Hi Bob,
The problem that still persist is how to use the values bond lengths to
assign the colors for each bond. I included a new variable to get the bond
length inside the for loop: y=x.bonds.length. However, I think the variable
colors[ ] just accept integer values, right? So, one possibility that I
check is to convert the bond length into an integer using "% 0". But in
most of the cases it is necessary to rescale the bond length to get more
decimal places before to convert into an integer. When I tried to run the
script with the values of bond length times 100 and rounded, this variable
used as argument to the colors fall out of the range. Do you have any other
idea of how to use the bond length as an argument for the colors()? The
script updated with the information of bond length is the following:
load $caffeine
var colors = color("rgb").colors // just a nice list of colors -- you can
make your own list
x=color("rwb", -3, 3)
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.
*y = ((x.bonds.length)*10) % 0* // convert the bond length into an
integer value with two digits
print " " + x + " " + y + " " + @{colors[y]} // arrays are 1-based
select @x
color bonds @{colors[y]}
}
I will appreciate any help on this issue.
Thanks!
2017-01-18 22:13 GMT-05:00 Max Pinheiro Jr <maxj...@gmail.com>:
> 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.
>>>>>>
>>>>>>
>>>>>> ------------------------------------------------------------
>>>>>> ------------------
>>>>>> Check out the vibrant tech community on one of the world's most
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>>>>>> _______________________________________________
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>>>>>> https://lists.sourceforge.net/lists/listinfo/jmol-users
>>>>>>
>>>>>
>>>>>
>>>>>
>>>>> --
>>>>> 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
>>>>
>>>>
>>>> ------------------------------------------------------------
>>>> ------------------
>>>> Check out the vibrant tech community on one of the world's most
>>>> engaging tech sites, SlashDot.org! http://sdm.link/slashdot
>>>> _______________________________________________
>>>> Jmol-users mailing list
>>>> Jmol-users@lists.sourceforge.net
>>>> https://lists.sourceforge.net/lists/listinfo/jmol-users
>>>>
>>>>
>>>
>>> ------------------------------------------------------------
>>> ------------------
>>> Check out the vibrant tech community on one of the world's most
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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
>>
>>
>> ------------------------------------------------------------
>> ------------------
>> Check out the vibrant tech community on one of the world's most
>> engaging tech sites, SlashDot.org! http://sdm.link/slashdot
>> _______________________________________________
>> Jmol-users mailing list
>> Jmol-users@lists.sourceforge.net
>> https://lists.sourceforge.net/lists/listinfo/jmol-users
>>
>>
>
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