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
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