As I said, the version of jmol I am running is the 14.6.3 of 2016-09-18. I
ran your script again using the cafeine molecule loaded directly from jmol
(File -> Get MOL), and, in this case, all bonds are colored as expected.
However, the same script has no effect when I run it over my xyz file. I
see that the jmol recognize the single and double bonds when loading the
cafeine structure but in my case this not happen because I am loading a xyz
file, I think. Is there some additional step missing in the case of xyz
files?
2017-01-18 13:33 GMT-05:00 Robert Hanson <hans...@stolaf.edu>:
> What version of Jmol are you running? Should be no problem running that
> exact script. Just did it again now.
>
>
>
>
> On Wed, Jan 18, 2017 at 11:44 AM, Max Pinheiro Jr <maxj...@gmail.com>
> wrote:
>
>> 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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>
>
> --
> 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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