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
>
>
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