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Re: [Jmol-users] problem with "set measureAllModels ON"
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From: Robert H. <ha...@st...> - 2011-03-29 13:04:54
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OK, I see. Right, now I understand the $ business -- these are PhP
substitutions. I see you need to identify these atoms by standard RasMol
format. That changes everything! You can't do this:
measure @a @ b
where a = "39:A.CA/1.1" and b = "40:A.CA/2.1"
what you have to do instead is create the entire measure command as a
string and then execute it, like this:
script inline @{"measure {" + a + "} {" + b + "}"}
Minor comment: I would put the set and font commands earlier, out of the for
loop; no need to repeat those.
If you have a reference atom and then a list of atoms from different models,
I think the function would be this, provided you create an array of strings
that look like ["35:a.ca", "36:b.ca","36:b.ca",...] that has the reference
atom in position 1, and the target atoms in :
function crossMeasure(atomList){
var n = atomList.length
measures delete
set measurementUnits angstroms
set measurements 3
font measure 16 serif bold
for (var i = 2; i <= n; i++) {
script inlne @{ "measure {" + atomList[1] + "/1.1}{" + atomList[i] +
"/" + i + ".1}" }
}
}
Or maybe, if the homology models all have the same group, just:
function crossMeasure(atom1, atom2){
var n = atomList.length
measures delete
set measurementUnits angstroms
set measurements 3
font measure 16 serif bold
for (var i = 2; i <= n; i++) {
script inlne @{ "measure {" + atom1 + "/1.1}{" + atom2 + "/" + i +
".1}" }
}
}
Bob
On Mon, Mar 28, 2011 at 5:00 AM, Daniel Carbajo <dan...@gm...>wrote:
> Thanks a lot! Sorry for not answering before, I have been away during the
> weekend... So this seems it should work. I indeed use Jmol.js, but the atoms
> are preselected (they are C-alphas from residues known to be catalytic by
> the Catalytic Site Atlas) and, actually, the corresponding residue number
> (and even the atom number) might not be the same between the native
> structure and the homology models (but it will be the same in all homology
> models), so I modified the function like this:
>
> function crossMeasure(atomListN, atomListM){
> var n = atomListM.length
>
> measures delete
> for (var i = 2; i <= n; i++) {
> set measurementUnits angstroms
> set measurements 3
> font measure 16 serif bold
> measure @{atomListN[1]} @{atomListM[i]}
> }
> }
>
> So the parameters passed will directly be something like "4:A.ca" and
> "6:A.ca" ($selectedRES_native and $selectedRES_models).
> I save the functions in myfunctions.spt, I call it when I launch the applet
> and it seems to launch properly, but when I try to load the models (that are
> loaded one by one after launching the applet via a series of checkboxes) I
> get an alert saying "could not find applet jmolApplet0" and the models do
> not show up. This is how I launch the applet:
>
> $JMOL = "<script type=\"text/javascript\">
> jmolInitialize(\"Jmol-12new\", true);
> jmolSetAppletColor(\"white\");
> var jmolcmds = [
> \"load $ZIPtoUSE|Models_$code/$pdb.pdb\",
> \"set frank off; select all; hbonds off; spin off;
> wireframe off; spacefill off; trace off; set ambient 40; set specpower 40;
> slab off; ribbons off; cartoons off; label off; monitor off\",
> \"set showAxes true\",
> \"set appendNew true\",
> \"frame all\",
> \"display all\",
> \"select 1.1; cartoon; color white\",
> \"select 1.1 and :$cadena; color red\"
> ];
> jmolApplet([580,580], jmolcmds.join(\"; \"), \"script
> myfunctions.spt\");
> </script>";
>
> Do I have to place myfunctions.spt in a particular place? What am I doing
> wrong? Thanks again for all your help Bob and everyone in the list!
> Cheers,
>
> Daniel
>
>
>
>
>
> 2011/3/25 Robert Hanson <ha...@st...>
>
>> OK, that's Jmol scripting, not JavaScript. Are you using Jmol.js for your
>> page (I hope)? How are you choosing the atoms -- is it a user click so it is
>> variable? Usually for that we use a pickCallback, from which you get an atom
>> index (a unique number for each atom in the full set of loaded atoms). I
>> would probably keep a set of useful Jmol script functions in a .spt file and
>> then load that when the applet loads. Like this:
>>
>>
>> jmolApplet(500,"set pickCallback 'myPickCallback'; script
>> myfunctions.spt")
>>
>> and then have a file myfunctions.spt:
>>
>> function crossMeasure(iAtom){
>>
>> // find the atom number that is associated with this atom
>> // I'm presuming all the measurements are between atoms
>> // with the same atom number.
>>
>> var atomNumber = {atomIndex = iAtom}.atomno
>> var atomList = {atomno=atomNumber}
>> var n = atomList.length
>> measures delete
>>
>> for (var i = 2; i <= n; i++) {
>> measure @{atomList[1]} @{atomList[i]}
>> }
>> }
>>
>>
>>
>> Then your pickCallback, which is a JavaScript function in the head of the
>> page, would look like this:
>>
>> function myPickCallback(appletID,atomID, atomIndex) {
>> jmolScript("crossMeasure(" + atomIndex + ")")
>> }
>>
>> See how that works? The main scripting is done in Jmol, but we do the
>> callback to JavaScript. Another option would be to do it all in Jmol:
>>
>> jmolApplet(500,"set pickCallback 'jmolScript:crossMeasure(-1)'; script
>> myfunctions.spt")
>>
>> and then have a file myfunctions.spt:
>>
>> function crossMeasure(iAtom){
>>
>> // find the atom number that is associated with this atom
>> // I'm presuming all the measurements are between atoms
>> // with the same atom number.
>> // _atomPicked is the atom index of the most recent atom clicked on
>>
>> if (iAtom < 0) { iAtom = _atomPicked }
>> var atomNumber = {atomIndex = iAtom}.atomno
>> var atomList = {atomno=atomNumber}
>> var n = atomList.length
>> measures delete
>>
>> for (var i = 2; i <= n; i++) {
>> measure @{atomList[1]} @{atomList[i]}
>> }
>> }
>>
>> Then you don't need any JavaScript.
>>
>> Of course, you might want something on your page to turn this off by
>> setting pickCallback to ""
>>
>>
>>
>>
>> <script type="text/javascript">
>>>
>>> </script>
>>>
>>> And I would like to call it like:
>>> jmolCheckbox("crossMeasure($selectedRES.ca)", \"measure OFF\", \"show
>>> distances\");
>>> Is it possible?
>>>
>>>
>> How are you assigning selectedRES? If it's really a Jmol selection, then
>> what you would do is substitute something like this, maybe:
>>
>> jmolCheckbox("crossMeasure('selectedRes')", \"measure OFF\", \"show
>> distances\");
>>
>> and then:
>>
>> function crossMeasure(iAtom){
>>
>> // find the atom number that is associated with this atom
>> // I'm presuming all the measurements are between atoms
>> // with the same atom number.
>>
>> if (iAtom == "selectedRes") { iAtom = {selected and *.ca}[1].atomIndex
>> }
>>
>> ...
>>
>>
>>
>>
>>
>>
>>> Thanks again,
>>> Daniel
>>>
>>>
>>> 2011/3/25 Robert Hanson <ha...@st...>
>>>
>>>> Here you go:
>>>>
>>>> var atomList = {46:A.ca}
>>>> var n = atomList.length
>>>> for (var i = 2; i <= n; i++) {
>>>> measure @{atomList[1]} @{atomList[i]}
>>>> }
>>>>
>>>>
>>>> Bob
>>>>
>>>> --
>>>> 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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>>>> _______________________________________________
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>>>>
>>>>
>>>
>>>
>>> ------------------------------------------------------------------------------
>>> 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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>>>
>>
>>
>> --
>> 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
>> _______________________________________________
>> Jmol-users mailing list
>> Jmo...@li...
>> https://lists.sourceforge.net/lists/listinfo/jmol-users
>>
>>
>
>
> ------------------------------------------------------------------------------
> 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
> _______________________________________________
> Jmol-users mailing list
> Jmo...@li...
> https://lists.sourceforge.net/lists/listinfo/jmol-users
>
>
--
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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