I would just do it in Jmol script. Why JavaScript? What exactly are you
trying to do? Get the distances from model one of a certain group to all the
other models? Seems to me it would be something like this:
function crossMeasure(groupNumber) {
Var n = {*}.modelIndex.max
for (Var i = 1; i<= n; i++) {
measure {*.ca and modelindex=0 and resno=groupNumber} {*.ca and
modelindex=i and resno=groupNumber}
}
}
On Thu, Mar 24, 2011 at 10:13 AM, Daniel Carbajo
<daniel.carb...@gmail.com>wrote:
> I see... I guess it should be a javascript function that takes as
> parameters the residue of interest in the native protein and the residue of
> interest in each of the protein homology models... then the function should
> be a foreach that runs the measure command for the native residue against
> one of the model residues at a time, isn't it?
> I am having problems though when passing this parameters... I am trying
> something like this (it is a checkbox, and the number of protein homology
> models is variable, and I should take only the displayed ones, cause some
> others might be hidden):
>
> <input type="checkbox" id="check_MAP_CREDO" onClick='var
> natMAP=jmolScriptWait("select 1.1 and $select_native_residue.ca;");
> JmolCrossMeasure(natMAP)'>
>
> JmolCrossMeasure is just an alert for now:
> function JmolCrossMeasure(x) {
> alert(x);
> }
>
> It and it shows all this:
> 2,scriptStatus,0,script 2 started
> 3,scriptStatus,0,Script completed
> 5,scriptStatus,0,Jmol script terminated
> 4,scriptTerminated,1,Jmol script terminated successfully
> 1,scriptStarted,2,select 1.1 and visible and 48:A.ca;
>
> I would need the output of the selection, only 48:A.ca/1.1 or something
> like that, how can I do it so I can pass it to the javascript function?
> Thanks
>
>
>
>
> 2011/3/24 Robert Hanson <hans...@stolaf.edu>
>
>> measureAllModels was designed to allow the same measurement WITHIN a model
>> to be applied to all models. So it isn't designed to do cross-model
>> measuring. You'll have to set up a little function yourself to do that.
>>
>>
>> On Thu, Mar 24, 2011 at 7:05 AM, Daniel Carbajo <daniel.carb...@gmail.com
>> > wrote:
>>
>>> Hello everybody,
>>> I have a little problem when measuring distances between C-alphas of
>>> residues belonging to different proteins.
>>> I have 3 proteins loaded (each with just one model, so: 1.1, 2.1 and
>>> 3.1), the first one is a native protein, and the other 2 are homology models
>>> for this protein.
>>> My objective is to measure the distance between a residue of the native
>>> protein (let's say residue 46, chain A) and the same residue in the 2
>>> models, at once.
>>>
>>> If I do:
>>> set measureAllModels ON; set measurementUnits angstroms; measure (1.1 and
>>> 46:A.ca) (not 1.1 and 46:A.ca)
>>> I get the output:
>>> measurementUnits = "angstroms"
>>> [[ASP]46:A.CA/1.1 #338, [ASP]46:A.CA/2.1 #362, 9.81 Å]
>>>
>>> As expected, it measures just between the native protein and the first
>>> model (the first occurrence of the second atom expression). So I need to use
>>> "set measureAllModels ON".
>>>
>>> But if I do:
>>> set measureAllModels ON; set measureAllModels ON; set measurementUnits
>>> angstroms; measure (1.1 and 46:A.ca) (not 1.1 and 46:A.ca)
>>> I get the output:
>>> measureAllModels = true
>>> measureAllModels = true
>>> measurementUnits = "angstroms"
>>> [[ASP]46:A.CA/1.1 #338, [SER]49:A.CA/1.1 #362, 9.27 Å]
>>> [[ASP]42:A.OD2/2.1 #338, [ASP]46:A.CA/2.1 #362, 14.85 Å]
>>> [[ASP]42:A.OD2/3.1 #338, [ASP]46:A.CA/3.1 #362, 11.89 Å]
>>>
>>> But I expect an output like:
>>> measureAllModels = true
>>> measurementUnits = "angstroms"
>>> [[ASP]46:A.CA/1.1 #338, [ASP]46:A.CA/2.1 #362, 9.81 Å]
>>> [[ASP]46:A.CA/1.1 #338, [ASP]46:A.CA/3.1 #362, x.xx Å]
>>>
>>>
>>> What am I doing wrong?? Where do these 49:A.CA/1.1, 42:A.OD2/2.1,
>>> 42:A.OD2/3.1 atoms come from if they do not meet the atom expression stated
>>> above???
>>> Thanks a lot for your help,
>>> Daniel
>>>
>>>
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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
>>
>>
>> ------------------------------------------------------------------------------
>> Enable your software for Intel(R) Active Management Technology to meet the
>> growing manageability and security demands of your customers. Businesses
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>>
>
>
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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
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