Re: [Jmol-users] Publishing enhanced figures in IUCr journals

[hansonr]

> The problem is - as you go on to point out - with scaling of fonts
> and other objects, such as unit cell axis widths, where the
> size is specified in pixels. From the same script I want to create
> both the online image (at about 100 pixels per inch) and a
> higher-resolution TIFF (~ 300 ppi). If I simply scale the
> output width and height to get the TIFF, my fonts are 1/3 the
> desired size.
>
>> Q: How did you solve the font scaling problem?
>
> It's not a solved problem. I was hoping Bob would say "Oh, it's just
> a half-hour's work to provide an export option that will scale all
> dimensions (in pixels) by a factor of n" :-)
>
> Failing that, we will look into post-processing the script to find
> any size-setting commands and scale them individually; and also to
> determine default sizes for fonts etc. and scale those defaults
> globally.
>

Definitely more than half an hour's work. Perhaps what we are going to
need is some sort of font size expressed in percent -- which would use the
Jmol default font size and offsets and some sort of default applet size
(height? width? 400?), and then calculate the font sizes on the fly from
that. Or what we will need is some sort of setting such as

 set fontScaleAutomatic 400

that would take whatever font sizes and offsets are present and apply the
ratio of this number to the zoom-determining dimension (height or width).
Might work

Bob



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Re: [Jmol-users] Zeroing delays, instant moveTo's for fast retesting

[hansonr]

I would certainly find this useful. Please submit a feature request.
It will be a setting. What was it in Chime?

> When I'm developing Jmol-based websites and scripts, I end up
> reloading/rerunning hundreds of times. Chime has a feature (that I
> requested) that was a huge time saver for these development cycles.
> There was a setting that made all delays go to zero, and all timed
> commands execute instantly.
>
> I'd love it if Jmol had something similar -- a setting that made all
> delays zero seconds, all moveTo's go in 0 time, etc. This would
> greatly speed up the process of testing, tweaking, retesting for
> hundreds of cycles.
>
> Then when you're ready for a release, you just turn off this proposed
> setting, and all your delays and moveTo's work as intended.
>
> If anyone else would find this useful, please "chime in".
>
> -Eric
>
> /* - - - - - - - - - - - - - - - - - - - - - - - - - - -
> Eric Martz, Professor Emeritus, Dept Microbiology
> U Mass, Amherst -- http://www.umass.edu/molvis/martz
>
> Top Five 3D MolVis Technologies http://Top5.MolviZ.Org
> Biochem 3D Education Resources http://MolviZ.org
> See 3D Molecules, Install Nothing! - http://firstglance.jmol.org
> Protein Explorer - 3D Visualization: http://proteinexplorer.org
> Workshops: http://workshops.proteinexplorer.org
> World Index of Molecular Visualization Resources: http://molvisindex.org
> ConSurf - Find Conserved Patches in Proteins: http://consurf.tau.ac.il
> Atlas of Macromolecules: http://atlas.proteinexplorer.org
> PDB Lite Macromolecule Finder: http://pdblite.org
> Molecular Visualization EMail List (molvis-list):
>http://bioinformatics.org/mailman/listinfo/molvis-list
> - - - - - - - - - - - - - - - - - - - - - - - - - - - */
>
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Re: [Jmol-users] Serious Memory Issue in Jmol/JTAT

[hansonr]

> Dear Bob and Angel and others,
>
>
> What I have seen indicates that some portion of memory from "dead and
> gone" Jmols fails to be freed for reuse, and that this continues to
> add up throughout each browser session. The only way I know to free
> all the java memory for new molecular views is to close/quit the
> browser, thereby quitting java. When you start a new browser session,
> the memory is cleared.

I tested this recently on MSIE/Windows, Firefox/Windows+Mac,
Opera/Windows, and all did a fine job of clearing memory for applets on
pages that had been  closed. This is not something you can easily test for
yourself. If you can give me some test pages, I can look at it with tools
that I have. There was an issue dating way back to at least 10.0, but
11.3.61 should have fixed that.


>
> I hope there are other ways that I don't yet know about!
>
> Bob wrote:
>>Or, alternatively, use code to deactivate applet divs that are not
>>in use.
>
> What code is that?
>

something like clearing the divs using
document.getElementById("theDiv").innerHTML = ""

> Here's what I am doing in JTAT currently. Please tell me how I can improve
> it.
>
> A. I have an HTML div for Jmol (id="jmolAppletsDiv") at the outset,
> and it remains in place throughout the JTAT session. Jmol.js is
> loaded at the outset.
>
> B. Before writing the first jmol object tag into the division, I
> execute (one time only)
>jmolInitialize(...);
>jmolSetCallback(); //for messageCallback
>jmolSetDocument(0); // because I gather HTML generated by Jmol.js
> functions into strings.
>
> C. Object tag HTML for Jmol(s) is gathered into a string variable
> jhtml using calls to
>jmolApplet( [s_jwidth, s_jheight], readySpt, jNameSuffix);
>
> D. The Jmol(s) are written into jmolAppletsDiv in this manner:
>document.getElementById("jmolAppletsDiv").innerHTML = jhtml;
>

all the above looks terrific.

> E. The initial script specified in jmolApplet() messages a
> recognizable token. When this token is seen in the messageCallback
> stream, I assume that the corresponding Jmol has loaded and is ready
> for action. (IS THERE A BETTER WAY TO DETECT JMOL READINESS?)

that's the way to do it.

>
> F. I then use jmolScript() to send a script to each Jmol that starts
> with a load command, and then renders, colors, etc. producing the
> initial molecular view.

You could also use the javaScript command to send a message yourself
anywhere in a script.

>
> SO FAR SO GOOD. We now have the first molecular display showing. I am
> generally using small coordinate sets, so I haven't used much java memory
> yet.
>
> G. Now, the user presses a button to display a different molecular view.
>
>   - If the new view uses the same PDB file(s) (coordinates), and the
> same number of Jmols (1-4), only a new rendering script(s) is sent to
> the EXISTING Jmol(s).
>
>   - If the new view uses different PDB file(s), but the same number
> of Jmols, the scripts start with a "load" command, loading new
> coordinates into the EXISTING Jmol(s).
>
> IT WOULD BE EASY TO PUT IN A ZAP HERE IF THAT WOULD HELP. Although
> the Jmol documentation is not explicit about what "load 1d66.pdb"
> does, I assume this does an implicit zap, replacing the previous
> coordinates with the new ones. If not, shouldn't it do an implicit zap?

right -- it does a zap so that if the file load fails, the warning message
is on a blank window.

>
>   - If the new view uses a different number of Jmols, new object HTML
> is generated using jmolApplet() call(s), and it is written into the
> existing jmolAppletsDiv.innerHTML SIMPLY REPLACING THE OBJECTS
> (JMOLS) THAT WERE THERE BEFORE. IS THERE SOME MORE EFFECTIVE WAY TO
> CLEAR OUT THE OLD JMOLS?

It could be that the applets are not properly unloaded in such a case. I
have not tested that. I could imagine that some browsers have problems
with that. Be sure none of your global JavaScript variables make reference
to an applet that might have been destroyed this way. For example, if you
keep

var theApplet = document.getElementById("jmolApplet0")

or something like that, there might be a problem unloading that applet
without unloading the page.



>
> H. When moving to a new chapter, a new chapter.htm file is loaded
> into the existing browser window, entirely replacing the old
> chapter.htm. This starts the entire process over again, from loading
> Jmol.js, setting up jmolAppletsDiv, to filling it with jmol
> object(s), and when they message their readiness, having them load
> PDB files and then scripting those coordinates.

My testing suggests that this totally unloads from memory all applets on
the replaced pages. Not so prior to 11.3.61, though.

>
> SHOULD I ZAP OR DO SOME OTHER JMOL CLEAN UP PROCESS BEFORE LOADING A
> NEW HTML DOCUMENT INTO THE WINDOW?

this should not be necessary. I'm not sure you can reliably check that a
page is unloading and then do these zaps.

>
> Currently, the links to new chapters are simple HTML links. If there
> is so

Re: [Jmol-users] debug print out for popup?

[hansonr]

> Hi Bob,
>
> Thank you so much for the help.  Adding
>
> viewer.setStringProperty("defaults", "Jmol");
>
> did removed the message.
>
>
> I have another question about loading a file using the script.  It used
> to be
>  load 1ubi.pbd
> will load the pdb file from current directory.  But now Jmol seemed to
> add the path of the directory where the application starts to the file
> name and it can not find the file even it is in current directory. Is
> this intended behavior?

Li Yang,

As far as I know nothing has changed. If you use "1ubi.pdb" Jmol has
always added the full path to that using simply

File file = new File(name);
fullPath = file.getAbsolutePath();

So perhaps it has something to do with Java versions and how
File.getAbsolutePath() is interpreted.

Note that you can designate a default directory, which could be your
application directory if you wish, using

viewer.setStringProperty("defaultDirectory", "file://some/directory/path");

That seems to me a good solution in this case.

Bob

>
> Thanks,
>
> Li Yang
>
> -Original Message-
> From: [EMAIL PROTECTED]
> [mailto:[EMAIL PROTECTED] On Behalf Of
> [EMAIL PROTECTED]
> Sent: Tuesday, January 22, 2008 7:37 AM
> To: jmol-users@lists.sourceforge.net
> Subject: Re: [Jmol-users] debug print out for popup?
>
> This is a bug. I've reported it and will fix it later next week when I
> return to the US. You can avoid the message by having your application
> send
>
>   viewer.setStringProperty("defaults", "Jmol");
>
> or
>
>   viewer.setBooleanProperty("perspectiveDepth", true);
>
> (or FALSE, if you prefer) prior to whatever command you have that is
> invoking
>
>   viewer.getBooleanProperty("perspectiveDepth")
>
> Bob
>
>> Hi Bob,
>>
>>
>>
>> I am embedding Jmol 11.4.RC in my applications.  Whenever I
> right-click
>> to bring up the context menu,  I got this line print to my log window.
>> It looks like a debug statement.
>>
>>
>>
>> viewer.getBooleanProperty(perspectivedepth) - unrecognized
>>
>> Thanks,
>>
>>
>>
>> Li Yang
>>
>>
> 
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>
>
>
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Re: [Jmol-users] Publishing enhanced figures in IUCr journals

[hansonr]

> Dear Jmol users
>
> The International Union of Crystallography has been developing a system
> to allow authors to publish interactive figures using Jmol in IUCr
> journals. This system is almost ready to go live as a beta release
> to our authors.
>
> You are invited to preview and comment on the Jmol authoring toolkit
> that will form part of this service. This preview version is available
> at http://sandbox.iucr.org/jtktalpha
>

Very good! I note that on my machine the menu items overlap.

You might consider adding some crystallographic-focused buttons to the
interface. Take a look at http://icsdweb.fiz-karlsruhe.de/ and
http://fusion.stolaf.edu/chemistry/jmol/xtalx/, for example, for some nice
options that allow checking and investigation of the symmetry, displaying
multiple unit cells, checking fractional coordinates, and more.

> Feel free to upload structures in CIF format to test this toolkit.
> You will find that saving your edits will take a very long time;
> the demonstration machine is a very low-powered one and struggles to
> render the saved view (the server that our authors will use is
> much faster). Nevertheless, you may find it interesting to explore
> the way that the interface is intended to work.
>
> The application will be integrated seamlessly into our submission
> and review system. Authors may create enhanced figures and make them
> accessible to referees as part of normal peer review. After
> acceptance, the enhanced figure is automatically managed within the
> electronic journal workflow. The initial rendering is saved as a TIFF
> image for incorporation in the PDF of the article (this is why I
> have a need to obtain, say, 300 dpi resolution output from jmol).
>
> The online figure contains the same static rendering, but also the
> Jmol applet and the set of Jmol scripts that the author has assembled.
> The page degrades well for readers with limited browsers; if they do
> not have Java or JavaScript, they will see only the static view.
>
> Much of the development effort has gone into the integration of
> this toolkit with the submission system. This is important in a
> journal production environment to provide capacity to accommodate
> large numbers of figures. Recently we have been publishing over
> 1000 crystal structures per month. We wish to be able to publish
> that many Jmol-enhanced figures if the community sees a need to do so.
>
> The next stage will be to collect user feedback and refine the
> palette of features offered within the toolkit interface. We are
> aiming to provide a service that will be quite usable by Jmol
> novices, but that can also be used to good effect by experts.
>
> I must pay tribute to the enormous developments in Jmol over the past
> few years that have made this project possible: the very clean export
> of the graphics state; the very powerful and useful Jmol.js library;
> the great improvement in handling crystallographic information
> (symmetry operations, coordination polyhedra etc.). I also acknowledge
> the inspiration of the many excellent tutorial and educational sites
> that are using Jmol, and the efforts of journals such as ACS Chemical
> Biology and the Biochemical Journals to incorporate enhanced figures
> into their publications. The Jmol community itself is a wonderful
> one, and thanks to all of you for your continuing contributions of
> tools, ideas and know-how!
>
> Enjoy
> Brian
> _
> Brian McMahon   tel: +44 1244 342878
> Research and Development Officerfax: +44 1244 314888
> International Union of Crystallographye-mail:  [EMAIL PROTECTED]
> 5 Abbey Square, Chester CH1 2HU, England
>
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Re: [Jmol-users] Need "show _memory" to work, with 3 values

[hansonr]

Eric,

>
> I am spending hours/days doing tests on the "total" (used) memory
> reported in the Jmol applet menu. For every step, I have to manually
> open the Jmol menu and hand record the "total memory" and "free memory"
> values.
>
> Although there is supposed to be a read-only "_memory", "show
> _memory" returns  in 11.4.RC1.
>
> It would be great if there were a show _memory command that returned
> all 3 values (in one line) that are displayed in the Jmol menu. Then
> I could accumulate them in a string variable, format them into a
> report, and run these tests many-fold faster.
>

That's a bug. From the console or a script you can use

 print _memory

Or, from JavaScript, use

var memUse = jmolEvaluate("_memory")

to get two of the three numbers you are looking for. These include the
Java measures:

 Runtime.getRuntime().totalMemory()
 Runtime.getRuntime().freeMemory()

But, as discussed in previous threads, these are only marginally useful,
because Java accesses memory dynamically. Just because Java reports a
certain amount of memory as "free" does not mean that is all that is
available, because in the next instance Java may request more, and both
these numbers may jump to higher values.

Java does not provide a reliable mechanism to find out exactly how much
memory is really available to an applet. The third number you are seeing
is only available on some systems, so it is not a reliable measure. It is

Runtime.getRuntime().maxMemory()

This in principle gives you some measure of the maximum, and do experiment
with it, but don't depend upon it being there for all users.

> The purpose of the tests is to try to deduce what it is about my Jmol
> Tutorial-Authoring Template's JTAT Demo Tutorial that gradually
> consumes all java memory in certain browsers and platforms. And if I
> can narrow it down, then can I find a trick to free up that memory?
> such as a "zap" at a critical time?
>

I'm presuming you are using the latest Jmol version, right? A major
long-standing memory leak was fixed in Jmol 11.3.61. I am not aware of any
additional memory leaks, but I'm always open to checking for them again if
you can give me a good test example.

As I recall, some browsers (Opera?) do not necessarily dispense with
applets when the page is closed or reloaded. Jmol might be able to do a
better job than the browsers do by unloading viewers found to be inactive
because their documents are no longer available. So that is definitely
something we could look into.

I'm glad you are working on this, Eric. It's possible you will find
something that we can work with to give better advice to web developers.
Let me know if you need any help.

Bob


> Thanks, -Eric
>
>
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Re: [Jmol-users] for loop question

[hansonr]

> At 1/21/08, you wrote:
>>Can a for loop in Jmol take two variables, as follows?
>>
>>for ( var i = -9, j = 2; i < -4.0; i = i + 0.2, j = j + 1 )
>>
no, can't do that. Eric's solution is what you need to do, although it
should read:

var j = 2;
for (var i = -9; i < -4.0; i = i + 0.2);
  # do your work here;
  j = j + 1;
end for;

Niether += nor ++ have been implemented in Jmol. Since they are simply
conveniences, I'm not seeing them as priority items.

Note that the above loop may not work the way you wish due to imperfect
representation of decimal numbers in binary. When I ran the following:

  FOR (VAR I = -9; I < -4;I = I + 0.2);PRINT I;END FOR;

I see:

-9
-8.8
-8.6
-8.41
-8.21
-8.01
-7.81
-7.613
-7.415
-7.217
-7.02
-6.82
-6.623
-6.425
-6.227
-6.03
-5.83
-5.632
-5.434
-5.236
-5.04
-4.84
-4.64
-4.444
-4.246
-4.05


Note especially the final value. This is a general problem with using
noninteger numbers in a for loop. Much better would be:


  FOR (VAR I = -45; I < -20;I = I + 1);PRINT I/5.0;END FOR;

which gives the expected:

-9.0
-8.8
-8.6
-8.4
-8.2
-8.0
-7.8
-7.6
-7.4
-7.2
-7.0
-6.8
-6.6
-6.4
-6.2
-6.0
-5.8
-5.6
-5.4
-5.2
-5.0
-4.8
-4.6
-4.4
-4.2


Bob




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Re: [Jmol-users] debug print out for popup?

[hansonr]

This is a bug. I've reported it and will fix it later next week when I
return to the US. You can avoid the message by having your application
send

  viewer.setStringProperty("defaults", "Jmol");

or

  viewer.setBooleanProperty("perspectiveDepth", true);

(or FALSE, if you prefer) prior to whatever command you have that is invoking

  viewer.getBooleanProperty("perspectiveDepth")

Bob

> Hi Bob,
>
>
>
> I am embedding Jmol 11.4.RC in my applications.  Whenever I right-click
> to bring up the context menu,  I got this line print to my log window.
> It looks like a debug statement.
>
>
>
> viewer.getBooleanProperty(perspectivedepth) - unrecognized
>
> Thanks,
>
>
>
> Li Yang
>
> -
> This SF.net email is sponsored by: Microsoft
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Re: [Jmol-users] Serious Memory Issue in Jmol/JTAT

[hansonr]

> RE: Jmol Tutorial-Authoring Template (JTAT), nearing release (I hope).
> Near final demo at http://bioinformatics.org/jmol-tutorials
>
> There is a major unresolved problem which calls into question the
> usability of tutorials using Jmol, and JTAT in particular: running
> out of java memory.

Eric, I think you will have to consider the strategy taken by others --
perhaps pop-up windows that can be closed. One way to do this is to put a
static picture in a div and then click on that to activate a pop-up
window. Or, alternatively, use code to deactivate applet divs that are not
in use.

It will take some thinking and experimentation to get this right. I think
there is no direct Chime-->Jmol solution, specifically because of the
known memory issues. You can save loads of memory just by using ZAP when a
model's  use is over.

Another idea would be to make sure that on page loading the applets are
NOT loading full models. This is very inefficient of resources.
>
> Suggestions are welcome: How does one force java to flush its memory?

Java does this automatically, as needed. Don't go there. Basically, get
rid of unnecessary memory-consuming objects, especially large molecular
systems, cartoons, isosurfaces, etc.

> Since Jmol can report memory used, I suppose it can message that
> somehow. Would it be possible to force the java memory flush FROM
> JAVASCRIPT when it becomes critical? Or better yet, from within Jmol
> itself, when it detects that memory is running out?
>

There is nothing to do but take care in how many objects you have live at
one time. Java will take care of the rest. I have taken great pains to
make sure that Jmol does not persist with objects that you think are gone.
If they are gone, they are gone.

> JTAT's design may make unnecessary demands on java memory: currently
> it restarts Jmol between chapters, even when the same molecule is
> used in both chapters. (This design, making each chapter independent
> of the others, greatly simplified the internal structure.) Keeping
> the same Jmol loaded between chapters would require major redesign of
> JTAT, and a more complicated internal structure. And it would only
> solve part of the problem. Using different PDB files in the same
> tutorial, and making comparisons side by side, will still be
> demanding on the memory limits.

It isn't much of a load to add applets, only models.

More later...
Bob

>
> The fact that IE7 works gives some hope that the java memory bug will
> eventually be solved without any changes in JTAT or Jmol. Apple java
> lags behind java development at Sun. It is currently at 1.5.0_13 vs.
> 1.6.0_3 on Windows. That may be part of the Safari problem. But I am
> mystified that in Windows, Firefox, using the same java as IE7, runs
> out of memory, while IE7 doesn't.
>
> In one test, IE6 did run out of memory, but lasted through the
> present 5 chapters before doing so. So it did better than Firefox,
> but not as well as IE7.
>
> I bring this up because you may want to give it consideration when
> you assign priorities to developing complex tutorials. The future is
> uncertain!
>
> -Eric
>
>
> -
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Re: [Jmol-users] POV-Ray export of stereo rendering and referencing Jmol

[hansonr]

> Dear Jmol developpers and users,
>
> The "POV-Ray export" feature have improved a lot
> since the last time (about two months among) I tried
> to use: high quality pictures and also lot of fun with !
> Many thanks to Pim and Bob for the very nice job !
>
> I am interested in exporting a stereo rendering of a
> molecule to POV-Ray but only one half of the view
> is exported (I would say the left one according to the
> test I made by exporting the view after having issued
> a "stereo 90" command).
> This actually also happens when the view is exported
> to an image (for instance, jpeg). The Jmol versions tested
> are 11.3.60,11.4.RC1 and 11.5.2.
> My question is: is it possible to export a stereo rendering ?
> Or is this feature missing ? If so, dear developpers, please
> consider my email as a wish ?
>

There are different sorts of stereo. What sort are you thinking of?
I would think that POV-Ray can support all sorts of stereo output.
Take a look at

http://www.cip.physik.uni-muenchen.de/~wwieser/render/stereo/create.html

and see if that works for you.

So in that case a standard Jmol export of POV-Ray should be adaptable to
stereo with the addition of a command or two.


> According to the FAQ, Jmol should be referenced by its
> website "www.jmol.org". I would like to know if there is a
> a paper or a book I could also cite.
>
> Best regards,
> Max
>
> --
> ***
> Latevi Max LAWSON DAKU
> Departement de chimie physique
> Universite de Geneve - Sciences II
> 30, quai Ernest-Ansermet
> CH-1211 Geneve 4
> Switzerland
>
> Tel: (41) 22/379 6548 ++ Fax: (41) 22/379 6103
> ***
>
>
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Re: [Jmol-users] Jmol 11.4.RC1

[hansonr]

Please file a bug report on this.
>
>
> I was playing with the new release (11.4.RC1) and believe I have found a
> bug. After set picking draw, the mouse will function correctly (using the
> shift or alt key to move a "draw" object, however the "show draw" command
> seems to be broken, it returns coordinates of {0.0 0.0 0.0} for all
> vertices.
>
> Rick Spinney
>
>
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Re: [Jmol-users] Bond formation in PDB files

[hansonr]

If you send me the PDB file, I will take a look. But because you are
defining the CONECT records, Jmol will respect that and not automatically
connect Ser 200 to the inhibitor (which is probably a HETATM, right?)
Try

set forceAutobond TRUE

prior to the load commmand and see if that does the trick.


> Hi All,
>
> I am making a tutorial to illustrate the mechanism of enzyme catalysis of
> hydrolysis of an ester.  The PDB file that I am using shows the Ser 200 at
> the active site covalently bonded to an inhibitor which is bound at the
> active site, and does not contain any hydrogen atoms. I added two hydrogen
> atoms to the file, one was identified as a Ser 200 atom and the other one
> as
> a His (also at the catalytic site) atom.  Both atoms were displayed at
> appropriate locations.  My problem is that the Ser is no longer bonded to
> the inhibitor, even though the Conect commands are still in the PDB file,
> and using the Jmol connect command I can show the Ser bonded to the
> inhibitor at the appropriate place in the mechanism.  I use the connect
> command to make, delete or change the nature of other bonds associated
> with
> the active site.  I do not understand how the information in a PDB file is
> used to make the covalent bonds well enough to know how I affected the Ser
> bonding by adding the hydrogens.  Any suggestions would be greatly
> appreciated.
>
> Karl
>
>
>
> Karl M. Oberholser, Ph.D. Phone:
> Professor of Chemistry Voice: 717-766-0512
> Chemistry & Biochemistry Dept.   Fax: 717-691-6046
> Messiah Collegee-mail: [EMAIL PROTECTED]
> P.O. Box 3049
> One College Avenue
> Grantham, Pa 17027
>
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Re: [Jmol-users] Can jmol initiate zoom change messages? (re: zoom slider)

[hansonr]

> I installed the very nice slab slider available from
> http://wiki.jmol.org:81/index.php/Recycling_Corner#Slider_control_for_Slabbing
> in my Jmol Tutorial-Authoring Template (JTAT).
>
> I have now adapted it to control either zoom or slab.
>
> I would like the zoom slider to auto-slide to match the current zoom
> percentage in Jmol, when the mouse is used for zooming.
>
> Is there any way to set up Jmol to automatically message a change in
> zoom? For example, I'd like Jmol to message two lines something like
> these whenever the zoom changes:
>
> zoom-change-report
> zoom 212.15
>
> I already have code that watches the message stream and resets the
> zoom slider when similar messages go by.
>
> If there is no way to get Jmol to initiate such a report, I can use
> javascript to initiate a query to jmol every one second. That will
> probably work satisfactorily. However, it seems that the ability to
> have Jmol initiate a report when something changes might be generally
> useful.
>

This is called polling, and there are numerous reports in Bugzilla that
Mozilla can't tolerate repeated polling of the applet. Believe it or not,
it totally messes up the typing in the URL line (words end up totally
backward.)

So that is not a feasible option. Zoom is just one of many types of
information that might be of value that way. Reports like this will really
slow down processing, though. I don't know a good solution.


> -Eric
>
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Re: [Jmol-users] Draw molecular HOMO

[hansonr]

Try checking frame 2 instead of frame 1.

Before loading the file, try

set loglevel 5

Then load the file and look in the Java console. You should see
information about what frames the orbitals are in and how many there are.
Gaussian output, for example, puts the MOs in frame 2.

Bob Hanson


>
> Hi all:
> I used the example on link
> http://chemapps.stolaf.edu/jmol/docs/examples-11/mo.htm
> to draw the MO. but I got the error message
> script ERROR: no MO basis/coefficient data available for this frame
> Could anybody help me?
>
> Thanks
> Xibin
>
> _
> ÊÖ»úÒ²ÄÜÉÏ MSN ÁÄÌìÁË£¬¿ìÀ´ÊÔÊÔ°É£¡
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Re: [Jmol-users] Changing the color of the residues is very slow

[hansonr]

>
> More testing:
> Instead of loading some residues at once and then painting all of
> them, I changed the script to select each residue individually and
> then change its colour;
>
> select C1; color [0,0,0];
> select N2; color [0,0,0];
> select C3; color [0,0,0];
> ...
> select N100; color [0,10,0];
> select C101; color [0,10,0];
> ...
>
> Then, the running time of the full script is 42 seconds (2.5 times
> slower). As the color commands are the same, I suppose that the issue
> is related do the selects.

the running time is related to parsing of the script. It's just a very
long script.

>
>
> Now for a bigger DNA (2000 bps)
> -with the script split each 100 lines: 2min 26sec
> -the full script (3000+ lines): i cancelled at 8 minutes...
>
>
> So, clearly, there is an issue with the selects. I think that the cost
> of the function isn't lineal but more like exponential, as multiplying
> the residues number by four doesn't multiply the script running time
> by four but by 12!
>
> How does jmol paint the molecule on load? Clearly it goes a different
> way, because the initial load+paint is just 5-6 seconds

Selecting is extremely fast. It must be the parsing of all those commands
that is slowing the process. You could speed this several ways, depending
upon where the data are coming from:

1) If you are creating these files yourself and you can assign group names
to the atoms in the PDB file, then you could assign colors to those group
names and be done with it.

2) If you can assign a number to the temperature column of the PDB file
corresponding to a color, you can then use a color scheme to assign a
given color to a given "temperature"

3) You don't need to select, then color. You can just

color {N30} [0,0,0]

4) If you know exactly what atoms you want to color, not just their names,
then you could use the (undocumented) color command:

color ({0 4:10 13:15 18:30}) [0,0,0]

The numbers in parentheses+braces are atom index numbers starting from 0.
This feature is used by the state scripts Jmol generates.

Bob Hanson


>
> Thanks for the help,
> Carles
>
> El 10/01/2008, a las 12:46, Angel Herraez escribió:
>
>> Hi Carles
>>
>> This sound strange indeed. I agree that it shouldn't take long.
>>
>> I think that maybe the 100 kB is too long for some unknown memory,
>> stack or cache (I'm just guessing). Try cutting the script file in
>> several pieces and see what happens when you call them one after
>> another (either manually or maybe with a master script)
>>
>> Another idea: test this in the Jmol application.
>>
>>
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>
> --
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> Barcelona Supercomputing Center / Life Sciences
> Nexus II / Jordi Girona, 29 / 08034 Barcelona
> +34 93 413 76 02
>
>
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Re: [Jmol-users] How to align more than two protein structures

[hansonr]

I think some sort of translateSelected might be what you need.

> Hello everyone!
>
>   I now am trying to display 3 proteins in a figures.
>   For example, I have 3 proteins, 1XBL.pdb, 1DKG.pdb, and 1DKX.pdb.
>   What I want to do is I want to display this 3 protein structures at same
> time, and some residues are combinded together such that for 1XBL there
> are 5 interface residues of which the residue IDs are 30 36 69 71 741,
> for 1DKG there are 3 interface residues of which the residue IDs are 13
> 116 174, and for 1DKX there are 4 interface residues of which the
> residue IDs are 6 405 447 483. Based on this information I want to put
> all three proteins are closed to each other.
>   I tried to use the commend: load append "1XBL.pdb" "1DKG.pdb"
> "1DKX.pdb", but I cannot move all the proteins independently.
>   Do you have any idea how to handle this problem? If so, please help me!!
>
>   Simpler example is shown below
>   If the structure of Protein A and B looks like this
>
>   Protein A:
>   |---|
>
>   Protein B:
>   ___|
> |
>
>   So, what I want to do is to combine Protein A and Protein B. Just like
> this.
>
>   Combine A and B
>   |---|
>  ___|
>|
>
>   Thanks
>
>
>
>
>  Send instant messages to your online friends
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Re: [Jmol-users] Message contents of .spt file without execution?

[hansonr]

So, Eric, I think by setting a variable to the contents of an spt file,
you could even select out segments you want to execute. (The simple way to
do this would be to set up a script file with functions and then only run
the functions that you specify.) For that the load("filename") Jmol math
function would be a starting point.


> Sometimes I wish that, from javascript in the browser, I could ask
> the Jmol applet to let me (javascript) peek into the contents of a
> Jmol command script (.spt) file, preferably before I execute it. Is
> there some way to do this?
>
> If not, do others think this would be useful?
>
> I'm envisioning something like this:
>
>  message file myscript.spt
>
> Rather than executing the script, it would simply message the
> contents of the .spt file. I could then parse the script and behave
> accordingly.
>
> This would be somewhat along the lines of "show pdbheader", which
> messages the PDB file header to the javascript messageCallback function.
>
> I am aware that the script file can set javascript variables using a
> "javascript ..." script command. However, if the purpose of that is
> to inform the browser that, for example, the script  plays a movie,
> it requires an additional knowledgable effort on the part of the
> script file author. If I could just preview the contents of the
> script file looking for e.g. delay or moveTo commands, I could tell
> whether there is movie in the script without troubling the author of
> the script file for (redundant) information in another form.
>
> -Eric
>
>
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Re: [Jmol-users] Detect opening of the Jmol console?

[hansonr]

> Is there any way for javascript to detect when the Jmol console is
> opened by the user?
>
No way to detect that. You could enter a feature request to supress
messages for reasons such as this.


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Re: [Jmol-users] Message contents of .spt file without execution?

[hansonr]

I have limited access to Eclipse from Jamaica throughout January. In the
mean time, you can use:

print load("initial-view.spt")


> Dear Paul,
>
> How nice to hear from you!
>
> I had not noticed show FILE -- thank you for
> pointing it out! However, I tried this from local
> files (not on a server) with Jmol 11.3.63 and I get:
>
> show FILE "initial-view.spt"
> pending
> script 8 started
> script ERROR: bad argument count
> line 2 command 1 of file null:
>   show file "initial-view.spt" <<
> Script completed
> Jmol script terminated
>
> On the other hand
>
> show FILE
>
> does work, messaging the entire PDB file currently loaded.
>
> I get the same "bad argument count" when Jmol 11.3.59 is on a server.
>
> Perhaps the "show FILE filepath" command is broken?
>
> -Eric
>
> At 1/13/08, you wrote:
>>Hello Eric, I think that the "show file" command does what you expect.
>> From the documentation :
>>show FILE filepath
>>
>> Delivers the entire contents of the
>> specified file on the server from which the
>> applet was loaded. The filename must be
>> relative to the current page (not necessarily
>> the directory containing the applet) and must be enclosed in quotation
>> marks.
>>
>>Paul
>>
>>Le 12 janv. 08 à 04:55, Eric Martz a écrit :
>>
>>>Sometimes I wish that, from javascript in the browser, I could ask
>>>the Jmol applet to let me (javascript) peek into the contents of a
>>>Jmol command script (.spt) file, preferably before I execute it. Is
>>>there some way to do this?
>>>
>>>If not, do others think this would be useful?
>>>
>>>I'm envisioning something like this:
>>>
>>>  message file myscript.spt
>>>
>>>Rather than executing the script, it would simply message the
>>>contents of the .spt file. I could then parse the script and behave
>>>accordingly.
>>>
>>>This would be somewhat along the lines of "show pdbheader", which
>>>messages the PDB file header to the javascript messageCallback function.
>>>
>>>I am aware that the script file can set javascript variables using a
>>>"javascript ..." script command. However, if the purpose of that is
>>>to inform the browser that, for example, the script  plays a movie,
>>>it requires an additional knowledgable effort on the part of the
>>>script file author. If I could just preview the contents of the
>>>script file looking for e.g. delay or moveTo commands, I could tell
>>>whether there is movie in the script without troubling the author of
>>>the script file for (redundant) information in another form.
>>>
>>>-Eric
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> /* - - - - - - - - - - - - - - - - - - - - - - - - - - -
> Eric Martz, Professor Emeritus, Dept Microbiology
> U Mass, Amherst -- http://www.umass.edu/molvis/martz
>
> Top Five 3D MolVis Technologies http://Top5.MolviZ.Org
> Biochem 3D Education Resources http://MolviZ.org
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> Atlas of Macromolecules: http://atlas.proteinexplorer.org
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Re: [Jmol-users] Message contents of .spt file without execution?

[hansonr]

definitely a bug. Please file a bug report.

>> show FILE "initial-view.spt"
>> pending
>> script 8 started
>> script ERROR: bad argument count
>> line 2 command 1 of file null:
>>   show file "initial-view.spt" <<
>
> Using both Jmol application and JmolApplet 11.0.3, both from local disk
> and from the server, show file "xx.spt"   works.
> Applets 11.1.29  and 11.4 fail with that same error.
>
> Testing with the application, the command broke somewhere between
> 11.1.7 and 11.1.22
>
>
>
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Re: [Jmol-users] bugs in set echo and its documentation

[hansonr]

Definitely bugs. Please file a bug report.

> I love the fact that you can name an echo, display it, then operate
> on a second named echo without affecting the first. This is a super
> feature!
>
> However:
>
> The following "invalid argument" results appear to me to be bugs in
> set echo, in Jmol applet 11.4.RC1, as it is documented:
>
> set echo off # works
> set echo on # invalid argument
>

> set echo username off # works, leaving other usernamed echos displayed
> set echo username on # invalid argument
>
> set echo top off # works, leaving "set echo bottom" displayed
> set echo top on # invalid argument
>
> -
> The documentation states:
>
> "Using percentages allows you to place text anywhere within the
> window and independently justify the text using set echo myecho LEFT,
> set echo myecho RIGHT, set echo myecho CENTER."
>
> However this is what I observe:
>
> set echo myecho 0% 85%
> echo hello
> set echo myecho center # hello remains at left edge, not centered
> echo blah # echo appears at left edge, not centered
>
> -
>
> How would I make a named echo at middle center?
>
> set echo username middle center # integer expected
>
> ---
> Maybe this should be deemed an error?
>
> set echo username 85% center # accepted without error, but no display
>
> -
>
> Documentation: "set echo TOP LEFT" is mentioned in the paragraph
> under percentages, but this syntax is not listed under "set echo".
>
> Thanks,
> -Eric
>
>
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Re: [Jmol-users] mopac2007 images

[hansonr]

note comments at

http://openmopac.net/manual/trouble_shooting.html#visualize%20results



> On 7/10/07, Gordon Ayers <[EMAIL PROTECTED]> wrote:
>>  I have installed Jmol 11.2.4 on my windows XP machine and am having a
>> problem displaying Mopac2007 files. When I open a *.out
>> file it appears to load but nothing is in the display window of Jmol.
>> I also tried loading a *gpt file with the same result. What am I doing
>> wrong?
>
> It might very likely be that there is something particular about your
> Mopac2007 file format. The best thing you can do, is make a demo .out
> file, for example for water or methane or so, using the parameters you
> would use otherwise too, and send this output to the list, or upload
> it into the bug track system, and assign it LGPL license (copyright
> remains with you), so that we can redistribute it in our SVN, and use
> it for future testing purposes.
>
> Egon
>
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Re: [Jmol-users] JmolViewer, Viewer

[hansonr]

Try checking

 if(viewer.haveFrame())

first, just to see if there is a model loaded. ("Frame" in this context
refers to a model, recently refactored as "ModelSet", not a Java Frame.) I
think your problem may be that you have a viewer but no model set. That's
usually what a null pointer exception from a method such as
viewer.getAtomCount() means. In general, when you create a viewer, you
should also call

setAppletContext(String htmlName, URL documentBase, URL codeBase,
String appletProxyOrCommandOptions)

So a typical instantiation might be:

JmolViewer viewer = JmolViewer.allocateViewer(display, modelAdapter);
viewer.setAppletContext("", null, null, "");

That second method includes a call to zap(), which instantiates a new
ModelSet, allowing viewer.getAtomCount() to return "0".

Bob



> I'm building a jmol embedded application which will allow me to open more
> than one molecules. Currently I'm able to open multiple molecules in a
> single application. However now I'm facing problems regarding Viewer. I
> have a jmolPanel which instantiate a SmarterJmolAdapter and also
> JmolViewer like what most people will do. I added this jmolPanel into a
> JInternalFrame (moleculeFrame) which will later be added to the main
> JDesktopPane. I have my own set of swing.GUi components that I want to use
> to access and manipulate the opened molecules which are shown in the
> jmolPanels contained in the moleculeFrames. Now the problem is whenever I
> try to access the viewer of each jmolPanel e.g viewer =
> (moleculeFrame.getJmolPanel()).getViewer();which will ask the jmolPanel of
> that particular moleculeFrame I'm referring to return the Viewer
> (JmolViewer).Then I tried to
> ...System.out.println(viewer.getAtomCount());I'm getting
> nullPointerException from the modelManager. I guess my Viewer is a
>  null when I'm doing this, so any better way of instantiating the viewers
> in order to make it work?Help and advice will be very much
> appreciated.RegardsKevin
> _
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Re: [Jmol-users] Spin fps popup menu bug?

[hansonr]

definitely a bug. Please enter a bug report.

> El 11 Jul 2007 a las 15:12, Nick Greeves escribió:
>
>> Issuing the commands from the popup menu leads to errors in console
>> e.g. Set X rate 10
>>
>> script ERROR: unrecognized SPIN = parameter: X
>> 
>> set spin >> X << 10
>>
>
> I can confirm the reported error in 11.2.4 and 11.3.4; uppercase X or
> Y are rejected.
>
> This is most surprising, as Jmol has never been case-sensitive.
>
>
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Re: [Jmol-users] jmol usability questions

[hansonr]

> Hi Volker
>
>> * After a fairly complex series of scripted commands in a large
>> molecule, I do
>> not see a simple way to "save" the current state of jmol - i.e. whenever
>> I'd
>> like to go back and reproduce my work, "all is lost" and I end up
>> starting
>> from scratch. Is that correct? (with the recent addition of "show set",
>> a
>> save option might not be too far off?)
>
> Well, this was not possible if former versions, but the latest 11.1.x
> (maybe even 11.0) can do exactly what you want. Please read "save
> STATE" at
> http://www.stolaf.edu/academics/chemapps/jmol/docs/?ver=11.1#save
>
> What it does not do is saving to a file, but you can "show state" and
> copy the output from the console.
>

from the Jmol application (not applet):

write state "somefile.spt"


then, at your leisure:

script "somefile.spt"

should get you back EXACTLY where you left off. If it doesn't I want to know!



>
>> Now, after some experimental work with jmol (I am not a java
>> programmer), I
>> find that some laborious hand conversion of my OpenBabel generated pdb
>> files
>> will suddenly activate all the nicer features in jmol if
>> (1) the pdb file contains the peptide identifier (ALA or the likes)
>

Jmol does not use the ALA names -- these are too unpredictable. It uses
the names of the atoms -- CA, N, O, etc. Particularly important is to
label the alpha carbon CA.

> Yes, I guess that's one of the keys.
>
>> (2) the pdb file assigns the peptide number to each atom
>
I think it IS important that the residues be numbered, yes. 1 for all the
atoms in the first residue, 2 for the next, etc. That field is critical.

>
>> (3) there is a MAIN at the end of each line of the pdb file
>
> I don't think this is relevant.
>

right, not relevant.

>> (4) "CA" and "CB" are properly identified.
>

CA is critical.

> Likely
>
>> Since jmol is able to create the correct wireframe geometry for all
>> these
>
> But wireframe, i.e. bond assignation, is only based on interatomic
> distance.
>
>> molecules, it should not be too far a stretch to be able to identify the
>> longest connected line in a wireframe, see whether the sequence
>> is -CCN-CCN-CCN- ... in a certain segment, and attempt to auto-recognize
>> a
>> peptide backbone (and activate all the nice eye-candy).
>

All that is needed is N and CA for this.

> As I said, as far as I know the backbone is assigned based not on
> elements, but on proper IDs. I guess there could be trouble with
> nonprotein molecules having -CCN-CCN-, maybe?
>
>> Is something like this possible / am I missing a shorter way here?
>
> I don't think there's any shorter way, it's just that XYZ was not
> meant for proteins. Why do you have xyz files of proteins?

Just use the PDB format, and you will be OK. Residue numbers, CA/N and C,O
if you want cartoons, and you will be all set.

>
Bob Hanson



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Re: [Jmol-users] Jmol 10.9.87 ...

[hansonr]

oh, except it's just

jmolLoadInline
jmolLoadInlineScript

as before -- no new command. What's new is that the first parameter can 
be a JavaScript Array of strings as well as a single string now.

Bob

Nicolas Vervelle wrote:

>... is available for download at http://www.jmol.org/files
>News:
>jmolLoadInlineFiles
>Nico
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Re: [Jmol-users] Jmol 10.9.86

[hansonr]

I see it now. Sure -- that clicking is doubling the zoom, so at some point
it crosses my "magic number" threashold, perspective depth is phased out,
and it gets super-magnified.

This effect is not seen if

 set perspectivedepth off


Rolf, Frieda, Tim, anyone interested:

Pick your favorite solution:

1) I don't like the double-clicking on the central atom to zoom in on it.
Please remove that.

2) I like the double-clicking on the central atom to zoom in on it, but
only under certain circumstances. (Specify)

3) I like the double-clicking to zoom in. Leave it there.

Separately, only if you answered (2) or (3):

4) Don't double the zoom if that would put it past the maximum for
perspective depth when perspective depth is turned on.

5) Don't double the zoom if that would (specify)

Bob





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

[hansonr]

I realize that. You are the first to try to use this information, I think.
Just tell me what you think "shapeInfo" should include.

> [EMAIL PROTECTED] wrote:
>>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.
>>
>>
>>
> The command works. But since it doesn't provide for which object the
> coordinates are, I guess I will have to use 'jmolGetPropertyAsJSON' to
> get all necessary information. I have to take a deeper look into that
> before I am able to use it, but I like the possibility to get all
> necessary information for all draw objects at once.
>
>>
>>
>>>[EMAIL PROTECTED] wrote:
>>>
>>>
>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.
>>>
>>>
> The freezing problem seems to depend additionally on other things. Today
> Firefox didn't freeze either with or without the timeout. I restarted
> the browser several times and never got a freeze. Yesterday I always got
> a freeze, but I am not aware of any change (not even a reboot or a new X
> server session). So 'jmolScriptWait' unfortunately still remains on my
> "don't use it" list.
>
>
> I noticed a strange behaviour of the 'show draw' command. If the
> definition command and the show command are provided within a single
> 'jmolScript' command, no coordinates are shown. Only if they are
> provided within different 'jmolScript' commands the coordinates are shown:
>
> jmolScript("draw line1 (atomno=1) (atomno=2);  draw line1; show draw;");
>-> WITHOUT COORDINATES
>
> jmolScript("draw line1 (atomno=1) (atomno=2);");
> jmolScript("draw line1; show draw;");
>-> WITH COORDINATES
>
> Sometimes the 'show draw' command freezes Jmol with the following error
> message (I couldn't figure out any specific condition, version 10.9.86):
>
> java.lang.NullPointerException
> at org.jmol.viewer.Draw.getDrawCommand(Draw.java:658)
> at org.jmol.viewer.Draw.getProperty(Draw.java:217)
> at org.jmol.viewer.Frame.getShapeProperty(Frame.java:1096)
> at
> org.jmol.viewer.ModelManager.getShapeProperty(ModelManager.java:393)
> at org.jmol.viewer.Viewer.getShapeProperty(Viewer.java:2475)
> at org.jmol.viewer.Eval.show(Eval.java:4720)
> at org.jmol.viewer.Eval.instructionDispatchLoop(Eval.java:610)
> 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)
>
>
> Besides the Java console shows sometimes the following error message (no
> freezing of Jmol):
>
> java.lang.IllegalArgumentException: null source
> at java.util.EventObject.(EventObject.java:34)
> at java.awt.AWTEvent.(AWTEvent.java:252)
> at java.awt.event.ComponentEvent.(ComponentEvent.java:94)
> at java.awt.event.WindowEvent.(WindowEvent.java:174)
> at java.awt.event.WindowEvent.(WindowEvent.java:211)
> at
> java.awt.DefaultKeyboardFocusManager.dispatchEvent(DefaultKeyboardFocusManager.jav

Re: [Jmol-users] Jmol 10.9.86

[hansonr]

When exactly is this unexpected zoom happening? I'm not seeing it.

>
> Like Frieda I also don't like the change of zoom when picking a new
> center. It was totally unpredictable for me, if there would be a very
> large or very small change in zoom and if it would zoom in or out.
>


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Re: [Jmol-users] [Jmol-developers] some advice regarding Jmol, Javascript & PHP

[hansonr]

you need 10.9.87, now up there, I think.

> On Fri, 2006-10-27 at 09:03 -0500, [EMAIL PROTECTED] wrote:
>> Better still, and (amazingly) it worked the first time. This will be in
>> 10.9.87 and can be tested at
>>
>> http://www.stolaf.edu/academics/chemapps/jmol/docs/examples-11/new.htm
>>
>> jmolLoadInline([model1, model2, model3...],target)
>> jmolLoadInlineScript([model1, model2, model3...],script,target)
>>
>> models may be of mixed type -- PDB, XYZ, MOL, SDF, etc.
>
> I followed the link above to get the latest version (10.9.86) - but am
> again getting stuck.
>
> I have a test page at
>
> http://156.56.90.245/~rguha/test.html
>
> which tries to load two structures.
>
> However the applet comes up, but the status bar says:
>
> Jmol script terminated
>
> but the Jmol console does not show anything (neither does the Jaavscript
> console of Firefox). And nothing shows up.
>
> Is it correct to use the following sequence load the applet:
>
>   jmolInitialize("./jmol");
>   jmolApplet(400, "console on");
>   jmolLoadInline([m3, m1]);
>
>
> ---
> Rajarshi Guha <[EMAIL PROTECTED]>
> GPG Fingerprint: 0CCA 8EE2 2EEB 25E2 AB04 06F7 1BB9 E634 9B87 56EE
> ---
> A hacker does for love what others would not do for money.
>
>
>
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Re: [Jmol-users] [Jmol-developers] some advice regarding Jmol, Javascript & PHP

[hansonr]

> El 27 Oct 2006 a las 9:03, [EMAIL PROTECTED] escribió:
>
>> What's our status on a description of how to use Jmol.js?
>
> Bob, are you meaning that we need a different, new, manual for
> Jmol.js?
>
no, no. I was just wondering how up to date it was. I haven't looked at it
myself in a long time. I just thought we shouldn't forget it on the way to
11.0.

That would be great if you looked it over, Angel.

> I was involved in the last update of
> http://jmol.sourceforge.net/jslibrary/
> although some commands are listed but yet undocumented.
>
> I can add this new multi-model inline loading to jmolLoadInline
> description tonight.
>
>
>
>
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Re: [Jmol-users] [Jmol-developers] some advice regarding Jmol, Javascript & PHP

[hansonr]

Better still, and (amazingly) it worked the first time. This will be in
10.9.87 and can be tested at

http://www.stolaf.edu/academics/chemapps/jmol/docs/examples-11/new.htm

jmolLoadInline([model1, model2, model3...],target)
jmolLoadInlineScript([model1, model2, model3...],script,target)

models may be of mixed type -- PDB, XYZ, MOL, SDF, etc.

Jmol recognizes that the first parameter is an array, and JavaScript
doesn't care. No changes needed in Jmol.js!

What's our status on a description of how to use Jmol.js?

Bob

:)

ps -- creating jmolLoadInline was the very first request I ever made of
Miguel when I posted my first message to this list back in May of 2004.
 It's a
pleasure now to be on the other end with implementing its extension to
multiple file types. Thanks again, Miguel!



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Re: [Jmol-users] [Jmol-developers] some advice regarding Jmol, Javascript & PHP

[hansonr]

correction!!! Duh.

I propose:

jmolLoadInlineFiles(modelData,script,target)

 target:optional applet extension
 script:a script to run -- required, but may be ""
 modelData: Array[] of string data

(I'm not exactly certain how one passes Array data to Java, but I'll look
into it.)



> correction:
>
>> Rajarshi,
>>
>> I have a solution for you. Don't convert your files yet.
>>
>> I propose:
>>
>> jmolLoadInlineFiles(modelData,separator,script,target)
>>
>> target:optional applet extension
>> separator: an explicit string of your choice indicating a new model
>> script: a script to run -- required, but may be ""
>> modelData: your model data, with each model separated by that separator
>>
>>
>> Sound OK?
>>
>> Bob
>>
>>
>>
>>
>>
>> -
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>
>
>
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Re: [Jmol-users] [Jmol-developers] some advice regarding Jmol, Javascript & PHP

[hansonr]

correction:

> Rajarshi,
>
> I have a solution for you. Don't convert your files yet.
>
> I propose:
>
> jmolLoadInlineFiles(modelData,separator,script,target)
>
> target:optional applet extension
> separator: an explicit string of your choice indicating a new model
> script: a script to run -- required, but may be ""
> modelData: your model data, with each model separated by that separator
>
>
> Sound OK?
>
> Bob
>
>
>
>
>
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Re: [Jmol-users] some advice regarding Jmol, Javascript & PHP

[hansonr]

Rajarshi,

I have a solution for you. Don't convert your files yet.

I propose:

jmolLoadInlineFiles(modelData,separator,target)

target:optional applet extension
separator: an explicit string of your choice indicating a new model
modelData: your model data, with each model separated by that separator


Sound OK?

Bob





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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
>
>
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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


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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
>
>
>
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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
>
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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


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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.
>
>
>
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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



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[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






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[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.






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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




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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
>
> ///
>
>
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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



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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
>
>
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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



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

[hansonr]

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}

:)

Bob



> yes, something like that might work:
>
> draw textID TEXT {whatever} "your text"
>
>
>> Implementation of the new draw object 'text', that places a text at a
>> specified position.
>> If I wanted to have for example a plane perpendicular to the line
>> between the alpha carbon atoms of 2 amino acid residues, labelled as
>> "boundary1", I could then define the following objects:
>>
>> draw boundary1 PERP PLANE (atomno=15) (atomno=25);
>> draw boundary1_label PERP TEXT (atomno=15) (atomno=25) OFFSET {x y z}
>> "boundary1"
>>
>> Regards,
>> Rolf
>>
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Re: [Jmol-users] initial zoom level

[hansonr]

set zoomLarge TRUE   #Jmol-default
set zoomLarge FALSE  #Chime-default


> I believe the zoom level in Jmol is tied to the larger of the two
> dimensions of the applet. Is this a setting that can be changed, to
> set it according to the lesser dimension of the applet?
>
> I usually like the default zoom, and was very happy it was set up
> that way because it maximizes the total amount of zoom available. But
> I have run into a situation where i would like it to behave the other
> way.
>
> Thanks,
> Frieda
>
> ///
>
> Frieda Reichsman, PhD
> Molecules in Motion
> Interactive Molecular Structures
> http://www.moleculesinmotion.com
>
> ///
>
>
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Re: [Jmol-users] JMOL/G03/MO

[hansonr]

Romuald:

Generally with Gaussian log files there are several models that load. The
entire course of the calculation is there, but only the final model has
the MOs. My guess is that you are only looking at the first model. Try
right-clicking on the applet and look for "models 1/n" -- there should be
a list there. Select the LAST model. Then using the popup menu again, look
under "surfaces --> molecular orbitals" and see if they are there. If you
have vibrations as well, then I think the MOs are in the model just before
the vibrations.

If this doesn't solve your problem, please send the log file to me offline
so I can look at it.

Bob Hanson


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

[hansonr]

yes, something like that might work:

draw textID TEXT {whatever} "your text"


> Implementation of the new draw object 'text', that places a text at a
> specified position.
> If I wanted to have for example a plane perpendicular to the line
> between the alpha carbon atoms of 2 amino acid residues, labelled as
> "boundary1", I could then define the following objects:
>
> draw boundary1 PERP PLANE (atomno=15) (atomno=25);
> draw boundary1_label PERP TEXT (atomno=15) (atomno=25) OFFSET {x y z}
> "boundary1"
>
> Regards,
> Rolf
>
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Re: [Jmol-users] Jmol prerelease 10.9.80

[hansonr]

sorry -- forgot to commit Labels.java


> I tried again with 10.9.83 and the result is still the same : the files
> from souceforge do not work whereas the ones from Bob's website are
> running well.
> Paul
>
> Nicolas Vervelle a écrit :
>
>>Paul Pillot wrote:
>>
>>
Can you try Jmol 10.9.81 ?
Be sure to clean the directory where you have installed Jmol.

Nico


-




>>>I solved the previous problem by using the files from Bob Hanson's
>>>website. Now, I've just tried the new files from sourceforge and I got
>>>the same message again :
>>>"Ignore
>>>Ignore
>>>java.lang.UnsupportedClassVersionError:
>>>org/jmol/translation/JmolApplet/Messages_fr (Unsupported major.minor
>>>version 49.0)
>>>at java.lang.ClassLoader.defineClass0(Native Method)
>>>at java.lang.ClassLoader.defineClass(Unknown Source)
>>>at java.security.SecureClassLoader.defineClass(Unknown Source)
>>>
>>>
>>>
>>>
>>Ok, I will try to find how to create the Messages classes with JDK 1.4
>>
>>Bob,
>>
>>which version of the JDK are you using to create the jars on your server
>> ?
>>
>>Nico
>>
>>
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Re: [Jmol-users] Jmol prerelease 10.9.80

[hansonr]

Sorry, this was my failure to commit Labels.java

> I tried again with 10.9.83 and the result is still the same : the files
> from souceforge do not work whereas the ones from Bob's website are
> running well.
> Paul
>
> Nicolas Vervelle a écrit :
>
>>Paul Pillot wrote:
>>
>>
Can you try Jmol 10.9.81 ?
Be sure to clean the directory where you have installed Jmol.

Nico


-




>>>I solved the previous problem by using the files from Bob Hanson's
>>>website. Now, I've just tried the new files from sourceforge and I got
>>>the same message again :
>>>"Ignore
>>>Ignore
>>>java.lang.UnsupportedClassVersionError:
>>>org/jmol/translation/JmolApplet/Messages_fr (Unsupported major.minor
>>>version 49.0)
>>>at java.lang.ClassLoader.defineClass0(Native Method)
>>>at java.lang.ClassLoader.defineClass(Unknown Source)
>>>at java.security.SecureClassLoader.defineClass(Unknown Source)
>>>
>>>
>>>
>>>
>>Ok, I will try to find how to create the Messages classes with JDK 1.4
>>
>>Bob,
>>
>>which version of the JDK are you using to create the jars on your server
>> ?
>>
>>Nico
>>
>>
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>
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Re: [Jmol-users] polyhedra and restrict, bug or feature ?

[hansonr]

Yes, I think so. Done.

Bob

> Hello,
> I've discovered that polyhedras are not cleared out of the screen after
> a restrict command.
> My guess was that they should be deleted when someone applies a restrict
> (?)
>
> - Is there another generic way (other than restrict) to clear all the
> objects from the screen and keep the model loaded in the meantime ?
> My aim is to reset the actual view before applying all the commands from
> the history except the last one, in order to have an undo effect.
>
> Paul
>
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Re: [Jmol-users] labels with pointers

[hansonr]

OK, you win!

set labelPointerBackground  # true: use background color (default)
set labalPointerBox # true: display pointer when boxed (default)
set labelPointerNoBox   # true: display pointer when not boxed (not def)

Bob


> On Oct 23, 2006, at 8:28 PM, [EMAIL PROTECTED] wrote:
>> offsetting the label and placing a box around it.
>> This will result in a pointer appearing from
>> the middle left edge of the label to the atom
>
> I am using this now in a couple of figures. Thanks, Bob, this is an
> excellent labeling option. A couple of things have come up -
>
> When using a label offset with a negative x value the pointer line
> disappears. I think this is a bug, and the desired behavior would be
> for the pointer line to extend from the middle right edge of the box.
>
> Using a background label color that is the same color as the applet
> background makes the pointer line invisible as well, since they are
> the same color. This may seem like a picky thing, but sometimes
> having the label background color contrast with the applet background
> color brings too much attention to the label. So it would be nice to
> be able to specify the pointer line color to match the label font
> color, optionally.
>
> Frieda
>
>
> ///
>
> Frieda Reichsman, PhD
> Molecules in Motion
> Interactive Molecular Structures
> http://www.moleculesinmotion.com
>
> ///
>
>
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Re: [Jmol-users] Problems with CIF Files

[hansonr]

I apologize if I've sent this already. My email it a bit hard to manage
when I'm out of town.

Bob

>
> I am very new to jmol but it is an excellent tool. I want to view
Fluorite
> and Bixbyite structures using it to create an applet. Basically, I want
to
> replicate what the American Mineralogists Crystal Structure database
does
> with these structures in a powerpoint presentation.
>
> However, when I download the CIF files from the applets on that website
I
> run into problems. With the fluorite structure, I only get two atoms
showing. Now, fluorite is very simple structure, is that all the
information
> the program actually needs and then I need to create a script to extend
it
> to get the full unit cell? When I try bixbyite, I only get three atoms
showing. Is it likewise the same problem?
>

right, same problem. You are seeing the data as given in the files. No
symmetry applied. To see one full unit cell, with symmetry, use:

load filename.cif {1 1 1}

If you play a little more, you can get some very nice effects. This
script, for example, displays polyhedra at


> I have uploaded the *.cif files I am trying to use (they are from the AMCSD
> Database - which I will of course reference) and any help in wrapping my
head around this program and how to display full unit cells would be
greatly
> appreciated.
>
> Sincerely,
>Justin Hood
>
> http://www.nabble.com/file/3782/fluorite.cif fluorite.cif
> http://www.nabble.com/file/3783/bixbyite.cif bixbyite.cif
> --
> View this message in context:
> http://www.nabble.com/Problems-with-CIF-Files-tf2490469.html#a6943217
Sent from the jmol-users mailing list archive at Nabble.com.
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Re: [Jmol-users] label line, plane ...

[hansonr]

this was in my drafts box. Not sure I sent it.

Rick,

Gotta think out of the box on this one.

>
> Is there a way to label a line or plane created by the "draw" command?
>
> i.e. draw line1 {0.0 0.0 0.0} {4.0 0.0 0.0}; select $line1; label "x";

Ahhh, custom axes, eh?

No, sorry, can't do that. Labels are strictly properties of atoms. And you
can only select atoms as well, not drawn objects.

Depends how much control you have over your subject matter. Here's what I
would do:

1) Create a file labels.xyz:

2
just 2 labels
He 4.1 0.0 0.0
Xe -0.1 0.0 0.0

2) load labels.xyz along with your file:


load "fileset" "myfile.xyz" "labels.xyz"
restrict */1001 # turn off all atoms in second "labels" frame
frame 0;
draw xaxis {0 0 0} {4 0 0}  #property of both frames
select _He; label x #label is in frame 2001
select _Xe; label 0 #label is in frame 2001

frame 1001   # no labels
frame 2001   # no molecule
frame 0  # everything


The frame command just prior to draw determines what you see when.


load "fileset" "myfile.xyz" "labels.xyz"
restrict */1001 # turn off all atoms in second "labels" frame
frame 1001;
draw xaxis {0 0 0} {4 0 0}  #property of frame 1001
select _He; label x #label is in frame 2001
select _Xe; label 0 #label is in frame 2001

frame 1001   # molecule, axis, but no labels
frame 2001   # just labels
frame 0  # everything


or


load "fileset" "myfile.xyz" "labels.xyz"
restrict */1001 # turn off all atoms in second "labels" frame
frame 2001
draw xaxis {0 0 0} {4 0 0}  #property of frame 2001
select _He; label x #label is in frame 2001
select _Xe; label 0 #label is in frame 2001

frame 1001   # no axis or labels
frame 2001   # no molecule
frame 0  # everything


Enjoy!

Bob


>
> Thanks, Rick
>
> Dr. Richard Spinney
> Department of Chemistry
> Ohio State University
> 100 West 18th Ave
> Columbus, OH
> 43210
> (614) 247-6847
>
>
>
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Re: [Jmol-users] sprouting Hydrogens, coloring isosurfaces

[hansonr]

Byrne Pedit wrote:

>I am resurrecting some RasMol/Chime scripts and have a couple commands I
can't duplicate. I have extensively searched the archives, documentation
and
>experimented to no avail.
>The "sprout hydrogen" command (Chime?) would calculate positions for
hydrogen atoms not resident in a pdb file so they could be displayed. I
see
>Jmol seems capable of such calculations for producing isosurfaces but I
can't find how to display them in simple spacefill mode. (I am trying to
emphasize the substrate-active site fit in a protein structure tutorial.)
>
Atom "sprouting" is not available except in the context of isosurfaces. 
For small systems or pieces of larger ones you can generate the JVXL  file
after creating the isosurface and, I think, the first 100 atoms are
dumped. So then you could read that -- but it's MOL file format, not PDB,
so you would lose PDB-type information. We could look into this more if it
is valued; hydrogens are  sprouted only for carbon atoms.

Bob Hanson

>I also cannot get the isosurface command to generate any other than a
uniformly colored surface. I previously generated, and colored, surfaces
with the "molesurface" command with such ancillary commands as:
>surface molsurface white 0.45; set mep distance 99.0; set charge function
gasteiger; calculate charges refresh; list molsurface color potential; (I
probably copied and tweaked this from others so don't think I'm ready
for
>too erudite a response on this!) The purpose here was to paint a picture
of
>the protein as this unique electromagnetic landscape ready to interact
with
>its environment in unique ways. The other purpose was, of course, because
it
>looks cool.
>I have tried the "colorscheme" parameter (again on a pdb file) without
luck.
>The "Jmol interactive scripting documentation" seems a bit short on how
some
>of these parameters should be specifically coded. For instance, it shows
the
>argument of COLORSCHEME in quotes which certainly doesn't work within a
jmolRadio call.
>Thanks for any help on this.
>Byrne Pedit
>[EMAIL PROTECTED]
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Re: [Jmol-users] labels with pointers

[hansonr]

Frieda Reichsman wrote:

> On Oct 23, 2006, at 8:28 PM, [EMAIL PROTECTED]
>  wrote:
>> offsetting the label and placing a box around it.
>> This will result in a pointer appearing from
>> the middle left edge of the label to the atom
> I am using this now in a couple of figures. Thanks, Bob, this is an 
excellent labeling option. A couple of things have come up -
> When using a label offset with a negative x value the pointer line 
disappears. I think this is a bug, and the desired behavior would be 
for the pointer line to extend from the middle right edge of the box.

Actually, it's intended that way, but for no particularly good reason
other than I was lazy. Feel free to recommend it as a  feature request.

> Using a background label color that is the same color as the applet 
background makes the pointer line invisible as well, since they are  the
same color. This may seem like a picky thing, but sometimes having  the
label background color contrast with the applet background color  brings
too much attention to the label. So it would be nice to be able  to
specify the pointer line color to match the label font color, 
optionally.

certainly could do that.

> Frieda
> ///
> Frieda Reichsman, PhD
> Molecules in Motion
> Interactive Molecular Structures
> http://www.moleculesinmotion.com
> ///
>
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Re: [Jmol-users] can't color triangle object

[hansonr]

> OK, I see now you said "PLANE" because you were only designating 3
> points. If you had used four points would "PLANE" become optional?

yes.

>
> Is there a means to draw curved objects such as spheres?
>

isosurface sphere

> Thanks,
> Frieda
>
>
> On Oct 23, 2006, at 11:04 PM, [EMAIL PROTECTED] wrote:
>
>> How curious!
>>
>> There is no keyword TRIANGLE, so this command is assigning the name
>> "TRIANGLE" to the draw object. The coloring command would then be
>>
>>   color TRIANGLE green
>>
>> But the solution is to just use
>>
>> draw triangle1 300 (atomno=1) (atomno=2) (atomno=3);color
>> $triangle1 green
>>
>> Bob
>>
>>
>>> but with
>>> draw triangle1 300 TRIANGLE (atomno=1) (atomno=2) (atomno=3);color
>> $triangle1 green
>>
>>
>>
>>>
>>> I get the default yellow-gold color triangle.
>>>
>>> This is with Jmol v 10.9.83
>>>
>>> Frieda
>>>
>>>
>>> ///
>>>
>>> Frieda Reichsman, PhD
>>> Molecules in Motion
>>> Interactive Molecular Structures
>>> http://www.moleculesinmotion.com
>>>
>>> ///
>>>
>>>
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>>
>>
>>
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> ///
>
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> Molecules in Motion
> Interactive Molecular Structures
> http://www.moleculesinmotion.com
>
> ///
>
>
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Re: [Jmol-users] label line, plane ...

[hansonr]

Rick,

Gotta think out of the box on this one.

>
> Is there a way to label a line or plane created by the "draw" command?
>
> i.e. draw line1 {0.0 0.0 0.0} {4.0 0.0 0.0}; select $line1; label "x";

Ahhh, custom axes, eh?

No, sorry, you can't do that. Labels are strictly properties of atoms. In
addition, you can only select atoms, not drawn objects, so "select $line1"
is out.

Depends how much control you have over your subject matter. Here's what I
would do:

...no, wait. I'm not going to tell you. ;)

Let me leave it as a puzzle to the Jmol users. We want:

1) to be able to draw any label of any sort, any font, any size, any
color, anywhere on any model, at a particular 3D molecular location, and

2) to be able to display and hide that label at will.

This can be done in Jmol. How would you do it?

If we don't hear a response in a suitable timeframe for Rick, I have a
sealed envolope here.

Bob



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Re: [Jmol-users] can't color triangle object

[hansonr]

How curious!

There is no keyword TRIANGLE, so this command is assigning the name
"TRIANGLE" to the draw object. The coloring command would then be

  color TRIANGLE green

But the solution is to just use

draw triangle1 300 (atomno=1) (atomno=2) (atomno=3);color $triangle1 green

Bob


> but with
> draw triangle1 300 TRIANGLE (atomno=1) (atomno=2) (atomno=3);color
$triangle1 green



>
> I get the default yellow-gold color triangle.
>
> This is with Jmol v 10.9.83
>
> Frieda
>
>
> ///
>
> Frieda Reichsman, PhD
> Molecules in Motion
> Interactive Molecular Structures
> http://www.moleculesinmotion.com
>
> ///
>
>
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Re: [Jmol-users] Feature request: set labels

[hansonr]

Eric, this would be an extremely difficult calculation. The labelsGroup
calculation is possible because it is not based on a distance measurement,
just a collective Z-ordering that is measured in a different sort of
"perspective space".

I'd like you to think more about the possibility of offsetting the label
and placing a box around it. This will result in a pointer appearing from
the middle left edge of the label to the atom, so, though nothing is
perfect, this might at least make it more obvious what a label is pointing
to.

Bob


> Dear Bob,
>
> I think we need a fourth "set labels" mode:
>
> set labels 
> e.g.
> set labels 10.0
>
> would hide a label only when an atom farther than 10 Angstroms from the
> labeled atom comes in front of it.
>
> Here is the kind of problem that I believe necessitates such a solution:
>
> I need to label some surface residues on a protein with numbers 1, 2, 3,
> etc. These residues are in a small contiguous patch (but are not
> continuous
> in the protein backbone chain). (They represent the epitope for binding an
> antibody.)
>
> When I use 'set labelsFront', and label only the alpha carbons, when you
> rotate the protein, you see the labels on the "wrong side", when all the
> atoms of the labeled residues are "behind". This is not useful.
>
> When I use 'set labelsGroup', and label only one atom per group (the alpha
> carbon), still often an atom outside the group hides the label. The result
> is that it is hard to find an orientation where all the labels can be seen
> at once. This makes it difficult to discern the sequence of numbered
> residues 1, 2, 3 etc., which is the goal of my labeling.
>
> The best solution I have come up with is to label every atom in each
> residue with the number, and use set labelsGroup on. This produces an ugly
> jumble of overlapping number labels, but does make it easy to see all the
> numbers at once, and thus to discern the sequence 1, 2, 3, etc.
>
> So, using an arbitrary user-settable distance, beyond which atoms hide the
> label, would solve this problem. I could label only alpha carbons, you
> could see all the labels at once, but when you turn the protein 180
> degrees
> and look at the "back", the labels would be obscured.
>
> -
> As a separate issue, it seems to me that there are now three "set label"
> modes (and I'm proposing a 4th), and that a better command syntax would be
>
> set labels atom
> set labels group
> set labels front
> set labels 
>
> or
>
> set labelsHiddenBehind atoms
> set labelsHiddenBehind groups
> set labelsHiddenBehind none
> set labelsHiddenBehind 
>
> Thanks, -Eric
>
> /* - - - - - - - - - - - - - - - - - - - - - - - - - - -
> Eric Martz, Professor Emeritus, Dept Microbiology
> U Mass, Amherst -- http://www.umass.edu/molvis/martz
>
> Biochem 3D Education Resources http://MolviZ.org
> See 3D Molecules, Install Nothing! - http://firstglance.jmol.org
> Protein Explorer - 3D Visualization: http://proteinexplorer.org
> Workshops: http://workshops.proteinexplorer.org
> World Index of Molecular Visualization Resources: http://molvisindex.org
> ConSurf - Find Conserved Patches in Proteins: http://consurf.tau.ac.il
> Atlas of Macromolecules: http://atlas.proteinexplorer.org
> PDB Lite Macromolecule Finder: http://pdblite.org
> Molecular Visualization EMail List (molvis-list):
>http://bioinformatics.org/mailman/listinfo/molvis-list
> - - - - - - - - - - - - - - - - - - - - - - - - - - - */
>
>
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Re: [Jmol-users] Problems with CIF Files

[hansonr]

Justin, the latest version of Jmol up now (10.9.82 or 10.9.83) should do
what you want.

Three thoughts:

1) If you have a Windows PC, for your PowerPoint presenation consider
using LiveWeb. (http://skp.mvps.org/liveweb.htm)

2) Take a look at some of the demos at http://icsd.ill.fr/icsd/index.html
They have a very nice installation of Jmol; you might get an idea or two
looking at those pages.

3) I recommend the following:

 load myfile.cif {444 666 1};display cell=555;zoom 300

What this does is display a complete unit cell for which all the atoms
have all the correct number of neighbors in all directions. So then you
could add, for example,

  polyhedra 2.5 (displayed and _Na)

to draw polyhedra at selected atoms.

These commands are explained further at

http://www.stolaf.edu/academics/chemapps/jmol/docs


Bob Hanson




>
> I am very new to jmol but it is an excellent tool. I want to view Fluorite
> and Bixbyite structures using it to create an applet. Basically, I want to
> replicate what the American Mineralogists Crystal Structure database does
> with these structures in a powerpoint presentation.
>
> However, when I download the CIF files from the applets on that website I
> run into problems. With the fluorite structure, I only get two atoms
> showing. Now, fluorite is very simple structure, is that all the
> information
> the program actually needs and then I need to create a script to extend it
> to get the full unit cell? When I try bixbyite, I only get three atoms
> showing. Is it likewise the same problem?
>
> I have uploaded the *.cif files I am trying to use (they are from the
> AMCSD
> Database - which I will of course reference) and any help in wrapping my
> head around this program and how to display full unit cells would be
> greatly
> appreciated.
>
> Sincerely,
>Justin Hood
>
> http://www.nabble.com/file/3782/fluorite.cif fluorite.cif
> http://www.nabble.com/file/3783/bixbyite.cif bixbyite.cif
> --
> View this message in context:
> http://www.nabble.com/Problems-with-CIF-Files-tf2490469.html#a6943217
> Sent from the jmol-users mailing list archive at Nabble.com.
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Re: [Jmol-users] Validate with Jmol

[hansonr]

(this probably should go to the developer list -- Eike, are you on that?)

Please feel free to experiment with this. Let me know on or off list if
you need any assistance. One thing that is not necessarily optimal in Jmol
is that processing occurs DURING script evaluation -- if there is an
error, say, at word 6 of "isosurface", then it is possible that you will
get a partially rendered isosurface. It's just the way it was done.

However, if you really wanted to work on this, I think it could work. What
you would do is write a class extension to Viewer and make your test
"viewer" an instance of that. All actions by Eval run through Viewer
methods, so all you have to do is create different versions of those
particular methods in your test version. You could have them do anything
(or nothing), as you wish. And certainly there's no need to render
anything. As a start, we have:

synchronized public String scriptCheck(String strScript)

This method does just the compilation, and checks for:

  a) improper syntax involving punctuation and operators.
  b) invalid commands.
  c) improper atom specifications.

So that's a lot already. But it has a flaw in that it passes
"unimplemented" commands to Eval right now. Actually, I think this could
be fixed without too much hassle.

public void setAppletContext(String htmlName, URL documentBase, URL
codeBase, String appletProxyOrCommandOptions)

This method allows you to set runtime parameters such as running silently,
running "headless" (turning off all frame rendering), etc.

That is, you can ALMOST do exactly what you describe now.

Bob


>
> My first approach (obviously?) was to look into the process flow
implemented
> by Jmol and then write a wrapper to reuse those classes and methods.
That
> is
> run the same tests as in the Jmol check on "compiler" level and
evaluation
> level. But as i figured out this might be impossible right now.
> E.g. in "Eval.java" an instance of "Viewer" is required, IIUC.
>
>
>> I don't think it's feasible to change this. So let's
>> figure out how to work with what we have.
> [...]
>> I think the primary request here was for a non-applet solution.  But if
>
> Indeed; my aim is to implement a java tool (syntax checker) that may run as
> a standalone (batch job / ant task) application as well as being
inserted
> as
> a filtering component on the server side *and* uses the same tests as Jmol.
>
> Regards
> EJ
> --
> Eike Jordan  <[EMAIL PROTECTED]>
>
> | FIZ CHEMIE BERLIN
> | Franklin Str. 11   --,__o
> | 10587 Berlin  --   _-\_<,
> |  --   (+)/'(+)
> | Tel. : 0049-30-39977 214
>
>
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[Jmol-users] 10.9.82

[hansonr]

Prerelease 10.9.82 is available. This is simply a correction to 10.9.81 --
scientific notation, ADF reader; multifile SDF reader.




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Re: [Jmol-users] Problems with CIF Files

[hansonr]

Justin, two issues:

1) If you downloaded 10.9.81, very sorry -- download again. Use 10.9.80 or
10.9.82 (when available). In responding to your message I realize that I
broke 10.9.81 for exactly what I wanted to tell you!

2) You are seeing the actual file data. To see the sort of thing displayed
at AMS, use

load fluorite.cif {1 1 1}

This loads a full unit cell, with symmetry.

Bob Hanson




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[Jmol-users] aargh! 10.9.81 is useless

[hansonr]

I broke 10.9.81. Please do not use.

Bob



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Re: [Jmol-users] [Fwd: Re: Validate with Jmol]

[hansonr]

>
> Tracing error behaviour is not a big problem for the script writer. But
> what about some-one else using the script for a structure file that the
> script writer has not tested ? My personal opinion is that Jmol should try
> to skip the problem command, write an error to the jmol window, but then
> continue with the remaining script commands and display something even if
> it is "wrong".

Just isn't going to happen with the error handling the way it is in Jmol.
Once an error is detected, it completely breaks from the evaluation
process. It would take some major rewrites (that I'm hesitant to even
think about) to be able to continue.

>
> I had this problem recently with underscores and _eof in foreign CIF
> files. Bob, efficient as ever, quickly corrected that. For these files my
> script just hung and displayed a blank Jmol window, and a naive user would
> have no clue as to where to look for the problem in his CIF file.
>

I understand. Specifically in the case of a file read error, where the
applet goes blank, I could imagine a message to the screen -- something
now enabled for ZAP.

Maybe an option that allows for a box to pop up that requires "OK" to be
pressed? Should I experiment with that?

Bob




> Alan.
> _
> Dr Alan Hewat, ILL Grenoble, FRANCE <[EMAIL PROTECTED]>fax+33.476.20.76.48
> +33.476.20.72.13 (.26 Mme Guillermet) http://www.ill.fr/dif/people/hewat/
> _
>
>
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Re: [Jmol-users] Problem loading ADF output

[hansonr]

The ADF reader was left out of Jmol 10; it will reappear in Jmol 10.9.81.
coordinates and vibrations only; the first several structures follow the
optimization; the last several are the vibrations.



> Hi,
>
> I'm having grief loading the output from ADF into jmol. I've tried both
> current stable release and the beta with no luck. Is ADF still supported
> by
> jmol?
>
> Thanks,
>
> --
> Donald Thomas
> Chemistry, School of Biomedical, Biomolecular and Chemical Sciences
> University of Western Australia
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Re: [Jmol-users] Validate with Jmol

[hansonr]

> On Oct 21, 2006, at 8:04 AM, [EMAIL PROTECTED] wrote:
>
>> Tim,
>>
>> Here are the arguments I would give for stopping the script.
>>
>> (1) You are certainly going to get an unsatisfactory result.
>>
> hi Bob,
>
> I agree. hopefully I did not give the wrong impression here: Miguel
> did a fine job of convincing me. :-)  I think it *is* better that
> Jmol does not fail silently.  I guess my concern is with the way Jmol
> tells me that it has failed (if you'll pardon the anthropomorphization).
>
>> (2) It is better to have a full stop than to pretend to read a
>> script that
>> can't really be read.
>>
> I agree.
>
>
>> (3) Programmatically, Jmol "throws an error" and it is simply not
>> possible
>> to continue from that point. These aren't just warnings -- they are
>> indications that the script command has failed.
>>
> this is why a 'buffer' might be useful, to check for command syntax
> errors.  naive filtering on the javascript side can account for the
> most obvious problems; a built-in filter might be more effective.  it
> might also be impossible or impractical to implement; I defer to  the
> Java programmers on that, of course.
>

All scripts are checked in two passes. The first is at the "compiler"
level, when the script is turned into "tokens". Failure here is due to
improper quotation, parentheses, invalid command names, but that's about
it. The second is at the evaluation level. We just have to evaluate to
find some errors. I don't think it's feasible to change this. So let's
figure out how to work with what we have.


>
>> (4) I can see that it might be a pain, but there are a finite
>> number of
>> differences between Chime and Jmol; when you find "set zoom center"
>> does
>> not work, and you develop a work-around, you apply that
>> modification to
>> all scripts and move on. Thus each such inconvenience should be a
>> singular
>> event. Once you have worked through your list, that should be it,
>> and then
>> when you get to the end and you have no further script stops, you know
>> that Jmol is reading the scripts.
>>
> when a long script is sent to the Jmol applet, and it fails, it has
> been difficult to determine exactly where the script is failing.

Yes, I've noticed that. However, recently I added the writing of the
current command line in the error message. This should go a long way to
helping in that.

> agree that fixing such failures should be easy enough, as long as one
> can quickly determine the point of termination.  an obvious error
> message from Jmol would be extremely helpful (i.e., file name if
> applicable, line number if applicable, offending command, and
> error).  of course, testing scripts in the app can help a lot, but
> sometimes that is not possible.  at times, I have resorted to
> watching the command stream in the browser status bar, which can be
> frustrating.
>
> an idea: is it possible for Jmol to echo error messages to the applet
> space itself?  that would be the most obvious, in my opinion, and
> certainly less annoying than a popup.

I think the primary request here was for a non-applet solution.  But if
you use scriptWait(), then the return from that has all error messages in
it. There shouldn't be any problem spotting them. They always have ERROR
in caps like that in them.


Bob



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Re: [Jmol-users] Validate with Jmol

[hansonr]

Tim,

Here are the arguments I would give for stopping the script.

(1) You are certainly going to get an unsatisfactory result.

(2) It is better to have a full stop than to pretend to read a script that
can't really be read.

(3) Programmatically, Jmol "throws an error" and it is simply not possible
to continue from that point. These aren't just warnings -- they are
indications that the script command has failed.

(4) I can see that it might be a pain, but there are a finite number of
differences between Chime and Jmol; when you find "set zoom center" does
not work, and you develop a work-around, you apply that modification to
all scripts and move on. Thus each such inconvenience should be a singular
event. Once you have worked through your list, that should be it, and then
when you get to the end and you have no further script stops, you know
that Jmol is reading the scripts.

Bob



 Timothy Driscoll wrote:On Oct 20, 2006, at 10:14 AM,
[EMAIL PROTECTED] wrote:  Thank You for this one!!! And
half way on the road. There is a slight drawback with this solution. Each
time my generated script contains an error, detected by Jmol, the
execution stops with a compileError:  --* console start *--
sh jmol -ons /tmp/test.mol.spt   Executing
script: /tmp/test.mol.spt FileManager opening /tmp/test.mol.spt
compileError(cannot SET:zoom) --* console stop *-- OK,
this is not a file-read issue; it's a chime script issue. There   have
been efforts to do this sort of conversion --
http://www.chem.umass.edu/people/cmartin/Jmol/Development/%
20CHIME2Jmol.html comes to mind. But this could be looked at again.
  one of my early requests was that Jmol *not* throw a compile error
 when it reads an invalid script command (set zoom center is Chime but
not Jmol).  it would be much more friendly if Jmol logged the   offending
command and continued with the rest of the script.  as I   recall, Miguel
convinced me that there were good programming reasons   not to do this. 
in the past, I have set up various kinds of filters to catch and   comment
such commands.  most of the time, it has been fairly
straightforward, because the commands were all coming through
javascript. since your source is an external file, though, it may be  
more tricky to implement.  but I can envision a simple server-side  
filter, perhaps using perl or php, if you have access to the server.  how
difficult would it be to add a scripting buffer to Jmol itself?that
would allow Jmol to strip out or comment invalid commands,   without user
intervention.   regards,  tim
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Re: [Jmol-users] Problem loading ADF output

[hansonr]

Donald,

It appears that ADF support never made it into Jmol 10. If you have the
file format specification and can send me a few files off-list, I'll get a
reader going for this. It should be no problem. Please be sure to give
examples of what you want to read -- coordinates, vibrational frequencies,
molecular orbitals, etc.

Bob Hanson


Donald Thomas wrote:

> Hi,
> I'm having grief loading the output from ADF into jmol. I've tried  both
current stable release and the beta with no luck. Is ADF still 
supported by jmol?
> Thanks,
> --
> Donald Thomas
> Chemistry, School of Biomedical, Biomolecular and Chemical Sciences
University of Western Australia
>
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Re: [Jmol-users] Validate with Jmol

[hansonr]

> [EMAIL PROTECTED] wrote:
>> 1) checking for file read errors:
>>
>>   jmol -ons cmd.spt >> log
>>
>
> Thank You for this one!!! And half way on the road.
> There is a slight drawback with this solution. Each time
> my generated script contains an error, detected by Jmol,
> the execution stops with a compileError:
>
> --* console start *--
>  > sh jmol -ons /tmp/test.mol.spt
> Executing script: /tmp/test.mol.spt
> FileManager opening /tmp/test.mol.spt
> compileError(cannot SET:zoom)
> --* console stop *--

OK, this is not a file-read issue; it's a chime script issue. There have
been efforts to do this sort of conversion --
http://www.chem.umass.edu/people/cmartin/Jmol/Development/%20CHIME2Jmol.html
comes to mind. But this could be looked at again.

Eric Martz or Tim Driscoll could probably help you better than anyone.
You shouldn't have to start from scratch on this.

I do note that "set zoom center" has not been requested or implemented.
And, frankly, from this description, I can't imagine what it does (or that
it would be particularly valuable:

Set Zoom

Syntax:  set zoom center 

The Chime set zoom center This command enables (and disables) the use of
automatic centering of the 'translation center' or 'center of rotation'
while zooming. If no boolean is specified than 'true' is assumed. See
'translate center' for more information. In Chime this defaults to ON
(TRUE) at startup.

This sounds like a crude implementation of what I just recently added:
"zoomTo".

This particular set of Chime commands -- set zoom, center, and translate
-- have been implemented in a considerably more flexible way in Jmol, so
getting Chime scripts that implement those commands to do the exact same
thing in Jmol is probably not desireable anyway.

I recommend taking a look at the latest documentation on moveTo, zoomTo,
and set windowCentered prior to converting these Chime commands.

http://www.stolaf.edu/academics/chemapps/jmol/docs


Bob Hanson



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Re: [Jmol-users] 10.9.80 fails if the Hall or H-M symbol contains underscores?

[hansonr]

1) Crystallogrphica should be encouraged to stick to CIF standards
2) I think Jmol is just giving a warning as well. If not, then I'll fix
that, but it should be a warning.

Bob

> Unfortunately Crystallographica also uses a CIF non-standard end-of-file
> line:
> _eof
> which also causes 10.9.80 to fail ( _eof should simply be ignored - it is
> flagged as a Warning by Encifer).
>
> Alan.
> _
> Dr Alan Hewat, ILL Grenoble, FRANCE<[EMAIL PROTECTED]>fax+33.476.20.76.48
> +33.476.20.72.13 (.26 Mme Guillermet)  http://www.ill.fr/dif/people/hewat/
> _
>
>
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Re: [Jmol-users] 10.9.80 fails if the Hall or H-M symbol contains underscores?

[hansonr]

> On 19-10-2006 9:08, [EMAIL PROTECTED] wrote:
>> disregarding the underscore is no problem. It is just extraneous, right?
>>
> Bob,
>
> Not so much disregard as simply transform it to a space.
>> also, Jmol should ignore this name and simply read the symmetry operator
>> information in those files. No?
>>
> If the explicit operators are present they should take precedence. I
> think the order should be:
>
> 1) operators
>
> 2) Hall symbol
>
> 3) H-M symbol, space group number
>
> with no effort to reconcile disagreements.

Yes, that's the order Jmol uses. In addition, if an H-M symbol is the only
symbol given, even if there are operators, it tries to assign a Hall name.

(3) is better than that! No time to detail now, but it's a sequence of
tests involving knowing the intl table number, knowing the cell
dimensions, identifying principal axes, etc.




>>
>>> Unfortunately CIFs produced with Crystallographica
>>> http://www.crystallographica.co.uk/ appear to have optional underscores
>>> in
>>> the Hall symbol which cause 10.9.80 to fail silently eg:
>>>
>>> _symmetry_space_group_name_Hall '-P_2'
>>>
>>> This underscore is equivalent to a space according to the CIF spec:
>>> http://www.iucr.org/iucr-top/cif/.checking/symmetry_checklist.html
>>> and is only needed if the symbol is not enclosed in quotes.
>>>
>>> In general, if the Hall space group symbol is not recognised perhaps
>>> Jmol
>>> should fall back on the H-M symbol. And if explicit operators are given
>>> these should be preferred.
>>>
>
> Alan,
>
> What does vcif say about these files?
>
> Rich
>
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Re: [Jmol-users] Validate with Jmol

[hansonr]

1) checking for file read errors:

  jmol -ons cmd.spt >> log

where cmd.spt is simply

  load filename.xyz

2) validating whatever

add to cmd.spt whatever validation you need that will give some output,
and then parse that output. For example,

select _C and connected(4)

You would have to figure out what sort of validation you require; feel
free to request additional information. But a good start might be

load filename.xyz
getproperty atominfo "all"

or

load filename.xyz
getproperty atominfo "all"
getproperty bondinfo "all"

and then work it out from there.
Basically, the "getproperty" command should give you everything you want.

Bob


> Due to migration from Chime-plugin to Jmol-applet it would be very
> handy, if one can validate molecule data files (and applied scripts)
> with Jmol.
>
> As we do have at last up to 4000 data files (mol, xyz, pdb, cub),
> validation
> should be done in a batch job.
>
> If anybody can give me a hint, where to start within the Jmol-API?
>
> thanks in advance
> EJ
>
> --
> Eike Jordan  <[EMAIL PROTECTED]>
>
> | FIZ CHEMIE BERLIN
> | Franklin Str. 11   --,__o
> | 10587 Berlin  --   _-\_<,
> |  --   (+)/'(+)
> | Tel. : 0049-30-39977 214
>
>
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Re: [Jmol-users] 10.9.80 fails if the Hall or H-M symbol contains underscores?

[hansonr]

disregarding the underscore is no problem. It is just extraneous, right?

also, Jmol should ignore this name and simply read the symmetry operator
information in those files. No?

> Unfortunately CIFs produced with Crystallographica
> http://www.crystallographica.co.uk/ appear to have optional underscores in
> the Hall symbol which cause 10.9.80 to fail silently eg:
>
> _symmetry_space_group_name_Hall '-P_2'
>
> This underscore is equivalent to a space according to the CIF spec:
> http://www.iucr.org/iucr-top/cif/.checking/symmetry_checklist.html
> and is only needed if the symbol is not enclosed in quotes.
>
> In general, if the Hall space group symbol is not recognised perhaps Jmol
> should fall back on the H-M symbol. And if explicit operators are given
> these should be preferred.

Definitely it should be reading the operators -- if it doesn't recognize
the name and has operators it should still be fine.

I'll take a look at some of these files when I get a chance.

Bob

>
> Unfortunately Crystallographica also uses a CIF non-standard end-of-file
> line:
> _eof
> which also causes 10.9.80 to fail ( _eof should simply be ignored - it is
> flagged as a Warning by Encifer).
>
> Alan.
> _
> Dr Alan Hewat, ILL Grenoble, FRANCE<[EMAIL PROTECTED]>fax+33.476.20.76.48
> +33.476.20.72.13 (.26 Mme Guillermet)  http://www.ill.fr/dif/people/hewat/
> _
>
>
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Re: [Jmol-users] Amino acids in "protein"-selection

[hansonr]

The key thing to understand is that Jmol uses no such catalog. The only
problems will be with "protein" groups that do not contain all three:

 1) a backbone carbonyl carbon "C"
 2) a backbone alpha carbon "CA"
 3) a backbone nitrogen "N"

If any one of these is missing, the group will be considered "other":
  not (protein, rna, dna, carbohydrate or hetero)

By the way, was someone at sometime interested in "lipid"? I don't think
that's worth it, probably, but I was wondering. It was on the menu but had
never been coded, so I deleted it from the menu. If someone has a
reasonable definition, I'm all ears. But my understanding it's a catch-all
term mostly meaning "greasy".

Bob


>>
>> Message: 1
>> Date: Tue, 19 Sep 2006 20:43:58 -0400
>> From: Eric Martz <[EMAIL PROTECTED]>
>> Subject: [Jmol-users] Lots of bugs in Jmol: fix some before v11?
>> To: jmol-users@lists.sourceforge.net
>> Message-ID: <[EMAIL PROTECTED]>
>> Content-Type: text/plain; charset="us-ascii"; format=flowed
>>
>>
>> Some standard amino acids are not included in protein.
>
> I agree with Eric that frequently found postranslational
> modifications such as phosphorylations
> and substitutions introduced to facilitate phasing such as
> Selenomethioneine in place of
> Methioneine should not prevent an amino acid from being treated as
> part of a protein.
> I do not have a comprehensive list, but the ones that come to my mind
> are:
>
> MSE Selenomethionine
> CSE Selenocysteine
> PTR Phosphotyrosine
> SEP Phosphoserine
> TPO Phosphothreonine
> HYP 4-hydroxyproline
> 5HP Pyroglutamic acid; 5-hydroxyproline
> PCA Pyroglutamic Acid
> LYZ 5-hydroxylysine
> GLX Glu or Gln
> ASX Asp or Asn
> GLA gamma-carboxy-glutamic acid
>
> Some programs also produce PDB files with different names for the His
> residues
> depending on which of the two nitrogen is protonated
>
>   Annemarie
>
>
>
>
>
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Re: [Jmol-users] Bugs that HIDE DOTS inappropriately

[hansonr]

The dots not changing color is certainly a bug that will be fixed in
10.9.47 (later today).

As for the action of restrict, this is intentional. (That is, a feature,
not a bug.) Let's discuss what we really mean by dots. Here's the deal:

Note that dots do not simply surround an atom. They take into account
neighboring atoms. Thus, unlike spacefill, dots are not just "displayed",
they are the result of a rather complex calculation -- essentially the
solvent-accessible-surface calculation. (They are not quite the
solvent-accessible surface, because they do not take into account all the
other atoms around the selected set. "isosurface sasurface" takes this
into account, but "dots" does not. In fact, "select *;dots +1.2" IS the
solvent-accessible surface.)

(Oh, I do so hate "restrict"!)

I'll look into whether restrict could properly restrict to part of the dot
surface, but the thinking on the part of Miguel and me up until now is
that since dots depend upon neighbors, and restrict changes neighborhoods,
dots should be completely removed if a restrict command is given.

The basic problem is that the following two will be different (which might
be OK):

select *;
dots on;
restrict (atomno < 10);
# this would be a partial surface, like the action of sasurface?

restrict (atomno < 10);
dots on;
# this would be a continous surface around those atoms.


Bob


> First, any restrict command (including "restrict not none" and "restrict
> all", which do not affect any renderings that I know of except dots) hides
> ALL dots. It seems to me that using "restrict" to hide a subset of atoms
> should not hide ALL dots -- it should hide dots only for the set hidden --
> just as it does for spacefill, etc.
>
> Second, "dots off" hides ALL dots, even when preceded with "select none".
>
> Working around these bugs in FirstGlance in Jmol has required adding a lot
> of messy javascript. It would be great to have them fixed!
>
> Thanks, -Eric
>
>
> 
> Eric Martz, Professor Emeritus, Dept Microbiology
> University of Massachusetts, Amherst MA US
> http://www.umass.edu/molvis/martz
>
>
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Re: [Jmol-users] CML and jmol

[hansonr]

Assadullah,

The problem is two-fold. First, we haven't set up Jmol for reading the
symmetry information in CML files. This is primarily because no one has
asked until now.

Be aware that some of your files are invalid because they contain <
instead of "<". For example:

http://www.xml-cml.org/dtdschema/cmlCore/EXAMPLES/crystal1.html


  


But some of the others are OK. Please enter this as a feature request at

http://sourceforge.net/tracker/?func=add&group_id=23629&atid=379136


Bob Hanson




> Greetings:
>
> I tried to load the sample crystals listed at
> http://www.xml-cml.org/dtdschema/cmlCore/EXAMPLES/
> including
> CRYSTAL1.XML, crystal1.html, and
> crystal2.html. jmol loaded the latter two fine, but
> did not display the crystals.
>
> I am wondering if I need to add addtional markup than
> what is in the sample files or if I need to configure
> jmol properly.
>
> Regards,
>
> Assadullah
>
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Re: [Jmol-users] Loading a local file using a remote server?

[hansonr]

>
> What is the easiest way of loading a local file using a remote server ?

No easy solution. Java security precludes reading a file from the user's
system directly. Two options I know of:

1) mirror it from your server:

a) Have a form with  with which the user can designate a
local file.
b) Have a server-side script that returns that text embedded in an applet
tag as part of a "loadInline" parameter. This removes the need to save the
file in any temporary way on your server. The trick here is that you need
to add a vertical line at the beginning of each line, because HTML will
strip lines from a parameter.

2) have the user clip the data into a text area. The code used at XTALX
uses this method. It is simpler, but it asks more of your user. The code
XTALX uses is:


function doloadcifdata() {
 var s=document.getElementById("cifdata").value.replace(/\n\ /g,"\n")
 
if(s.indexOf("")>0)
{
   var i =
s.lastIndexOf("")
   s=s.substring(i,s.length)
 }
 jmolScriptWait(getlatticeinfo("set defaultlattice "))
 lastinlineload=s
 jmolLoadInlineScript(s,loadscript)
}


Here "cifdata" is the ID of the textarea. That first replace isn't
necessary. The business of the # is that certain CIF files from a
certain database can't be read directly (right now) because they have too
many bytes of comment at the top. You could probably dispense with that as
well. The jmolScriptWait command simply reads the current lattice info
(from another function) and then finally loads the script. The following
will probably work just fine for you:

 jmolLoadInlineScript(document.getElementById("cifdata"))

where we have




on the page somewhere.

So this method asks a bit more of the user but is far easier to implement.

Bob



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Re: [Jmol-users] labeloffset behavior of post 10.2 versions of Jmol?

[hansonr]

> Thanks, Bob, for your amazingly quick response and fix of the refresh bug.
>
> Now,  I've encountered a second changed behavior of the newer versions
> compared to 10.2 with respect to "labeloffset."  In 10.2, one could,
> very conveniently, select an atom, label it, and offset the label to a
> specified coordinate independent of other labels on other atoms that
> might be offset to different relative positions vis a vis their selected
> atoms. In post-10.2 versions, it seems that the last labeloffset governs
> all labels that had been previously assigned. Is there any way to
> restore the labeloffset independence of 10.2 in 11-beta?

David, I appreciate your giving this a workout. Keep it coming! Another
easy fix.
A new Jmol-11-beta.zip is being uploaded at this moment. (Give it a few
minutes to complete, please).

10.x.46d

in http://www.stolaf.edu/academics/chemapps/jmol/docs/examples-11

Bob

>
> Thanks for considering this.
>
> David
>
> [EMAIL PROTECTED] wrote:
>
>>Thanks very much for spotting that, David. This was an easy fix.
>>
>>10.x.46c
>>
>>See Jmol-11-beta.zip 21-Aug-2006 19:46 and associated files in
>>
>>  http://www.stolaf.edu/academics/chemapps/jmol/docs/examples-11
>>
>>For the record, it was a failure of Jmol to do a (newly required)
>>"refresh" before the move or moveto command.
>>
>>
>>
>
> --
> <<>><<>><<>><<>><<>><<>><<>><<>><<>><<>><<>><<>><<>>
> David Marcey
> Fletcher Jones Professor of Developmental Biology
> Chair, CLU Biology Department
> 60 W. Olsen Rd., MC3700
> Thousand Oaks, CA 91360
> (805)-493-3263, 3590
> [EMAIL PROTECTED]
> <<>><<>><<>><<>><<>><<>><<>><<>><<>><<>><<>><<>><<>>
>
>
>
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Re: [Jmol-users] Curious spacefill behavior of post 10.2 versions of Jmol?

[hansonr]

Thanks very much for spotting that, David. This was an easy fix.

10.x.46c

See Jmol-11-beta.zip 21-Aug-2006 19:46 and associated files in

  http://www.stolaf.edu/academics/chemapps/jmol/docs/examples-11

For the record, it was a failure of Jmol to do a (newly required)
"refresh" before the move or moveto command.



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Re: [Jmol-users] surfaces and JVXL files

[hansonr]

>
> On Aug 18, 2006, at 9:24 PM, Bob Hanson wrote:
>
>> Frieda, what sort of surfaces are you particularly interested in
>> displaying?
>>
>> Bob
>
> Solvent-accessible surfaces of macromolecules are what I am
> accustomed to using vis Chime, hence what I am seeking to create.
> However I have to admit that I am not aware of what the distinction
> is between "isosurface" and solvent-accessible surface...

There are two subtle distinctions now being made in Jmol --

"Solvent-accessible" which means the probe center position when rolled
around the molecule. This is:

  isosurface SAsurface 1.2

where 1.2 is the solvent probe radius.

"solvent-excluded" or "molecular" which means the set of all points on the
solvent sphere that touch the Van der Waals radius along with the portions
of the solvent sphere that form "caveties" when the solvent sphere touches
the molecule at more than one point. This is:

  isosurface solvent 1.2

Both are called isosurfaces because they represent the points in space
that have the same measurement, in this case the same distance from the
solvent probe (and as described above).

"SAsurface" display is far faster than "solvent" and probably what you want.

Sorry, earlier I forgot about the SAsurface option.

Bob

>
> Frieda
>
>
>
>>
>> Frieda Reichsman wrote:
>>
>>> Hi All,
>>>
>>> I am interested in fast rendering of surfaces for large molecules. It
>>> seems that Bob Hanson has invented a file format for this purpose,
>>> called JVXL. I have seem Angel Herraez's and Bob's test pages for
>>> surfaces, but I am still puzzled as to how to get started in doing
>>> this.
>>>
>>> To create a JVXL surface file in Jmol, do you first have to load a
>>> CUBE file into Jmol? I have started to read a little about CUBE files
>>> but am unfamiliar with them. How do you generate a CUBE file?
>>>
>>> Frieda
>>>
>>> ///
>>>
>>>
>>> Frieda Reichsman, PhD
>>>
>>> Molecules in Motion
>>>
>>> Interactive Molecular Structures
>>>
>>> http://www.moleculesinmotion.com
>>>
>>>
>>> ///
>>>
>>>
>>>
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>>
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>
> ///
>
> Frieda Reichsman, PhD
> Molecules in Motion
> Interactive Molecular Structures
> http://www.moleculesinmotion.com
>
> ///
>
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Re: [Jmol-users] Pop-up documentation not working on Mac

[hansonr]

Same cheat. (Really just loading an HTML file.) It's not that pop-ups
don't work, it's that pop-ups that dump HTML code to the window instead of
sending a page do not work. If no one comes up with a solution for the Mac
bug (I have to say) that prevents on the fly writing HTML directly to a
new window and having a LiveConnect applet, I will consider it a loss and
cheat as well. :)

Bob


> One further example of (working) UI in Jmol applets in a pop-up
> window in Safari:
>
> On Angel Herraez's page,
> http://biomodel.uah.es/pruebas/jmol/pop-up_Jmol/v6_1/pop-up_Jmol.htm
>
> - select the radio button for generating a pop-up
> - then click the link to view the structure
>
> the UI controls work in that pop-up window on Safari.
>
> Frieda
> ///
>
> Frieda Reichsman, PhD
> Molecules in Motion
> Interactive Molecular Structures
> http://www.moleculesinmotion.com
>
> ///
>
>
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[Jmol-users] 10.x.39 -- message command

[hansonr]

10.x.39 introduces the "message" command, which sends the text to the
console and to the messageCallback function, if defined, and also logs the
message on the scriptStatus queue. No message is sent to the user.

http://www.stolaf.edu/people/hansonr/jmol/test/proto/new.htm



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Re: [Jmol-users] Jmol's cartoon rendering needs improvements

[hansonr]

Eric, as I think about this, I realize that you are referring to the
rockets rather than the cartoons. Is there something about the *cartoons*
that you don't like? -- They are the objects that are meant to "replace"
the Chime cartoons. Jmol cartoons behave as you describe you wish the
rockets behaved. The rockets that you are comparing are another thing
altogether. I guess I'm wondering why you are not comparing cartoons.

Q: Are ROCKETS (as opposed to CARTOONS) common to these other programs?

Bob

> At 8/12/06, Bob Hanson [Jmol team] wrote:
>>Eric, please submit this as a feature request, and I will take a look at
>>it.
>
> Done.
>
>>My first reaction to the Word document is that I think the Chime
>>rendition looks horrible, but that may be just because they used a poor
>>algorithm. I think we would have to experiment a bit, but I'm willing to
>>try. I've recently streamlined the graphics part of Jmol, so redoing the
>>cartoon business is not out of the question.
>
> I agree that the RasMol/Chime cartoon rendering is ugly. However, it
> reflects the reality of the protein structure much better than the
> oversimplified but "beautiful" straight Jmol cartoon rendering.
>
> Of the 3 I looked at, I like Protein Workshop's beta strands the best, but
> I think they are overly smoothed, also tending towards unrealistic beauty.
> Something similar, less smoothed than Protein Workshop, and more smoothed
> than RasMol/Chime, seems ideal to me.
>
> Protein Workshops alpha helix cylinders are way too fat, and have no
> coneheads. I don't like them. For Jmol, it is presently crucial to show
> both trace backbone and the cartoon so one can see where the former
> deviates, showing when the latter is unrealistic (as shown in my
> snapshots).
>
> Generally speaking, Protein Workshop's renderings are stunningly beautiful
> (publication quality). But when the number of atoms gets reasonable (more
> than a single small protein domain) rotation begins to suffer. With
> something as large as an antibody, rotation becomes unacceptably slow. I
> think Jmol's renderings need to look better (more like those of Protein
> Workshop -- which is open source java by the way) but only if we can
> preserve the rotation speed Jmol now has, which is vastly superior to that
> of Protein Workshop (for medium-sized proteins), but significantly
> inferior
> to that of Chime.
>
> Has the decision not to use openGL in Jmol been revisited? Should it be?
>
> I'm glad you think some improvements are feasible!
>
> -Eric
>
>
> /* - - - - - - - - - - - - - - - - - - - - - - - - - - -
> Eric Martz, Professor Emeritus, Dept Microbiology
> U Mass, Amherst -- http://www.umass.edu/molvis/martz
>
> Biochem 3D Education Resources http://MolviZ.org
> See 3D Molecules, Install Nothing! - http://firstglance.jmol.org
> Protein Explorer - 3D Visualization: http://proteinexplorer.org
> Workshops: http://workshops.proteinexplorer.org
> World Index of Molecular Visualization Resources: http://molvisindex.org
> ConSurf - Find Conserved Patches in Proteins: http://consurf.tau.ac.il
> Atlas of Macromolecules: http://atlas.proteinexplorer.org
> PDB Lite Macromolecule Finder: http://pdblite.org
> Molecular Visualization EMail List (molvis-list):
>http://bioinformatics.org/mailman/listinfo/molvis-list
> - - - - - - - - - - - - - - - - - - - - - - - - - - - */
>
>
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Re: [Jmol-users] Picking groups (elements or equivalent sites)]

[hansonr]

> [EMAIL PROTECTED] said:
>> Alan Hewat wrote:
>>>What would be great would be to have additional picking commands: "set
> picking ELEMENT"  (select all atoms of that element)
>
>> easy.
>
> That would already be very helpful. I would then click on any Aluminum
> atom for example and so select all (visible) aluminum atoms.

This won't be just the visible ones, though. You can add that designation
when you process the selection. So whatever your JavaScript is going to do,
you would add "and visible" to that. OK? Or we could institute something like

  set pickingVisibleOnly

that would restrict the picking groups, etc. to only those atoms that are
visible.

>
>>>"set picking SITE" (select all symmetry related atoms for
>>>that particular site)
>
>> hmm. That might be a challenge. How exactly do you define "site"?
>
> With "set picking SITE" I would like to click on a particular aluminum
> atom eg Al2 as listed in the CIF file, and so select all (visible) Al2
> atoms but not Al1 or Al3.

so, for example, we have:

loop_
_atom_site_label
_atom_site_fract_x
_atom_site_fract_y
_atom_site_fract_z
Si   0.46970   0.0   0.0
O   0.41350   0.26690   0.11910

"site 1" is Si, "site 2" is O, right? And then when we apply symmetry (in
this case) all the Si are "site 1" and all the O are "site 2". Yes? If so,
this will require a new atom field "site" I think. We should probably then
also add the label field %S for "site"


>
>> Are you referring to the selection halo that works with "set display
> selected"?
>
> No. I mean those atoms that are visible after a restrict command like:
> load \"y12367.cif\" {3 3 3};restrict cell={2 2 2};
>
> I don't want atoms from the invisible cells, that are only there to allow
> construction of complete octahedra.

I'm wondering if we also need a select option for element. Maybe just

  within(element, selected)

for example. "within" sounds a bit strange, but it is already in place and
will work. That way the user doesn't necessarily have to use the mouse to
effect this element-based selection, and multiple elements can be selected
at the same time. Similarly:

 within(site, selected)

would select all of the same site.

It's great to have you thinking about this, Alan.

Bob


>
> Alan.
> _
> Dr Alan Hewat, ILL Grenoble, FRANCE <[EMAIL PROTECTED]>fax+33.476.20.76.48
> +33.476.20.72.13 (.26 Mme Guillermet) http://www.ill.fr/dif/AlanHewat.htm
> _
>
>
>
>
> _
> Dr Alan Hewat, ILL Grenoble, FRANCE <[EMAIL PROTECTED]>fax+33.476.20.76.48
> +33.476.20.72.13 (.26 Mme Guillermet) http://www.ill.fr/dif/AlanHewat.htm
> _
>
>
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Re: [Jmol-users] messaging arbitrary signal strings

[hansonr]

Right, OK. 10.x.39 will incorporate the "message" command. It will output
to the messageCallback function as well as the scriptMessage status queue.

Unrelated: Eric, you are the RasMol expert. What do you think of
"restrict"? I've been thinking that restrict is too brute force. All it
does is turn off wireframe and balls. Would there be use for a different
kind of restrict, (perhaps "limitDisplay") that just does not display the
atoms, but doesn't change their wireframe/spacefill settings?

Bob Hanson


> At 8/11/06, you wrote:
>>Eric, the command is "echo". Just make sure you have "set echo off" so
>>that the user does not get the message as well.
>
> I see that this does not require 'set debugscript on', which is good.
>
> However, 'set echo off' erases the current message for the user (in Jmol).
> This is definitely not what I need.
>
>>messages is a possible idea as well if you really think echo won't do
>> the
>>job for you.
>
> Yes, I still advocate a new command 'message arbitrary signal string' that
> sends the 'arbitrary signal string' to messageCallback, regardless of set
> debugscript mode.
>
> For now, I'll stick with my 3 command workaround with a bogus define
> command following set debugscript on.
>
>
>>  Note that
>>10.2 has errors in how it depicts RasMol structures for some
>>muliple-chain systems. These are corrected in the prototype, which is
>>soon to be 11.0.
>
> Could you please tell me where I can read what these errors are, or what
> terms to search for?
>
> And what do you mean by "RasMol structures"??
>
> Thanks, -Eric
>
>
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Re: [Jmol-users] Jmol's cartoon rendering needs improvements

[hansonr]

Eric, please submit this as a feature request, and I will take a look at
it. My first reaction to the Word document is that I think the Chime
rendition looks horrible, but that may be just because they used a poor
algorithm. I think we would have to experiment a bit, but I'm willing to
try. I've recently streamlined the graphics part of Jmol, so redoing the
cartoon business is not out of the question.

Bob


> I would like to request that Jmol's rendering of secondary structure
> cartoons be improved. In my opinion, its 'cartoon' rendering is very
> important but unsatisfactory. With increased exposure (Nature is working
> on
> installation of FirstGlance in Jmol), the present rendering may diminish
> Jmol's acceptance/reputation.
>
> Presently, Jmol draws beta planks as absolutely straight. In reality, beta
> strands are often curved and usually somewhat twisted.
>
> In some cases, Jmol's beta strand planks not only largely miss the correct
> positions, but end up crossing through each other. This happens for 1APM
> (restrict 42-75 to see the relevant portion).
>
> Similarly, many alpha helices are curved, and Jmol's rockets need to
> reflect this.
>
> Also, the cone-heads of Jmol's rockets (very nice) sometimes "flap"
> annoyingly when the molecule is rotating. Though less important, it would
> be great if this could be fixed.
>
> I have put an MS Word 2002 file, ss-cartoon.doc, containing snapshots of
> some cases where Jmol's rendering is unsatisfactory at:
> http://www.umass.edu/microbio/chime/beta/jmol/
> Snapshots there compare the renderings of Jmol, Chime, and Protein
> Workshop.
> (If anyone has trouble displaying the .doc file, let me know.)
>
> -Eric
>
>
> /* - - - - - - - - - - - - - - - - - - - - - - - - - - -
> Eric Martz, Professor Emeritus, Dept Microbiology
> U Mass, Amherst -- http://www.umass.edu/molvis/martz
>
> Biochem 3D Education Resources http://MolviZ.org
> See 3D Molecules, Install Nothing! - http://firstglance.jmol.org
> Protein Explorer - 3D Visualization: http://proteinexplorer.org
> Workshops: http://workshops.proteinexplorer.org
> World Index of Molecular Visualization Resources: http://molvisindex.org
> ConSurf - Find Conserved Patches in Proteins: http://consurf.tau.ac.il
> Atlas of Macromolecules: http://atlas.proteinexplorer.org
> PDB Lite Macromolecule Finder: http://pdblite.org
> Molecular Visualization EMail List (molvis-list):
>http://bioinformatics.org/mailman/listinfo/molvis-list
> - - - - - - - - - - - - - - - - - - - - - - - - - - - */
>
>
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Re: [Jmol-users] messaging arbitrary signal strings

[hansonr]

Eric Martz wrote:

>I am beginning to try to use messageCallback for FirstGlance in Jmol. It
appears to me that Jmol 10.2.00 does not message comments, even with
set
>debugscript on.
>
that is correct.

>In the past (Protein Explorer) I have extensively used comments messaged
by
>Chime to detect where Chime is in executing a command script.
>Can someone tell me how I can message an arbitrary signal string in Jmol?
If not, I would like to request a new command "message" that would simply

>message whatever follows after the word message, e.g.
>message this arbitrary signal text
>
Eric, the command is "echo". Just make sure you have "set echo off" so 
that the user does not get the message as well. This works both at 
http://www.stolaf.edu/people/hansonr/jmol/test/10.2/new.htm and at 
http://www.stolaf.edu/people/hansonr/jmol/test/proto/new.htm, so it 
should be useable for either version 10.2 or upcoming 11.0. Note that 
10.2 has errors in how it depicts RasMol structures for some
muliple-chain systems. These are corrected in the prototype, which is 
soon to be 11.0.

messages is a possible idea as well if you really think echo won't do  the
job for you.

>Alternatively, comments could be messaged with set debugscript on.
However,
>this seems less desirable since one then needs three commands to insert a

>marker string into the message stream:
>set debugscript on
># arbitrary signal string
>set debugscript off
>(but in Jmol 10.2.00, "# arbitrary signal string" is not messaged.)
>
right, comments are never processed.

>As a temporary workaround for messaging an arbitrary string, I am using 
this scheme:
>set debugscript on
>define arbitrary_signal_1 none
>set debugscript off
>Thanks, -Eric
>/* - - - - - - - - - - - - - - - - - - - - - - - - - - -
>Eric Martz, Professor Emeritus, Dept Microbiology
>U Mass, Amherst -- http://www.umass.edu/molvis/martz
>Biochem 3D Education Resources http://MolviZ.org
>See 3D Molecules, Install Nothing! - http://firstglance.jmol.org
>Protein Explorer - 3D Visualization: http://proteinexplorer.org
>Workshops: http://workshops.proteinexplorer.org
>World Index of Molecular Visualization Resources: http://molvisindex.org
ConSurf - Find Conserved Patches in Proteins: http://consurf.tau.ac.il
Atlas of Macromolecules: http://atlas.proteinexplorer.org
>PDB Lite Macromolecule Finder: http://pdblite.org
>Molecular Visualization EMail List (molvis-list):
>   http://bioinformatics.org/mailman/listinfo/molvis-list
>- - - - - - - - - - - - - - - - - - - - - - - - - - - */
>-
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Re: [Jmol-users] Release notes for Jmol 10.3 or 11?

[hansonr]

   Eric Martz wrote:I see that Jmol prerelease 10.3.1 is
available for download.  Can someone give me the URL for the
notes about what the changes are in  10.3 and 10.3.1?

10.3.1 is not particularly useful.

Ditto for Jmol 11 (and where is the download?)?

The full file set
of 11.0 beta (10.x.38) is at
http://www.stolaf.edu/people/hansonr/jmol/test/proto
 Look for the most recent ZIP file there.



 Thanks, -Eric
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Re: [Jmol-users] Picking groups (elements or equivalent sites)

[hansonr]

   Alan Hewat wrote: I am now trying (unrelated) to use
picking to switch on/off bonding/polyhedra for elements
selected by clicking. I am using CIF files where
atoms are generated according to symmetry operations. One
problem is that I want to select all atoms of a particular
kind. I looked at "set picking ATOM" but that selects just one
atom. "set picking GROUP" seems to select all atoms even though
I have defined things like: 'define ~anions (oxygen or nitrogen
or fluorine or sulphur or chlorine or bromine or iodine);'+ I
assumed this would define a "group" called ~anions, but
apparently not. What is a "group" then?  "set picking"
refers to what should happen when a user clicks an atom.

What would be great would be to have additional picking commands: "set
picking ELEMENT"  (select all atoms of that element) easy.

"set picking SITE"  (select all symmetry related atoms for
that particular site) hmm. That might be a challenge. How exactly do
you define "site"?
I would also like to be able to qualify this with "and VISIBLE" since
I have invisible atoms that I want to stay unselected and invisible.
  Are you referring to the selection halo that works with "set display
selected"? We should probably talk about how that should display. I see
what you mean  -- it pops up regardless of whether the atom is actually
visible.

 Bob

 Alan.   _
Dr Alan Hewat, ILL Grenoble, FRANCEfax+33.476.20.76.48
+33.476.20.72.13 (.26 Mme Guillermet)
http://www.ill.fr/dif/AlanHewat.htm
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Re: [Jmol-users] Animating concatenated CIF files

[hansonr]

> Getting back to this after a hard week in HI :-) My mistake was to
> separate the CIF data blocks by literally "model 1", "model 2" etc as for
> PDB, when it was sufficient just to concatenate the CIF data_ blocks ie
> separate them by "data_model_1", "data_model_2" etc.
>
> However, I find that the script that I load together with the concatenated
> CIF file to draw specific bonds and polyhedra only applies to the first
> data block. The second data block is drawn with default bonds.
> Interestingly if I send an instruction like 'connect 2.6' after the
> animation has started, it applies to both data blocks. (Yes I tried
> turning animation on before loading the concatenated CIFs). And I can't
> issue all the bond/polyhedra instructions after loading the CIF file
> because I want to load multiple cells with:
> "load \"y12367.cif\" {3 3 3};restrict cell={2 2 2};set unitcell {1 1
> 1};etc..."
> Alan.

I'd have to look at the script carefully. Here's what I do know:

 load {3 3 3}

works for all frames

 restrict cell=666

works for all frames

 unitcell {1 1 1}

works only for the CURRENT frame, so for that, you will need:

 frame 1;unitcell {1 1 1};frame 2;unitcell {1 1 1};

etc. This is because just about anything could be in any frame, and each
frame has its own unit cell, or not

 connect

works for all frames at once

 polyhedra

works for all frames at once

So I don't know exactly what part of your script might not be working.
What's the problem with issuing the connect commands after file loading or
along with the file load command?

Bob



>
> At 21:08 21/07/2006, you wrote:
3) I can see how to animate a PDB drawing to switch between different
 structures separated by "model n" statements, but I can't get that
 syntax to work for CIF files. Am I missing something simple ?
>>>Do your CIF files have multiple data_ lines?
>>>Show me your cif file. Should just be
>>>model 1
>>>model 2
>>>model 3
>
> _
> Dr Alan Hewat, ILL Grenoble, FRANCE<[EMAIL PROTECTED]>fax+33.476.20.76.48
> +33.476.20.72.13 (.26 Mme Guillermet) http://www.ill.fr/dif/AlanHewat.htm
> _
>
>
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Re: [Jmol-users] Selecting residues with incomplete sidechains

[hansonr]

> I am writing scripts within FirstGlance in Jmol to display residues with
> incomplete sidechains. (Sometimes, crystallographers may omit the gamma
> carbon and beyond when the electron density is too blurry for a given
> sidechain.) The scripting is fussy but doable. Requires separate lines for
> each amino acid and nucleotide.
>
> Is there a built-in way to select residues with incomplete sidechains in
> Jmol?
>
> Example of my concept of how to select Glu's lacking either sidechain
> oxygen:
>
> select glu and not within(group, glu.oe1)
> select selected or (glu and not within(group, glu.oe2))
>
> Is there an easier way?
>

I think so. the "chaininfo" property provides an array:

chainInfo=new Array()
chainInfo.models=new Array()
chainInfo.models[0]=new Array()
chainInfo.models[0].chains=new Array()
chainInfo.models[0].chains[0]=new Array()
chainInfo.models[0].chains[0].residues=new Array()
chainInfo.models[0].chains[0].residues[0]=new Array()
chainInfo.models[0].chains[0].residues[0].atomInfo2="[THR]1.CG2 #7"
chainInfo.models[0].chains[0].residues[0].atomInfo1="[THR]1.N #1"
chainInfo.models[0].chains[0].residues[0]._apt2=6
chainInfo.models[0].chains[0].residues[0]._apt1=0
chainInfo.models[0].chains[0].residues[0].groupID=17
chainInfo.models[0].chains[0].residues[0].seqCode="1"
chainInfo.models[0].chains[0].residues[0].visibilityFlags=0
chainInfo.models[0].chains[0].residues[0].groupIndex=0
chainInfo.models[0].chains[0].residues[1]=new Array()
chainInfo.models[0].chains[0].residues[1].atomInfo2="[THR]2.CG2 #14"
chainInfo.models[0].chains[0].residues[1].atomInfo1="[THR]2.N #8"
chainInfo.models[0].chains[0].residues[1]._apt2=13
chainInfo.models[0].chains[0].residues[1]._apt1=7


Except for the issue of insertion codes, you could match the residue code
"THR" with the difference in atom pointers (13 - 7) + 1 to get the number
of atoms in THAT particular residue (7 in this case). The "groupID" is
also indicative of the residue type, based on this array:

  public final static String[] predefinedGroup3Names = {
// taken from PDB spec
"", //  0 this is the null group

"ALA", // 1
"ARG",
"ASN",
"ASP",
"CYS",
"GLN",
"GLU",
"GLY",
"HIS",
"ILE",
"LEU",
"LYS",
"MET",
"PHE",
"PRO", // 15 Proline
"SER",
"THR",
"TRP",
"TYR",
"VAL",
"ASX", // 21 ASP/ASN ambiguous
"GLX", // 22 GLU/GLN ambiguous
"UNK", // 23 unknown -- 23

// if you change these numbers you *must* update
// the predefined sets in script.Token.java

"A", // 24 the purines
"+A",
"G", // 26
"+G",
"I", // 28
"+I",
"C", // 30 the pyrimidines
"+C",
"T", // 32
"+T",
"U", // 34
"+U",

"1MA", // 36
"AMO",
"5MC",
"OMC",
"1MG", // 40
"2MG",
"M2G",
"7MG",
"G7M",
"OMG", // 45
"YG",
"QUO",
"H2U",
"5MU",
"4SU", // 50
"PSU",

"AMP",
"ADP",
"ATP",

"GMP", // 55
"GDP",
"GTP",

"IMP",
"IDP",
"ITP", // 60

"CMP",
"CDP",
    "CTP",

"TMP",
"TDP", // 65
"TTP",

"UMP",
"UDP",
"UTP", // 69

// water && solvent
"HOH", // 70
"DOD", // 71
"WAT", // 72
// ions && solvent
"PO4", // 73 phosphate ions
"SO4", // 74 sulphate ions

  };


So a simple correlation there would probably work.

But I think insertion codes might complicate this.



> I am assuming that if it lacks any atoms in the sidechain, it must lack at
> least one terminal oxygen. That is, I'm assuming that all sidechain atoms
> are connected covalently. I may be wrong.

"group" does not depend upon any covalency, so that is not an issue here,
I think.

>
> A PDB file that has many incomplete sidechains is 1APM.

Yes, firing that into
http://www.stolaf.edu/people/hansonr/jmol/test/proto/new.htm using the St.
Olaf relay (just under the applet) and then clicking on "[chaininfo]"
gives a list that can be processed by Excel to provide the following pivot
table (sorry if this doe

Re: [Jmol-users] Jmol Documentaton broken for IE

[hansonr]

> Hi, Bob,
>
> When I access
> http://www.stolaf.edu/people/hansonr/jmol/docs
> All is OK until I click an item in the contents.
>
> Then in IE-Windows I get a js error "number expected", and the page
> remains
> blank.
>

This is an IE/Win bug I thought I had worked around. I guess not. It
should work now.

Bob

> In Firefox-Windows I get no js errors, and I can see the manual (Whew!).
>
> -Eric
>
>
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Re: [Jmol-users] Echoing %selected and other global status items?

[hansonr]

> Thanks for your suggestion, Bob.
>
> I remind you that I am not using jmol.js in FirstGlance in Jmol.
>

that's fine. No problem, Eric. If you don't want to use Jmol-new.js, you
can go directly to the Java property itself using:

var nResidues = applet.getProperty("atominfo","(selected and (*.ca,
*.p))").size()

where "applet" is how you have defined the applet -- usually (but not
reliably, "document.jmolApplet0")


>
> According to the manual, getProperty depends on messagecallback.

That's when you use it as a script command, as in:

  applet.script("getProperty ")

I don't recommend that usage, because, as you say, it requires callback.
The getProperty method itself is far more useful. I think that's what you
in particular should be using.

Bob



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