Oh thanks a lot! But returning to the thread question (ie, how to echo,
alert or prompt the distance results)...
This is the best I came up with but it does not work, and I cannot figure
out why:
var atomListN='4:A'
var atomListM='7:A'
set measurementUnits angstroms
set measurements 3
font measure 16 serif bold
var n = atomListM.length
for (var i = 2; i <= n; i++) {
script inline @{"measure @{{" + atomListN + ".ca/1.1}} @{{" + atomListM +
".ca/" + i + ".1}}"}
var j = i-1
prompt "DISTANCE: " + getProperty("measurementinfo[j].atoms[1].info") + "
AND " + getProperty("measurementinfo[j].atoms[2].info") + " = " +
getProperty("measurementinfo[j].strMeasurement")
}
measurementinfo[1] or whatever number works, but introducing the j does
not... I tried with double and single quotes, without quotes and everything,
I even tried to define j like @{i-1}
So which is the problem here?
I also have problem with atoms[i].model as I told you... It is always 1
Thanks again!
Daniel
2011/4/11 Robert Hanson <hans...@stolaf.edu>
> first, I would use double quotes in PHP, not single. Makes life a lot
> easier:
>
> $content .= "<td><script>
> jmolCheckbox(\"myfunction('$residue')\", .......... ";
>
>
>
> On Mon, Apr 11, 2011 at 4:52 AM, Daniel Carbajo
> <daniel.carb...@gmail.com>wrote:
>
>> Apart from the atoms[i].model problem, I always find trouble when passing
>> the variables from php to a function...
>> If I pass '104:A' like this:
>> $content .= '<td><script>
>> jmolCheckbox("myfunction(\' '.$residue.' \')", ..........
>>
>> How can I, inside the function, especify 104:A.ca as a variable that I can
>> use in the function? I try this:
>>
>> function myfunction(res){
>> var atoms="{" + res + ".ca}"
>> var n = atoms.length
>> var fileNameArray = getProperty("modelInfo.models.file")
>> for (var i = 1; i <= n; i++) {
>> atoms[i].label = "***%M - " + atoms[i].model + " - lig bin res
>> %n_%c_%r temperature=%b"
>> }
>> }
>>
>> But this obviously does not work... so which should be the correct way to
>> define "atoms" (104:A.ca) out of "res" (104:A)? Thanks!
>> Daniel
>>
>>
>>
> If you really need to do that, you have to use script inline or select:
>
> var atoms = "" + res + ".ca"
> script inline "atoms = {" + atoms + "}"
> # now atoms is that set of atoms
>
> or select can take a string as a variable:
>
> select @{"" + res + ".ca"}
> var atoms = {selected}
>
>
>
>
>
>>
>>
>>
>>
>>
>>
>>
>> 2011/4/8 Daniel Carbajo <daniel.carb...@gmail.com>
>>
>>> I am close to it but a strange things happens; I apply this on console
>>> when I have 3 proteins loaded (the native structure plus two homology
>>> models):
>>> var natmod = "MOD"
>>> var desc = "SS"
>>> var atoms = {104:A.ca}
>>> var info = "lig bin res"
>>>
>>> var fileNameArray = getProperty("modelInfo.models.file")
>>> var n = atoms.length
>>> if (desc == "SS"){
>>> var sarray = ["H","B","E","G","I","T","S","U"]
>>> for (var i = 1; i <= n; i++) {
>>> atoms[i].label = "***%M - " + atoms[i].model + " - " + info
>>> + " %n_%c_%r " + desc + ":" + sarray[atoms[i].temperature]
>>>
>>> }
>>> }
>>> else{
>>> for (var i = 1; i <= n; i++) {
>>> atoms[i].label = "***%M - " + atoms[i].model + " - " + info
>>> + " %n_%c_%r " + desc + ":%b"
>>>
>>> }
>>> }
>>> font label 14 serif bold
>>> color label black
>>>
>>>
>>> So I get correclty 3 atoms labeled, but atoms[i].model turns out to be 1
>>> in all three situations, I get the following labels:
>>>
>>> ***1.1 - 1 - lig bin res PHE_A_104 SS:H
>>> ***2.1 - 1 - lig bin res PHE_A_104 SS:H
>>> ***3.1 - 1 - lig bin res PHE_A_104 SS:H
>>>
>>> And so when I extract the file name I get always the same... (by the way:
>>> can I parse the file name removing everything before the last "/" and the
>>> ".pdb" at the end?). What am I doing wrong? I do not get it...
>>> Thanks!
>>>
>>
>>
>>
>> ------------------------------------------------------------------------------
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>>
>>
>
>
> --
> Robert M. Hanson
> Professor of Chemistry
> St. Olaf College
> 1520 St. Olaf Ave.
> Northfield, MN 55057
> http://www.stolaf.edu/people/hansonr
> phone: 507-786-3107
>
>
> 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
>
>
> ------------------------------------------------------------------------------
> Xperia(TM) PLAY
> It's a major breakthrough. An authentic gaming
> smartphone on the nation's most reliable network.
> And it wants your games.
> http://p.sf.net/sfu/verizon-sfdev
> _______________________________________________
> Jmol-users mailing list
> Jmol-users@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/jmol-users
>
>
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And it wants your games.
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