option, but that requires "atom/bond set" syntax:
>
> select bond ({0}) # first bond
> select bond ({1}) # second bond
>
> etc.
>
> Now, the trick here is that that syntax doesn't allow for variables. For
> example, you cannot say:
>
> select bond ({ i })
>
> HOWEVER, you can get around this by using a variable and setting the value
> using an *bond set*, using a which does accept variables:
>
> load $caffeine
> var colors = color("rgb").colors // just a nice list of colors -- you can
> make your own list
> for (var i = {*}.bonds.count; --i >= 0;) {
> var x = eval("[{"+i + "}]") // note that this bond-set syntax is
> 0-based. You must use eval() to create it.
> print " " + x + " " + @{colors[i + 1]} // arrays are 1-based
> select @x
> color bonds @{colors[i + 1]}
> }
>
> Bob
>
> On Tue, Jan 17, 2017 at 11:38 AM, Angel Herráez <angel.herr...@uah.es>
> wrote:
>
>> Hi Max
>>
>> Two issues here. One is the way to achive this in Jmol scripting. The
>> other is
>> to specify what you are expecting to achieve, i.e. which is your criteria
>> of
>> bond ordering + coloring.
>>
>> Atoms are indexed as the file is read, and so there is no issue: they
>> receive a
>> sequential number and you can refer to it. They also have many properties
>> associated to each atom.
>>
>> Bonds, on the one hand, have no properties attached to them except
>> thickness and color. On the other hand, it is not so easy to define their
>> ordering and indexing. Among other things, each bond "belongs" to 2 atoms
>> and each atom "has" several bonds, so what should their index/order be?
>> (We recently experienced a case: the same protein, when read from a pdb
>> file and when read from a cif file, has the same atom indexing in Jmol but
>> different bond indexing)
>>
>> I believe that yes, most probably you can iterate or loop over the bonds
>> collection and assign a color to each bond, read from your data file. But
>> still
>> the question is in which order those bonds will come, every time you have
>> a
>> new file.
>> What are you expecting in this regard when you define your color-data
>> file?
>>
>>
>> > Good question. Since in the case of coloring atoms by the partial
>> charge I don't need to specify
>> > the atoms, i.e, I think there is a direct correspondence of each line
>> of the file for each atom in the
>> > respective ordering,
>>
>> YES
>>
>> > I thought that in the case of bonds we would have the same kind of
>> > correspondence.
>>
>> NOT THE SAME (see above)
>>
>>
>> > I have checked in the manual that specific bonds can be selected by the
>> command "select[{i}]" or
>> > a set of bonds could be attributed to a variable by "x = {atomno <
>> 30}.bonds"
>>
>> Right, but that x will be a collection of bonds -- in which order, is
>> difficult to
>> anticipate.
>>
>>
>> > and I could change
>> > the color of the selected bonds to red, for example.
>>
>> That would mean all bonds attached to that atom get the same red color.
>> But each bond will also be attached to another atom, then which is the
>> last
>> color applied to it?
>>
>> So, in summary, I believe some of these "philosophical" or "logical"
>> questions
>> need to be answered before trying to find Jmol commands to do what you
>> want.
>>
>>
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>
>
>
> --
> Robert M. Hanson
> Larson-Anderson Professor of Chemistry
> St. Olaf College
> Northfield, MN
> http://www.stolaf.edu/people/hansonr
>
>
> 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
Larson-Anderson Professor of Chemistry
St. Olaf College
Northfield, MN
http://www.stolaf.edu/people/hansonr
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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