So what I am trying to do is the following: I have a native structure plus a
variable number of homology models. I want to measure all the distances
between a certain residue in the native structure, to its corresponding
residue in each model.
Instead of:
measure (1.1 and 46:A.ca) (not 1.1 and 46:A.ca)
Do:
foreach MODEL{
measure (1.1 and 46:A.ca) (MODEL and 46:A.ca)
}
where MODEL is 2.1, 3.1, 4.1...
All at once when clicking a checkbox.
The function you suggest is something similar to what I was thinking, but I
do not really know how to set it up.
Thanks again!
2011/3/24 Robert Hanson <hans...@stolaf.edu>
> 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
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>>> 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
>
>
> ------------------------------------------------------------------------------
> Enable your software for Intel(R) Active Management Technology to meet the
> growing manageability and security demands of your customers. Businesses
> are taking advantage of Intel(R) vPro (TM) technology - will your software
> be a part of the solution? Download the Intel(R) Manageability Checker
> today! http://p.sf.net/sfu/intel-dev2devmar
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>
>
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