Re: [Jmol-users] Jmol 10.9.86

[hansonr]

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 , 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=lnk&kid=120709&bid=263057&dat=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=lnk&kid=120709&bid=263057&dat=121642
___
Jmol-users mailing list
Jmol-users@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/jmol-users

[Jmol-users] Jmol 10.9.86

[Nicolas Vervelle]

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=lnk&kid=120709&bid=263057&dat=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

[hansonr]

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=lnk&kid=120709&bid=263057&dat=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

[hansonr]

If you really have to use strings, that is what you have to do. If these
could be separate files on your server, you can just use


load "fileset" "file1.pdb" "file2.mol"

Bob


> 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=lnk&kid=120709&bid=263057&dat=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=lnk&kid=120709&bid=263057&dat=121642
___
Jmol-users mailing list
Jmol-users@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/jmol-users

Re: [Jmol-users] label line, plane ...

[hansonr]

ah, one more thought!


Try

var infoString = jmolScriptWait("shapeInfo")

or

var V = jmolGetPropertyAsArray("shapeInfo").Draw.obj[0].vertices

array V will now be a full list of the vertices for all models.


Bob


> [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
>
> -
> 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=lnk&kid=120709&bid=263057&dat=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=lnk&kid=120709&bid=263057&dat=121642
___

Re: [Jmol-users] label line, plane ...

[hansonr]

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=lnk&kid=120709&bid=263057&dat=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

[Rajarshi Guha]

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=lnk&kid=120709&bid=263057&dat=121642
___
Jmol-users mailing list
Jmol-users@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/jmol-users

Re: [Jmol-users] sprout hydrogens

[Byrne Pedit]

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=lnk&kid=120709&bid=263057&dat=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

[hansonr]

Rajarshi,

The question is:

How important is it that you load the models one at a time?

That is NOT possible in Jmol 10.9.85. There are a couple of ways around this:

1) Provided these are SDF files, a line containing just  separates
different models. So you could:

 var m1 = "...";
 jmolAppletLoadInline(400, m1, "spacefill on;");
 var m2 = "...";
 jmolLoadInline(m1 + "\n\n" + m2);

or, if you want to be a little fancier and load the second model so that
it just magically "appears" with the first model, you could use:

 jmolLoadInline("save orientation;"
  +"data \"model data\""
  +m1+"\n\n"+m2
  +" end \"model data\";"
  +"frame 0;"
  +"restore orientation;")

The key here is that we are loading the first model AGAIN, this time with
the second model. The data command allows you to bracket an inline load
with script on both sides. In this case, we save and restore the
orientation, and we use frame 0 to display both models.

Maybe this isn't what you had in mind, but I'm using it as an illustration
anyway.

Bob Hanson



> 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=lnk&kid=120709&bid=263057&dat=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=lnk&kid=120709&bid=263057&dat=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

[hansonr]

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=lnk&kid=120709&bid=263057&dat=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

[Rajarshi Guha]

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=lnk&kid=120709&bid=263057&dat=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

[Rajarshi Guha]

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  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=lnk&kid=120709&bid=263057&dat=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

[Angel Herraez]

Hi
Your page works OK in my Firefox and in IE  (WinXP)

You have a nonclosed tag http://sel.as-us.falkag.net/sel?cmd=lnk&kid=120709&bid=263057&dat=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

[Rajarshi Guha]

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=lnk&kid=120709&bid=263057&dat=121642
___
Jmol-users mailing list
Jmol-users@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/jmol-users

[Jmol-users] Jmol [EMAIL PROTECTED] team

[Nicolas Vervelle]

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=lnk&kid=120709&bid=263057&dat=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

[Timothy Driscoll]

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
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=lnk&kid=120709&bid=263057&dat=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

[Angel Herraez]

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=lnk&kid=120709&bid=263057&dat=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 Huehne]

[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

-
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=lnk&kid=120709&bid=263057&dat=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

[Timothy Driscoll]

On Oct 26, 2006, at 11:15 AM, Rajarshi Guha wrote:
>
> 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?
>
as far as I know, yes - you will need to concatenate the structures  
as independent MODEL (or perhaps FRAME) records.


> * 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)
>
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:



then in the applet tag, you can use php to write the coordinates,  
like this:




this has worked for me in the past.  just be sure to append each line  
with a bar (|) to fit the syntax for loadinline.


hope that helps,

tim
-- 
Timothy Driscollem: [EMAIL PROTECTED]
molvisions - see. grasp. learn. ph: 919-368-2667
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=lnk&kid=120709&bid=263057&dat=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

[Rajarshi Guha]

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=lnk&kid=120709&bid=263057&dat=121642
___
Jmol-users mailing list
Jmol-users@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/jmol-users

Re: [Jmol-users] initial zoom level

[Frieda Reichsman]

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=lnk&kid=120709&bid=263057&dat=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=lnk&kid=120709&bid=263057&dat=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=lnk&kid=120709&bid=263057&dat=121642___
Jmol-users mailing list
Jmol-users@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/jmol-users

Re: [Jmol-users] zoom

[Frieda Reichsman]

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=lnk&kid=120709&bid=263057&dat=121642___
Jmol-users mailing list
Jmol-users@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/jmol-users

[Jmol-users] sprout hydrogens

[hansonr]

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=lnk&kid=120709&bid=263057&dat=121642
___
Jmol-users mailing list
Jmol-users@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/jmol-users

[Jmol-users] zoom

[hansonr]

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=lnk&kid=120709&bid=263057&dat=121642
___
Jmol-users mailing list
Jmol-users@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/jmol-users

Re: [Jmol-users]

[nvervell]

De: "Rzepa, Henry" <[EMAIL PROTECTED]>

>In the mediawiki invocation of Jmol,  how might one address
>different instances of a jmol.  Might it be eg
>
>  or  ?
>
>Would either of these be supported by your code?

The following should work

  
first
  


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=lnk&kid=120709&bid=263057&dat=121642
___
Jmol-users mailing list
Jmol-users@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/jmol-users

[Jmol-users] history - commands separation

[Paul Pillot]

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;ihttp://sel.as-us.falkag.net/sel?cmd=lnk&kid=120709&bid=263057&dat=121642
___
Jmol-users mailing list
Jmol-users@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/jmol-users

Re: [Jmol-users] label line, plane ...

[hansonr]

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




-
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=lnk&kid=120709&bid=263057&dat=121642
___
Jmol-users mailing list
Jmol-users@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/jmol-users

[Jmol-users]

[Rzepa, Henry]

Nico,

In the mediawiki invocation of Jmol,  how might one address
different instances of a jmol.  Might it be eg

  or  ?

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  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=lnk&kid=120709&bid=263057&dat=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 Huehne]

[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


-
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=lnk&kid=120709&bid=263057&dat=121642
___
Jmol-users mailing list
Jmol-users@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/jmol-users

Re: [Jmol-users] initial zoom level

[hansonr]

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=lnk&kid=120709&bid=263057&dat=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=lnk&kid=120709&bid=263057&dat=121642
___
Jmol-users mailing list
Jmol-users@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/jmol-users

Re: [Jmol-users] initial zoom level

[Frieda Reichsman]

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=lnk&kid=120709&bid=263057&dat=121642___
Jmol-users mailing list
Jmol-users@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/jmol-users

Re: [Jmol-users] lines in frames

[hansonr]

this is fixed for 10.9.86.

Be sure to indicate "and /n" or "and visible" if you only want drawn
objects in a specific frame.

> 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?

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=lnk&kid=120709&bid=263057&dat=121642
___
Jmol-users mailing list
Jmol-users@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/jmol-users

[Jmol-users] lines in frames

[Hens Borkent]

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=lnk&kid=120709&bid=263057&dat=121642
___
Jmol-users mailing list
Jmol-users@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/jmol-users

Re: [Jmol-users] lines in frames

[hansonr]

> 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=lnk&kid=120709&bid=263057&dat=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=lnk&kid=120709&bid=263057&dat=121642
___
Jmol-users mailing list
Jmol-users@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/jmol-users

Re: [Jmol-users] lines in frames

[hansonr]

> 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=lnk&kid=120709&bid=263057&dat=121642
___
Jmol-users mailing list
Jmol-users@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/jmol-users