[Jmol-users] Jmol prerelease 10.9.85
Hi, Jmol 10.9.85 is available at http://www.jmol.org/files -move command zoom fixed -o for unitcell axes -3D positionable echos -fix for i18n classes version - Using Tomcat but need to do more? Need to support web services, security? Get stuff done quickly with pre-integrated technology to make your job easier Download IBM WebSphere Application Server v.1.0.1 based on Apache Geronimo http://sel.as-us.falkag.net/sel?cmd=lnkkid=120709bid=263057dat=121642 ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] lines in frames
A short question, concerning lines and planes in an animation (multiple XYZ file). When I call a script like frame 1 draw line1 120 (atomno=1) (atomno=2) draw plane1 200 PERP PLANE $line1 the line is shown in all frames of the animation, while the plane turns out to be attached to frame1 only. that must be a bug. Is there a way to confine a line to a particular frame too? And vice versa, to show the plane in all frames? draw FIXED/MODELBASED Sets whether the surface [BH: should say object] generated is to be associated with the fixed window -- and thus appear with all frames/models -- or is to be associated with the currently displayed model (the default). but I don't think it's working. Bob - Using Tomcat but need to do more? Need to support web services, security? Get stuff done quickly with pre-integrated technology to make your job easier Download IBM WebSphere Application Server v.1.0.1 based on Apache Geronimo http://sel.as-us.falkag.net/sel?cmd=lnkkid=120709bid=263057dat=121642 ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
[Jmol-users] lines in frames
A short question, concerning lines and planes in an animation (multiple XYZ file). When I call a script like frame 1 draw line1 120 (atomno=1) (atomno=2) draw plane1 200 PERP PLANE $line1 the line is shown in all frames of the animation, while the plane turns out to be attached to frame1 only. Is there a way to confine a line to a particular frame too? And vice versa, to show the plane in all frames? (Context: I'd like to show in an animation that eclipsed 2,3-dichlorobutane has a plane of symmetry, while the most stable all trans conformation has an inversion center, visualized by drawing lines between related atoms). Hens - Using Tomcat but need to do more? Need to support web services, security? Get stuff done quickly with pre-integrated technology to make your job easier Download IBM WebSphere Application Server v.1.0.1 based on Apache Geronimo http://sel.as-us.falkag.net/sel?cmd=lnkkid=120709bid=263057dat=121642 ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] lines in frames
A short question, concerning lines and planes in an animation (multiple XYZ file). When I call a script like frame 1 draw line1 120 (atomno=1) (atomno=2) draw plane1 200 PERP PLANE $line1 OK, disregard the fixed/modelbased business. Here is the problem: 1) You select atomno=1 which is all the first atoms in all the models. So lines are drawn in all models. If you want to draw lines in only one model, be sure to only select atoms in one model. 2) The PERP PLANE operation is a bug. Bob the line is shown in all frames of the animation, while the plane turns out to be attached to frame1 only. Is there a way to confine a line to a particular frame too? And vice versa, to show the plane in all frames? (Context: I'd like to show in an animation that eclipsed 2,3-dichlorobutane has a plane of symmetry, while the most stable all trans conformation has an inversion center, visualized by drawing lines between related atoms). Hens - Using Tomcat but need to do more? Need to support web services, security? Get stuff done quickly with pre-integrated technology to make your job easier Download IBM WebSphere Application Server v.1.0.1 based on Apache Geronimo http://sel.as-us.falkag.net/sel?cmd=lnkkid=120709bid=263057dat=121642 ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users - Using Tomcat but need to do more? Need to support web services, security? Get stuff done quickly with pre-integrated technology to make your job easier Download IBM WebSphere Application Server v.1.0.1 based on Apache Geronimo http://sel.as-us.falkag.net/sel?cmd=lnkkid=120709bid=263057dat=121642 ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] initial zoom level
On Oct 25, 2006, at 9:50 PM, [EMAIL PROTECTED] wrote:set zoomLarge TRUE #Jmol-defaultset zoomLarge FALSE #Chime-defaultIs this a very newly implemented option? In Jmol 10.9.83, these cause a script error: unrecognized set option.Frieda ///Frieda Reichsman, PhDMolecules in MotionInteractive Molecular Structureshttp://www.moleculesinmotion.com/// - Using Tomcat but need to do more? Need to support web services, security? Get stuff done quickly with pre-integrated technology to make your job easier Download IBM WebSphere Application Server v.1.0.1 based on Apache Geronimo http://sel.as-us.falkag.net/sel?cmd=lnkkid=120709bid=263057dat=121642___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] initial zoom level
10.9.85 On Oct 25, 2006, at 9:50 PM, [EMAIL PROTECTED] wrote: set zoomLarge TRUE #Jmol-default set zoomLarge FALSE #Chime-default Is this a very newly implemented option? In Jmol 10.9.83, these cause a script error: unrecognized set option. Frieda /// Frieda Reichsman, PhD Molecules in Motion Interactive Molecular Structures http://www.moleculesinmotion.com /// - Using Tomcat but need to do more? Need to support web services, security? Get stuff done quickly with pre-integrated technology to make your job easier Download IBM WebSphere Application Server v.1.0.1 based on Apache Geronimo http://sel.as-us.falkag.net/sel?cmd=lnkkid=120709bid=263057dat=121642___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users - Using Tomcat but need to do more? Need to support web services, security? Get stuff done quickly with pre-integrated technology to make your job easier Download IBM WebSphere Application Server v.1.0.1 based on Apache Geronimo http://sel.as-us.falkag.net/sel?cmd=lnkkid=120709bid=263057dat=121642 ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] label line, plane ...
[EMAIL PROTECTED] wrote:
Well, what do you know! The new echo x y capability easily extends to 3D
set echo myecho {x y z}
set echo myecho (atomno=3)
set echo myecho (*)
It wasn't draw, it wasn't text or label -- it was just the idea of a
3D-echo
You have to love it when it's THAT easy. When you
set echo myecho (*)
set echo myecho center
echo X
you get an X as nearly as I can place it centered on the geometric center
of the molecule. Note that fractional coordinates are allowed.
set echo myecho {1/2 1/2 1/2}
:)
In contrast to the 'draw object' solution there remains one problem to
be solved.
How do I know which coordinates I must provide to echo to label a
specific draw object?
The 'show draw' command is supposed to show the command to generate the
draw object that is considered as current, including the coordinates of
the reference points. (By the way, it would be more secure if the name
of the draw object could be specified directly, e.g. show draw $plane1.)
But this only works extremely rare and unpredictable in version 10.9.85
(also in 10.9.79, I havn't checked others).
Take for example this command (PDB entry 1deh):
draw border1 PERP 150 PLANE (5:A and carbon and alpha) (6:A and carbon
and alpha);
The plane is drawn correctly but 'show draw' only outputs draw border1
most of the time. (Actually it only worked once, with exactly this
example and a few others in version 10.9.79 but never again that the
four coordinates of the corners were shown.)
The next issue (if 'show draw' works correctly) is to read the
information from Jmol and to generate the corresponding 'echo' command.
To avoid parsing the message callback stream, I tried the
'jmolScriptWait' command for the first time. But it totally freezes
Firefox 1.5.0.7 with Java 1.4.2_11 on SuSE linux 9.3. The browser
freezes independant of the script command I used.
Regards,
Rolf
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[Jmol-users] jmol
Nico, In the mediawiki invocation of Jmol, how might one address different instances of a jmol. Might it be eg jmol name=first or jmol id=first? Would either of these be supported by your code? Much of http://wiki.jmol.org/index.php/MediaWiki#Simple_usage seems to assume only one jmol per page? -- Henry Rzepa. +44 (020) 7594 5774 (Voice); +44 (0870) 132 3747 (eFax); [EMAIL PROTECTED] (iChat) http://www.ch.ic.ac.uk/rzepa/ Dept. Chemistry, Imperial College London, SW7 2AZ, UK. (Voracious anti-spam filter in operation for received email. If expected reply not received, please phone/fax). - Using Tomcat but need to do more? Need to support web services, security? Get stuff done quickly with pre-integrated technology to make your job easier Download IBM WebSphere Application Server v.1.0.1 based on Apache Geronimo http://sel.as-us.falkag.net/sel?cmd=lnkkid=120709bid=263057dat=121642 ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] label line, plane ...
Rolf,
draw border1 PERP 150 PLANE (5:A and carbon and alpha) (6:A and carbon
and alpha);
easier, BTW:
draw border1 PERP 150 PLANE (5:A.CA) (6:A.CA)
The plane is drawn correctly but 'show draw' only outputs draw border1
most of the time. (Actually it only worked once, with exactly this
example and a few others in version 10.9.79 but never again that the
four coordinates of the corners were shown.)
when you use show draw you don't add any qualifiers
draw border1 #sort of a select for DRAW -- sets current object
show draw #shows current draw object
should give something like:
draw border1 {23.890585 32.710503 10.786414} {21.773388 34.16974 10.07222}
{20.224413 32.710503 11.682588} {22.34161 31.251266 12.396782}
I suspect the reason it seems unpredictable is that sometimes you had the
object selected, and sometimes not. But if I'm wrong, reply with the exact
wording of the script that is causing the problem.
Also, something I keep doing is I sometimes accidentally put the $ in:
draw $border1
DON'T DO THAT.
The next issue (if 'show draw' works correctly) is to read the
information from Jmol and to generate the corresponding 'echo' command.
To avoid parsing the message callback stream, I tried the
'jmolScriptWait' command for the first time. But it totally freezes
Firefox 1.5.0.7 with Java 1.4.2_11 on SuSE linux 9.3. The browser
freezes independant of the script command I used.
Interesting -- this means that those browsers are using the event queue.
David Evans at Eli Lilly had this problem with the application (as opposed
to the applet). The solution for applications was to make sure you call
scriptWait() from a new thread rather than the one associated with a user
action, like clicking a button.
Something to try: If the jmolScriptWait function is being run because the
user has clicked on a link or button, try making sure that the button
method looks like this:
onClick=setTimeout('clickAction()', 100)
the 100-ms delay won't be noticed by the user, but a new thread is started
that isn't the event queue thread. So it shouldn't hang the program. Then
function clickAction() {
var info = jmolScriptWait(draw $border1;show draw)
}
If anything will work, that stands the best chance.
I seem to remember having this sort of problem with Opera browsers some
eons ago, even with regular scripting, and the only solution was to use
setTimeout() this way with every user-derived action.
Bob
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[Jmol-users] history - commands separation
I have been working on a javascript function in order to cancel the last
actions performed by the user (an undo function). I think it might
interest some of the Jmol users :
- the new history command gives the succession of all the commands that
have been sent to the applet.
- the consecutive sets of commands sent are separated by a | character.
- if 2 commands are separated by a semi-colon and are sent to the applet
(eg: select all; cpk on;) they appear in the history as a single
command (eg: previous command; | select all; cpk on; | next command...).
To make an undo function I choose to split the history based on the |
character, and to concat the different pieces except the last one. The
new script preceded by a command which reset the interface is then sent
to the applet and it works great.
The problem begins when you want to perform a second undo command : as
all the previous commands are sent as one set, they are no longer
separated by a | in the history and they appear as a single command.
I found a workaround (there might be some others) by inserting a #|;
between the commands from the history in order to keep a separation
between these consecutives commands.
In my opinion, the easyest way would be that the | character is
understood by Jmol as a separator for the history, then one would only
have to send a substring of the history in order to perform an undo, and
it could be used recursively. I don't know if it could be easily
implemented but I think it should help a lot.
By the way, if some are interested by the javascript I used, here it is :
function undo() {
answer = jmolScriptWaitAsArray('show history; history on;');
script = answer[0][0][3];
pieces = script.split(' #|;');
fin = pieces[pieces.length-1].split('|');
debut = pieces.slice(0,-1);
script = debut.concat(fin);
while (script[script.length-1]==' ') {
script.length--;
}
spt='';
for (i=0;iscript.length-1;i++) {
if(script[i]!='')
spt += script[i]+' #|;' ;
}
if (script[0].indexOf(initscript)==-1) {
spt = initscript + ' #|;' + spt;
}
//alert(spt);
executer(spt);
}
Paul
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Re: [Jmol-users] jmol
De: Rzepa, Henry [EMAIL PROTECTED] In the mediawiki invocation of Jmol, how might one address different instances of a jmol. Might it be eg jmol name=first or jmol id=first? Would either of these be supported by your code? The following should work jmol jmolApplet namefirst/name /jmolApplet /jmol See http://wiki.jmol.org/index.php/MediaWiki#Reference Nico - Using Tomcat but need to do more? Need to support web services, security? Get stuff done quickly with pre-integrated technology to make your job easier Download IBM WebSphere Application Server v.1.0.1 based on Apache Geronimo http://sel.as-us.falkag.net/sel?cmd=lnkkid=120709bid=263057dat=121642 ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
[Jmol-users] zoom
I was playing with 1d66.pdb and realizing again that in such cases the zoom maxes out too soon. Way back I had tried allowing for a larger maximum zoom setting, but that fails to do the job. Just now I implemented locally what I think is an ideal solution. The problem is not that zoom can't go very high, it's that the perspective depth calculation undoes the zoom. So here's my idea: Starting with a certain zoom setting and going up to the maximum (20), we scale out the perspective depth. If you think about it, once you have such huge zoom settings, the subtlely of perspective depth is probably not necessary. This work. The question is, what is that magic zoom setting where this effect kicks in? I've tried 5000 and 1, and both work fine. Q: What is the highest zoom setting you use IN YOUR SCRIPTS? I'd like to set this above whatever those are so that scripts don't change. I'd like this number to lower, not higher, so that its a smoother transition. Too close to 20 and what you see is a sudden increase in zoom capability as you approach the max. - Using Tomcat but need to do more? Need to support web services, security? Get stuff done quickly with pre-integrated technology to make your job easier Download IBM WebSphere Application Server v.1.0.1 based on Apache Geronimo http://sel.as-us.falkag.net/sel?cmd=lnkkid=120709bid=263057dat=121642 ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
[Jmol-users] sprout hydrogens
I've been looking into sprouting hydrogens, and it's no problem. The only thing is what do people really want. Please start discussing what you want. 1) Only PDB models (like Chime)? 2) Only the 20 common amino acids (like Chime)? 3) Just carbons or all atoms? 4) If not just PDB residues, suggestions for resolving oxidation state ambiguities like -CCCO, which could be CH2CH2CH2OH or several other possibilities. 5) If not just carbons, suggestions for resolving pKa issues. 6) If not just carbons, suggestions for resolving dihedral selection. 7) full model or selected subsets? Bob - Using Tomcat but need to do more? Need to support web services, security? Get stuff done quickly with pre-integrated technology to make your job easier Download IBM WebSphere Application Server v.1.0.1 based on Apache Geronimo http://sel.as-us.falkag.net/sel?cmd=lnkkid=120709bid=263057dat=121642 ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] zoom
On Oct 26, 2006, at 10:18 AM, [EMAIL PROTECTED] wrote:Q: What is the highest zoom setting you use IN YOUR SCRIPTS?In my scripts the highest zoom has probably been well under 5000, perhaps around 2000 or 3000. If there are occurences that are higher, I would gladly re-write them in order to be able to increase the effective zoom levels.Sounds great, looking forward to trying it out.Frieda ///Frieda Reichsman, PhDMolecules in MotionInteractive Molecular Structureshttp://www.moleculesinmotion.com/// - Using Tomcat but need to do more? Need to support web services, security? Get stuff done quickly with pre-integrated technology to make your job easier Download IBM WebSphere Application Server v.1.0.1 based on Apache Geronimo http://sel.as-us.falkag.net/sel?cmd=lnkkid=120709bid=263057dat=121642___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] initial zoom level
OK, works very nicely, thanks!On Oct 26, 2006, at 8:26 AM, [EMAIL PROTECTED] wrote:10.9.85 On Oct 25, 2006, at 9:50 PM, [EMAIL PROTECTED] wrote: set zoomLarge TRUE #Jmol-defaultset zoomLarge FALSE #Chime-default Is this a very newly implemented option? In Jmol 10.9.83, these causea script error: unrecognized set option.Frieda///Frieda Reichsman, PhDMolecules in MotionInteractive Molecular Structureshttp://www.moleculesinmotion.com///-Using Tomcat but need to do more? Need to support web services, security?Get stuff done quickly with pre-integrated technology to make your jobeasierDownload IBM WebSphere Application Server v.1.0.1 based on Apache Geronimohttp://sel.as-us.falkag.net/sel?cmd=lnkkid=120709bid=263057dat=121642___Jmol-users mailing listJmol-users@lists.sourceforge.nethttps://lists.sourceforge.net/lists/listinfo/jmol-users -Using Tomcat but need to do more? Need to support web services, security?Get stuff done quickly with pre-integrated technology to make your job easierDownload IBM WebSphere Application Server v.1.0.1 based on Apache Geronimohttp://sel.as-us.falkag.net/sel?cmd=lnkkid=120709bid=263057dat=121642___Jmol-users mailing listJmol-users@lists.sourceforge.nethttps://lists.sourceforge.net/lists/listinfo/jmol-users ///Frieda Reichsman, PhDMolecules in MotionInteractive Molecular Structureshttp://www.moleculesinmotion.com/// - Using Tomcat but need to do more? Need to support web services, security? Get stuff done quickly with pre-integrated technology to make your job easier Download IBM WebSphere Application Server v.1.0.1 based on Apache Geronimo http://sel.as-us.falkag.net/sel?cmd=lnkkid=120709bid=263057dat=121642___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
[Jmol-users] some advice regarding Jmol, Javascript PHP
Hi, all this time I've been using the Jmol application from the command line. However I now have to use it in a web page. I can place the applet in a HTML page pretty easily. However my situation is a little more involved and I was wondering if anybody could provide any hints as to how to solve this: I have a PHP page that will pull a PDB file and SD file from a database. So both the structures are in the form of strings. What I'd like to do is generate a link on the PHP page that when clicked, brings up a window with Jmol showing the PDB SDF structures simultaneously (they are docked ligand and receptor so the coordinate system is the same). So there are a number of issues: * Since Jmol cannot show multiple structures, I need to convert my SDF to PDB and concatenate it to the protein PDB. Is this correct? * The PHP page needs to write out a HTML page that contains the code for the applet. But ordinarily I cannot write a file to disk from my PHP page. * How do I specify that Jmol should load the structures - which are in a string. Do I need to write out a temporary file? I have a feeling that Javascript comes in somewhere (!), but never having done this, it's not clear as to how I attack this problem (at least in an elegant/efficient manner) Any pointers would be appreciated Thanks, --- Rajarshi Guha [EMAIL PROTECTED] GPG Fingerprint: 0CCA 8EE2 2EEB 25E2 AB04 06F7 1BB9 E634 9B87 56EE --- Q: What do you get when you cross a mosquito with a mountain climber? A: Nothing. You can't cross a vector with a scaler. - Using Tomcat but need to do more? Need to support web services, security? Get stuff done quickly with pre-integrated technology to make your job easier Download IBM WebSphere Application Server v.1.0.1 based on Apache Geronimo http://sel.as-us.falkag.net/sel?cmd=lnkkid=120709bid=263057dat=121642 ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] label line, plane ...
[EMAIL PROTECTED] wrote:
when you use show draw you don't add any qualifiers
draw border1 #sort of a select for DRAW -- sets current object
show draw #shows current draw object
should give something like:
draw border1 {23.890585 32.710503 10.786414} {21.773388 34.16974 10.07222}
{20.224413 32.710503 11.682588} {22.34161 31.251266 12.396782}
I suspect the reason it seems unpredictable is that sometimes you had the
object selected, and sometimes not. But if I'm wrong, reply with the exact
wording of the script that is causing the problem.
Also, something I keep doing is I sometimes accidentally put the $ in:
draw $border1
DON'T DO THAT.
This didn't make a difference. But I found out that the coordinates are
only provided if a specific frame is displayed, not with 'frame all' set
before.
Since we add amino acid variants as new models in our Jmol viewer,
'frame all' is always set initially.
In this context I noticed that Jmol freezes if the frame number is not
specified and not all atoms specified in the 'draw' command are present
in all frames. The java console shows the following error message:
java.lang.NullPointerException
at javax.vecmath.Tuple3f.sub(Tuple3f.java:225)
at org.jmol.viewer.Draw.scaleDrawing(Draw.java:462)
at org.jmol.viewer.Draw.setProperty(Draw.java:197)
at org.jmol.viewer.Frame.setShapeProperty(Frame.java:1092)
at org.jmol.viewer.ModelManager.setShapeProperty(ModelManager.java:386)
at org.jmol.viewer.Viewer.setShapeProperty(Viewer.java:2463)
at org.jmol.viewer.Eval.draw(Eval.java:5039)
at org.jmol.viewer.Eval.instructionDispatchLoop(Eval.java:634)
at org.jmol.viewer.Eval.runEval(Eval.java:104)
at org.jmol.viewer.Viewer.evalStringWaitStatus(Viewer.java:2289)
at org.jmol.viewer.ScriptManager.runScript(ScriptManager.java:130)
at org.jmol.viewer.ScriptManager.runNextScript(ScriptManager.java:119)
at
org.jmol.viewer.ScriptManager$ScriptQueueRunnable.run(ScriptManager.java:147)
at java.lang.Thread.run(Thread.java:534)
The next issue (if 'show draw' works correctly) is to read the
information from Jmol and to generate the corresponding 'echo' command.
To avoid parsing the message callback stream, I tried the
'jmolScriptWait' command for the first time. But it totally freezes
Firefox 1.5.0.7 with Java 1.4.2_11 on SuSE linux 9.3. The browser
freezes independant of the script command I used.
Interesting -- this means that those browsers are using the event queue.
David Evans at Eli Lilly had this problem with the application (as opposed
to the applet). The solution for applications was to make sure you call
scriptWait() from a new thread rather than the one associated with a user
action, like clicking a button.
Something to try: If the jmolScriptWait function is being run because the
user has clicked on a link or button, try making sure that the button
method looks like this:
onClick=setTimeout('clickAction()', 100)
the 100-ms delay won't be noticed by the user, but a new thread is started
that isn't the event queue thread. So it shouldn't hang the program. Then
function clickAction() {
var info = jmolScriptWait(draw $border1;show draw)
}
If anything will work, that stands the best chance.
I seem to remember having this sort of problem with Opera browsers some
eons ago, even with regular scripting, and the only solution was to use
setTimeout() this way with every user-derived action.
Unfortunately it doesn't work. Without 'jmolScriptWait' in 'clickAction'
the method works, but with it the browser freezes.
Regards,
Rolf
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Re: [Jmol-users] some advice regarding Jmol, Javascript PHP
Timothy Driscoll answered to Rajarshi Guha: * Since Jmol cannot show multiple structures, I need to convert my SDF to PDB and concatenate it to the protein PDB. Is this correct? as far as I know, yes - you will need to concatenate the structures as independent MODEL (or perhaps FRAME) records. Wrong. Recent versions of Jmol CAN load multiple structures, so there is no need to concatenate files. Don't know if different formats will be trouble, but get a current prerelease version of Jmol and try. * The PHP page needs to write out a HTML page that contains the code for the applet. But ordinarily I cannot write a file to disk from my PHP page. I don't know any PHP, but at least javascript can write an html page on-the-fly without saving any temp files. * How do I specify that Jmol should load the structures - which are in a string. Do I need to write out a temporary file? you should be able to use php to write the Jmol applet and provide the structure(s) as an inline param; in other words, I don't think you need a tmp file anywhere. for example, if you assign your coordinates to a php var, like this: I'm quite sure that Jmol has inline loading abilities, but I haven't used them. Check the documentation. - Using Tomcat but need to do more? Need to support web services, security? Get stuff done quickly with pre-integrated technology to make your job easier Download IBM WebSphere Application Server v.1.0.1 based on Apache Geronimo http://sel.as-us.falkag.net/sel?cmd=lnkkid=120709bid=263057dat=121642 ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] some advice regarding Jmol, Javascript PHP
On Oct 26, 2006, at 1:38 PM, Angel Herraez wrote: Timothy Driscoll answered to Rajarshi Guha: * Since Jmol cannot show multiple structures, I need to convert my SDF to PDB and concatenate it to the protein PDB. Is this correct? as far as I know, yes - you will need to concatenate the structures as independent MODEL (or perhaps FRAME) records. Wrong. Recent versions of Jmol CAN load multiple structures, so there is no need to concatenate files. Don't know if different formats will be trouble, but get a current prerelease version of Jmol and try. and move them independently? that's news to me. * The PHP page needs to write out a HTML page that contains the code for the applet. But ordinarily I cannot write a file to disk from my PHP page. I don't know any PHP, but at least javascript can write an html page on-the-fly without saving any temp files. if you are using php anyway, to query your server-side database, then js is a needless complication IMO. you could use php to write the coordinates as a js variable, then use js to write your applet tag - but why bother? php works outright. * How do I specify that Jmol should load the structures - which are in a string. Do I need to write out a temporary file? you should be able to use php to write the Jmol applet and provide the structure(s) as an inline param; in other words, I don't think you need a tmp file anywhere. for example, if you assign your coordinates to a php var, like this: I'm quite sure that Jmol has inline loading abilities, but I haven't used them. Check the documentation. Jmol does, in fact; my example was actual working code. but I could find no documentation about loadinline. tim -- Timothy Driscollem: [EMAIL PROTECTED] molvisions - see. grasp. learn. ph: 919-368-2667 http://www.molvisions.com/im: molvisions usa:virginia:blacksburg tx: [EMAIL PROTECTED] - Using Tomcat but need to do more? Need to support web services, security? Get stuff done quickly with pre-integrated technology to make your job easier Download IBM WebSphere Application Server v.1.0.1 based on Apache Geronimo http://sel.as-us.falkag.net/sel?cmd=lnkkid=120709bid=263057dat=121642 ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
[Jmol-users] Jmol [EMAIL PROTECTED] team
Hi, I'd like to welcome recent new members in the Jmol Folding At Home team [1] (team 44383), and tell you that we are almost in the top 500 teams (currently 501st) :) Folding At Home [2] is a distributed computing project to understand protein folding, misfolding, and related diseases. If you are interested in participating, you can join the Jmol team (n° 44383). Nico [1] http://folding.extremeoverclocking.com/team_summary.php?s=t=44383 [2] http://folding.stanford.edu/ - Using Tomcat but need to do more? Need to support web services, security? Get stuff done quickly with pre-integrated technology to make your job easier Download IBM WebSphere Application Server v.1.0.1 based on Apache Geronimo http://sel.as-us.falkag.net/sel?cmd=lnkkid=120709bid=263057dat=121642 ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
[Jmol-users] problems bringing up the applet
Hi, I'm have a problem in bringing up the applet on a web page. The page is located at http://156.56.90.245/~rguha/jmol.html when I click on the page I get a flash of black then an empty box for the applet. The Java console shows me: load: class JmolApplet not found. java.lang.ClassNotFoundException: JmolApplet at sun.applet.AppletClassLoader.findClass(AppletClassLoader.java:168) at java.lang.ClassLoader.loadClass(ClassLoader.java:306) at sun.applet.AppletClassLoader.loadClass(AppletClassLoader.java:119) at java.lang.ClassLoader.loadClass(ClassLoader.java:251) at sun.applet.AppletClassLoader.loadCode(AppletClassLoader.java:599) at sun.applet.AppletPanel.createApplet(AppletPanel.java:721) at sun.plugin.AppletViewer.createApplet(AppletViewer.java:1760) at sun.applet.AppletPanel.runLoader(AppletPanel.java:650) at sun.applet.AppletPanel.run(AppletPanel.java:324) at java.lang.Thread.run(Thread.java:595) Caused by: java.io.IOException: open HTTP connection failed. at sun.applet.AppletClassLoader.getBytes(AppletClassLoader.java:271) at sun.applet.AppletClassLoader.access$100(AppletClassLoader.java:44) at sun.applet.AppletClassLoader$1.run(AppletClassLoader.java:158) at java.security.AccessController.doPrivileged(Native Method) at sun.applet.AppletClassLoader.findClass(AppletClassLoader.java:155) ... 9 more and my httpd error log says: File does not exist: /home/rguha/public_html/rguha/jmol.html/ JmolApplet.class The directory contains JmolApplet.jar and JmolApplet?.jar as well as Jmol.js. The page and the jar files are all in the same directory. I've looked at other simple pages that were posted on the list, but I can't see any difference in the HTML Javascript. I'm assuming that it has something to do with my paths, but I can't see whats going wrong. Any pointers would be appreciated I'm using Firefox 1.5, Fedora Core 5 (64 bit) and the jar files from the 10.9.85 tarball. --- Rajarshi Guha [EMAIL PROTECTED] GPG Fingerprint: 0CCA 8EE2 2EEB 25E2 AB04 06F7 1BB9 E634 9B87 56EE --- Q: Why did the mathematician name his dog Cauchy? A: Because he left a residue at every pole. - Using Tomcat but need to do more? Need to support web services, security? Get stuff done quickly with pre-integrated technology to make your job easier Download IBM WebSphere Application Server v.1.0.1 based on Apache Geronimo http://sel.as-us.falkag.net/sel?cmd=lnkkid=120709bid=263057dat=121642 ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] problems bringing up the applet
Hi Your page works OK in my Firefox and in IE (WinXP) You have a nonclosed tag /script on the third line. - Using Tomcat but need to do more? Need to support web services, security? Get stuff done quickly with pre-integrated technology to make your job easier Download IBM WebSphere Application Server v.1.0.1 based on Apache Geronimo http://sel.as-us.falkag.net/sel?cmd=lnkkid=120709bid=263057dat=121642 ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] problems bringing up the applet
On Thu, 2006-10-26 at 22:17 +0200, Angel Herraez wrote: Hi Your page works OK in my Firefox and in IE (WinXP) You have a nonclosed tag /script on the third line. Yes, my mail was too hasty. I was initializing in the wrong directory :( --- Rajarshi Guha [EMAIL PROTECTED] GPG Fingerprint: 0CCA 8EE2 2EEB 25E2 AB04 06F7 1BB9 E634 9B87 56EE --- So the Zen master asked the hot-dog vendor, Can you make me one with everything? - TauZero on Slashdot - Using Tomcat but need to do more? Need to support web services, security? Get stuff done quickly with pre-integrated technology to make your job easier Download IBM WebSphere Application Server v.1.0.1 based on Apache Geronimo http://sel.as-us.falkag.net/sel?cmd=lnkkid=120709bid=263057dat=121642 ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] some advice regarding Jmol, Javascript PHP
On Thu, 2006-10-26 at 19:38 +0200, Angel Herraez wrote: Timothy Driscoll answered to Rajarshi Guha: * Since Jmol cannot show multiple structures, I need to convert my SDF to PDB and concatenate it to the protein PDB. Is this correct? as far as I know, yes - you will need to concatenate the structures as independent MODEL (or perhaps FRAME) records. Wrong. Recent versions of Jmol CAN load multiple structures, so there is no need to concatenate files. Don't know if different formats will be trouble, but get a current prerelease version of Jmol and try. How would this be done? Currently I do: var mol1 = ...; jmolAppletLoadInline(400, m1, spacefill on;); To load the next one would I do var m2 = ...; jmolLoadInline(m2); Or is there some other approach? --- Rajarshi Guha [EMAIL PROTECTED] GPG Fingerprint: 0CCA 8EE2 2EEB 25E2 AB04 06F7 1BB9 E634 9B87 56EE --- Every nonzero finite dimensional inner product space has an orthonormal basis. It makes sense, when you don't think about it. - Using Tomcat but need to do more? Need to support web services, security? Get stuff done quickly with pre-integrated technology to make your job easier Download IBM WebSphere Application Server v.1.0.1 based on Apache Geronimo http://sel.as-us.falkag.net/sel?cmd=lnkkid=120709bid=263057dat=121642 ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] some advice regarding Jmol, Javascript PHP
An (older) example of using jmolLoadInline() is at http://www.stolaf.edu/people/hansonr/jmol/inline/ Bob - Using Tomcat but need to do more? Need to support web services, security? Get stuff done quickly with pre-integrated technology to make your job easier Download IBM WebSphere Application Server v.1.0.1 based on Apache Geronimo http://sel.as-us.falkag.net/sel?cmd=lnkkid=120709bid=263057dat=121642 ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] sprout hydrogens
Bob, Thanks for looking into this. I am not a sophisticated user so I can;t comment on 4, 5, 6. I mostly am making tutorials for my AP Biology students which also are used by other teachers for general Biology students at the high school level. That said, here's what would work for me. I've only used PBD models. I'm trying to emphasize the fit between substrate and active site as well as hydrogen bonding. So it would be nice to extend the sprouted hydrogen set from carbons to at least include those involved in hbonding. The ideal would also include hydrogens involved between residues in the specificity pocket and those on the non-residue substrate. I extensively searched the archives and found no mention of sprouted hydrogens. If I the only one asking, please don't go out of your way on this. Thanks, Byrne On 10/26/06 7:24 AM, [EMAIL PROTECTED] [EMAIL PROTECTED] wrote: I've been looking into sprouting hydrogens, and it's no problem. The only thing is what do people really want. Please start discussing what you want. 1) Only PDB models (like Chime)? 2) Only the 20 common amino acids (like Chime)? 3) Just carbons or all atoms? 4) If not just PDB residues, suggestions for resolving oxidation state ambiguities like -CCCO, which could be CH2CH2CH2OH or several other possibilities. 5) If not just carbons, suggestions for resolving pKa issues. 6) If not just carbons, suggestions for resolving dihedral selection. 7) full model or selected subsets? Bob ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users - Using Tomcat but need to do more? Need to support web services, security? Get stuff done quickly with pre-integrated technology to make your job easier Download IBM WebSphere Application Server v.1.0.1 based on Apache Geronimo http://sel.as-us.falkag.net/sel?cmd=lnkkid=120709bid=263057dat=121642 ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] some advice regarding Jmol, Javascript PHP
On Thu, 2006-10-26 at 18:36 -0500, [EMAIL PROTECTED] wrote: Rajarshi, The question is: How important is it that you load the models one at a time? Not really. Basically I have a protein structure and multiple SD files of docked ligands. So at any one time I'd like to bring up Jmol with the protein and the ligand. If this is done by separate calls or in one call (by creating a single structure file) doesn't really matter 1) Provided these are SDF files, a line containing just separates different models. So you could: Hmm, one is a PDB. I could convert it to SDF but I figured that I'd loose information (such as secondary structure etc) - is that correct? If so, then it appears that converting the SDF to PDB and then concatenating would be the way to go (?) --- Rajarshi Guha [EMAIL PROTECTED] GPG Fingerprint: 0CCA 8EE2 2EEB 25E2 AB04 06F7 1BB9 E634 9B87 56EE --- Breadth-first search is the bulldozer of science. -- Randy Goebel - Using Tomcat but need to do more? Need to support web services, security? Get stuff done quickly with pre-integrated technology to make your job easier Download IBM WebSphere Application Server v.1.0.1 based on Apache Geronimo http://sel.as-us.falkag.net/sel?cmd=lnkkid=120709bid=263057dat=121642 ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] label line, plane ...
Ah, right, if you have multiple models, and the one draw command was used to create all the lines at once, show draw may not work as advertised. This didn't make a difference. But I found out that the coordinates are only provided if a specific frame is displayed, not with 'frame all' set before. Since we add amino acid variants as new models in our Jmol viewer, 'frame all' is always set initially. In this context I noticed that Jmol freezes if the frame number is not specified and not all atoms specified in the 'draw' command are present in all frames. The java console shows the following error message: java.lang.NullPointerException at javax.vecmath.Tuple3f.sub(Tuple3f.java:225) at org.jmol.viewer.Draw.scaleDrawing(Draw.java:462) found and fixed. Bob - Using Tomcat but need to do more? Need to support web services, security? Get stuff done quickly with pre-integrated technology to make your job easier Download IBM WebSphere Application Server v.1.0.1 based on Apache Geronimo http://sel.as-us.falkag.net/sel?cmd=lnkkid=120709bid=263057dat=121642 ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] some advice regarding Jmol, Javascript PHP
OK, so the problem here is that we don't have a multiple-file-format loadInline function. I suggest something like: [some PDB data] ~~~JMOL~EOF~~~ [some other data] ~~~JMOL~EOF~~~ [some more data] What would be the appropriate thing for ~~~JMOL~EOF~~~ ? Bob - Using Tomcat but need to do more? Need to support web services, security? Get stuff done quickly with pre-integrated technology to make your job easier Download IBM WebSphere Application Server v.1.0.1 based on Apache Geronimo http://sel.as-us.falkag.net/sel?cmd=lnkkid=120709bid=263057dat=121642 ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
[Jmol-users] Jmol 10.9.86
Hi, Jmol 10.9.86 is available for download at http://www.jmol.org/files/ News: - Turkish translation; - draw, isosurface; - new high zoom option allows nearly infinite zoom; - fix minor selected/hidden bug Nico - Using Tomcat but need to do more? Need to support web services, security? Get stuff done quickly with pre-integrated technology to make your job easier Download IBM WebSphere Application Server v.1.0.1 based on Apache Geronimo http://sel.as-us.falkag.net/sel?cmd=lnkkid=120709bid=263057dat=121642 ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Jmol 10.9.86
I encourage all to try this out, particularly the zoom. take the biggest, strangest PDB file you can and see what you can do with it. Any problems? Like it? Notice anything different? Too strange? Try it with set windowcentered OFF; set picking center and start picking atoms and rotating the model; and with set windowcentered ON just to see what that does differently. Zoom in and out to the extreme. You should be able to zoom to 20, but I doubt you will ever ever need that. I was playing with http://www.rcsb.org/pdb/files/1d66.pdb, myself. Bob Hi, Jmol 10.9.86 is available for download at http://www.jmol.org/files/ News: - Turkish translation; - draw, isosurface; - new high zoom option allows nearly infinite zoom; - fix minor selected/hidden bug Nico - Using Tomcat but need to do more? Need to support web services, security? Get stuff done quickly with pre-integrated technology to make your job easier Download IBM WebSphere Application Server v.1.0.1 based on Apache Geronimo http://sel.as-us.falkag.net/sel?cmd=lnkkid=120709bid=263057dat=121642 ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users - Using Tomcat but need to do more? Need to support web services, security? Get stuff done quickly with pre-integrated technology to make your job easier Download IBM WebSphere Application Server v.1.0.1 based on Apache Geronimo http://sel.as-us.falkag.net/sel?cmd=lnkkid=120709bid=263057dat=121642 ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
