Hi Bob,
Thank for the tips. I tried to run your script right now, but something
seems to be wrong with the color assignment. Jmol is returning the
following error message:
script ERROR: invalid argument
----
color bonds <<<<""
----
for ( var i = { all } . bonds . count ; -- i >= 0 ; )
I have tried the same script with a fixed color (red, for example) and the
script ran normally. I checked the manual and I found a reference to the
function "x=y.color" instead "something.colors", but I tested this former
option and it didn't work anyway. I also tried to assign a color from the
variable "var colors = color("rgb").colors" for a single bond selected
manually with "select bond ({2})" but the "color bonds" command do not
accept the argument for the color ("@{colors[5]}", for example). Do you
think that this problem could be related to the version of jmol? I am using
the version 14.6.3.
Besides this problem, I still could not see (in your script) how the colors
can be assigned based on the length or a difference in length as I have
mentioned in the previous message. Supposing that the variable
color("rgb").colors works, can it receive no integer numbers as argument?
2017-01-18 11:18 GMT-05:00 Robert Hanson <hans...@stolaf.edu>:
> 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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> ------------------
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