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, I thought that in the case of bonds we would have the same kind
of correspondence.
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" and I could change the color of the selected
bonds to red, for example. But I don't know how to use these commands to
associate the intensity of the color with the specific value of strain in
the data file. In this case, should I try a looping over the bonds for the
selection? Is there a keyword equivalent to "property_partialcharge" for
the case of bonds? Do you have some simple example to start with?
Thanks!
2017-01-17 11:39 GMT-05:00 Robert Hanson <hans...@stolaf.edu>:
> How are you determining which bonds go with which properties in your file?
>
>
> On Mon, Jan 16, 2017 at 10:14 AM, Max Pinheiro Jr <maxj...@gmail.com>
> wrote:
>
>> Dear Jmol team,
>>
>> I am trying to make a figure of a molecule in which the bonds are colored
>> by a RGB scale according to the values read from a data file. I have done
>> something similar to this idea in the case of coloring atoms by the value
>> of partial charges:
>>
>> x = load("charges.dat")
>> set propertydatafield 1
>> data "property_partialcharge @x"
>> {y>0}.label = load("charges.dat").split()
>> color property_partialcharge "bwr" range 0.7 1.3
>> write IMAGE PNG "color_by_charges.png"
>>
>> It worked pretty well in this case but I couldn't find a way to update my
>> script for the case of coloring bonds. I tried to use the "
>> property_bond_lengths" but it seems to have the same effect as in the
>> partialcharge. Is there a way to do such color maps of bonds in jmol? If
>> yes, could somebody, please, give me a suggestion of how to do that?
>>
>> I will be grateful for any help you can provide.
>>
>> All the best,
>>
>> Max Pinheiro Jr
>>
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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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