[Jmol-users] Mol-graphics: Jmol VB ?
[ This follows a post and discussion held partly in jmol-developers
and partly privately; I am posting it here since it may be of help to
other users ]
Michael Marden wrote:
thanks for your comments on the applet size.
In my case Visual Basic (VB) is providing the Web-window and Bob's
script is providing communication - via the hard disk. I added an
explicit VB button (command) to reset the applet to a new size, based on
the current window size; this works, but of course resets the molecule.
It was not reasonable to do it during resizing, since the round trip to
the disk is too slow.
I did try to paste in the suggestion by Angel H.:
script type=text/javascript
function resize(n)
{
document.getElementById(jmolApplet0).width = n
document.getElementById(jmolApplet0).height = n
}
function resizeCSS(n)
{
document.getElementById(jmolApplet0).style.width = n+px
document.getElementById(jmolApplet0).style.height = n+px
}
/script
but I got errors. Maybe Bob can tell me what exact form I need within
the current script he setup.
Overall we need an applet size that follows a percentage of the
Web-window (without having to pass external messages via the disk).
hopefully I can now respond via the Jmol users group.
thanks again,
Michael, if you just need an applet that is sized a percent of the
web page window, that can be done easily (I can send you my
JavaScript code that works). The tricky part is to have the applet
resize when the browser is resized. As pointed out by Miguel, this
probably involves too many resize events and can choke Jmol, or the
browser.
But a per-request resize should also be easy to have.
Please, advise
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Re: [Jmol-users] Mol-graphics: Jmol VB ?
good call, Angel -- yes, this is a Jmol-user issue, not a developer one,
since it involves no Jmol code issues.
Michael, if you Google
apple resize
you will get a number of solutions for automatically resizing an applet
-- Sounds like Angel has one.
See for example
http://blog.taragana.com/index.php/archive/resizing-applets-dynamically-within-browser-frames/
It uses something like this (MSIE only here). One trick might be that on
load the applet may not be fully initiallized. My quick an dirty
solution based on that JavaScript code is at
http://www.stolaf.edu/academics/chemapps/jmol/docs/examples-11/resize.htm
Note that I issue
zoomLarge = false
at the beginning of my script -- That's to ensure that as the applet
resizes the molecule stays within the window.
There's also a hack in there because Jmol.js doesn't support
proportional size windows. [We should fix that, Angel. Perhaps just
allowing: jmolApplet([50%,50%]) or jmolApplet(50%) -- I think it's
one line of code.]
There is no issue of flood Jmol with refreshes. Jmol just ignores a
resize if it is the same dimensions as it already has.
And if it is currently in the process of refreshing, it ignores a
refresh request. So that's not an issue. Especially in a
case like this where you know for a fact the browser is MSIE because it
is a component of your Visual Basic program.
Again, window resizing is standard procedure with the application -- the
Jmol end of things has been capable of this for a long time. This is
just the first time anyone has thought about it in terms of the applet.
Angel Herraez wrote:
[ This follows a post and discussion held partly in jmol-developers
and partly privately; I am posting it here since it may be of help to
other users ]
Michael Marden wrote:
thanks for your comments on the applet size.
In my case Visual Basic (VB) is providing the Web-window and Bob's
script is providing communication - via the hard disk. I added an
explicit VB button (command) to reset the applet to a new size, based on
the current window size; this works, but of course resets the molecule.
It was not reasonable to do it during resizing, since the round trip to
the disk is too slow.
I did try to paste in the suggestion by Angel H.:
script type=text/javascript
function resize(n)
{
document.getElementById(jmolApplet0).width = n
document.getElementById(jmolApplet0).height = n
}
function resizeCSS(n)
{
document.getElementById(jmolApplet0).style.width = n+px
document.getElementById(jmolApplet0).style.height = n+px
}
/script
but I got errors. Maybe Bob can tell me what exact form I need within
the current script he setup.
Overall we need an applet size that follows a percentage of the
Web-window (without having to pass external messages via the disk).
hopefully I can now respond via the Jmol users group.
thanks again,
Michael, if you just need an applet that is sized a percent of the
web page window, that can be done easily (I can send you my
JavaScript code that works). The tricky part is to have the applet
resize when the browser is resized. As pointed out by Miguel, this
probably involves too many resize events and can choke Jmol, or the
browser.
But a per-request resize should also be easy to have.
Please, advise
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Re: [Jmol-users] JmolAppletLite
Sebastian Lisken said: Wouldn't it be possible though to split the applet into several Jars and arrange for all but the first to be loaded on demand? Loading only the jar files necessary for the features requested would be great if it were possible. I can see the point of a Jmol-light, but ADSL is becoming so ubiquitous (I now watch TV over my telephone line) that downloading the present Jmol jar file is not a problem even from home. On the other hand several versions of Jmol would be more difficult to maintain, and more confusing to users. I already have trouble keeping up with all the new features, but am looking forward to finding time to try out the math package. _ 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/ _ - Take Surveys. Earn Cash. Influence the Future of IT Join SourceForge.net's Techsay panel and you'll get the chance to share your opinions on IT business topics through brief surveys-and earn cash http://www.techsay.com/default.php?page=join.phpp=sourceforgeCID=DEVDEV ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] resize applet with window (was: Mol-graphics: Jmol VB ?)
I changed the subject line to make this a bit easier to find in
future, if someone is looking on the archives - and wow, it works
beautifully-- what a great enhansonment! ;^)
Frieda
On Mar 6, 2007, at 7:46 AM, Bob Hanson wrote:
good call, Angel -- yes, this is a Jmol-user issue, not a developer
one,
since it involves no Jmol code issues.
Michael, if you Google
apple resize
you will get a number of solutions for automatically resizing an
applet
-- Sounds like Angel has one.
See for example
http://blog.taragana.com/index.php/archive/resizing-applets-
dynamically-within-browser-frames/
It uses something like this (MSIE only here). One trick might be
that on
load the applet may not be fully initiallized. My quick an dirty
solution based on that JavaScript code is at
http://www.stolaf.edu/academics/chemapps/jmol/docs/examples-11/
resize.htm
Note that I issue
zoomLarge = false
at the beginning of my script -- That's to ensure that as the applet
resizes the molecule stays within the window.
There's also a hack in there because Jmol.js doesn't support
proportional size windows. [We should fix that, Angel. Perhaps just
allowing: jmolApplet([50%,50%]) or jmolApplet(50%) -- I think
it's
one line of code.]
There is no issue of flood Jmol with refreshes. Jmol just ignores a
resize if it is the same dimensions as it already has.
And if it is currently in the process of refreshing, it ignores a
refresh request. So that's not an issue. Especially in a
case like this where you know for a fact the browser is MSIE
because it
is a component of your Visual Basic program.
Again, window resizing is standard procedure with the application
-- the
Jmol end of things has been capable of this for a long time. This is
just the first time anyone has thought about it in terms of the
applet.
Angel Herraez wrote:
[ This follows a post and discussion held partly in jmol-developers
and partly privately; I am posting it here since it may be of help to
other users ]
Michael Marden wrote:
thanks for your comments on the applet size.
In my case Visual Basic (VB) is providing the Web-window and Bob's
script is providing communication - via the hard disk. I added an
explicit VB button (command) to reset the applet to a new size,
based on
the current window size; this works, but of course resets the
molecule.
It was not reasonable to do it during resizing, since the round
trip to
the disk is too slow.
I did try to paste in the suggestion by Angel H.:
script type=text/javascript
function resize(n)
{
document.getElementById(jmolApplet0).width = n
document.getElementById(jmolApplet0).height = n
}
function resizeCSS(n)
{
document.getElementById(jmolApplet0).style.width = n+px
document.getElementById(jmolApplet0).style.height = n+px
}
/script
but I got errors. Maybe Bob can tell me what exact form I need
within
the current script he setup.
Overall we need an applet size that follows a percentage of the
Web-window (without having to pass external messages via the disk).
hopefully I can now respond via the Jmol users group.
thanks again,
Michael, if you just need an applet that is sized a percent of the
web page window, that can be done easily (I can send you my
JavaScript code that works). The tricky part is to have the applet
resize when the browser is resized. As pointed out by Miguel, this
probably involves too many resize events and can choke Jmol, or the
browser.
But a per-request resize should also be easy to have.
Please, advise
-
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///
Frieda Reichsman, PhD
Molecules in Motion
Interactive Molecular Structures
http://www.moleculesinmotion.com
///
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[Jmol-users] New Window with resizable applet command?
I agree this works well and made me think about how it could be used more widely. In ordinary web pages I often use the Open Link in New Window(Frame) feature of my browser (Safari) to create a new window of the content I want to scrutinise in more detail without losing the initial page. Or when you click on thumbnail image to see the full size picture So how about a command for Jmol (and in the menu) that creates a New Window with a resizable Jmol frame. That way we can keep small windows as embedded items in web pages but have the capability to blow them up if required. All the best Nick -- WWW Pages: http://www.liv.ac.uk/Chemistrywww/Staff/greeves.html Tel: +44 (0)151-794-3506 (3500 secretary) On 6 Mar 2007, at 13:28, [EMAIL PROTECTED] wrote: From: Frieda Reichsman [EMAIL PROTECTED] Subject: Re: [Jmol-users] resize applet with window (was: Mol-graphics: Jmol VB ?) To: jmol-users@lists.sourceforge.net Cc: Bob Hanson [EMAIL PROTECTED] Message-ID: [EMAIL PROTECTED] Content-Type: text/plain; charset=us-ascii I changed the subject line to make this a bit easier to find in future, if someone is looking on the archives - and wow, it works beautifully-- what a great enhansonment! ;^) - Take Surveys. Earn Cash. Influence the Future of IT Join SourceForge.net's Techsay panel and you'll get the chance to share your opinions on IT business topics through brief surveys-and earn cash http://www.techsay.com/default.php?page=join.phpp=sourceforgeCID=DEVDEV___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
[Jmol-users] Mac: copying from script window of Jmol application?
Hi all, On a Mac it seems impossible to get the wonderful show state text out of the script window of the Jmol application. Copy/paste is disabled, and drag drop is impossible because after selecting the text, the click inside the script window de-selects the text. (In terms of how other windows work on Mac, this second click should not de-select the text, if the click is held down and the mouse is dragged - it should carry the text and drop it into your waiting shiny new empty text file window. IOW, it is the difference between a mouse-down event and a mouse-up.) I dug up an old post on the list because I remembered someone saying that I could get the output from the Mac OSX Console.app's console.log. But the info does not appear in the log. Anyone solve this mystery already? Frieda /// Frieda Reichsman, PhD Molecules in Motion Interactive Molecular Structures http://www.moleculesinmotion.com /// - Take Surveys. Earn Cash. Influence the Future of IT Join SourceForge.net's Techsay panel and you'll get the chance to share your opinions on IT business topics through brief surveys-and earn cash http://www.techsay.com/default.php?page=join.phpp=sourceforgeCID=DEVDEV___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
[Jmol-users] Bond lengths valence sum calculation with Jmol?
[Sorry, I am still not getting Jmol-users messages. So I'm slow on the
take here. I'll look through some recent archives for messages I might
have something to say about]
Alan, the latest incarnation of Jmol, 11.1.17, includes just the sort of
thing you want, although not sorted. (Come now, you can do that on your
own, right? :) )
I will use 11.1.17 syntax since this wouldn't work on earlier versions
anyway. Basically what you do is:
1) choose bondmodeOR = true or bondmodeOR = false and create a bond
set for the atoms you are interested in. Then format the label for the
set anyway you want.
bondmodeOR = true
theBonds = {_Si}.bonds.label(%2a1%-3i1 %2a2%-3i2 %6.3LENGTH)
The code in there is format code
%2a1 atom 1 identifier, 2 characters, right-justified
%-3i2 atom 2 index, 3 characters, left-justified
%6.3LENGTH bond length set in 6 characters, right-justified, rounded
to 3 decimal places
(another bond option is %ORDER)
now if you say
message @theBonds
you get your information:
O11 Si101.605
O9 Si5 1.614
O8 Si7 1.605
Si7O2 1.614
Si7O9 1.605
O6 Si5 1.605
O4 Si7 1.614
Si3O111.614
Si3O4 1.605
O2 Si1 1.605
Even easier, using the new Jmol.js jmolEvaluate() funcation (only at St.
Olaf, I think? -- not sure if this got into the package), on your web
page use:
var mybonds = new Array()
mybonds = jmolEvaluate('{_Si}.bonds.label(%2a1%-3i1 %2a2%-3i2
%6.3LENGTH').split(\n)
Then you have them in a nice JavaScript array you can sort anyway you
want to.
Bob
Alan Hewat
Sun, 25 Feb 2007 09:31:19 -0800
Jmol already calculates bond-lengths to decide which atoms are bonded
according to distance criteria. It would be very nice to be able to output
a list of these bond-lengths, sorted according to central bonded sites.
For example, the output obtained from
http://icsd.ill.fr/icsd/index.php?action=Bondsid[]=72989
http://icsd.ill.fr/icsd/index.php?action=Bondsid%5B%5D=72989
Then of course it would be an extra bonus to be able to output a list of
the bond angles as well, as can be done from the above URL.
Finally :-) if you have a list of bond lengths, it would be very useful
for inorganic/ionic structures to be able to calculate the bond-valence
sum around the different cations. This is simply the sum of the individual
bond valences = exp((Ro-R)/B) where R is the bond length and Ro and B are
parameters for given cation-anion oxidation states obtained from a look-up
table such as http://icsd.ill.fr/icsd/help/valence.html
The valence states would be extracted from the CIF file, as used for
drawing ionic radii. (Actually in my calculation I have a self-consistency
loop, which assumes intial valence states, calculates the valence sum for
comparison, and then if it is significantly different, uses this new value
as the supposed valence state to select new Ro and B parameters).
The bond valence sum is a very important check on the correctness of a
structure. If it unreasonable then almost certainly something is wrong
(atom coordinates, disorder, stoichiometry etc...)
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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[Jmol-users] Bond lengths valence sum calculation with Jmol?
Alan Hewat
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Re: [Jmol-users] a treat for you -- Jmol in motion
you would just add to the script a new connect() command somewhere in the loop, being careful only to adjust bonds to the molecule you are moving. Yes, that would be cool. C Anthony Lewis Wed, 28 Feb 2007 08:18:29 -0800 Bob, Funky! I found that with both hydrogen bonds and movement on the H-bonds just got longer and longer but if the H-bonds were turned off and then on again another set formed. I'm wondering if its possible to update the H-bonds as the individual molecules move, i.e. breaking and forming them on the fly? Just a thought, Anthony Lewis - Take Surveys. Earn Cash. Influence the Future of IT Join SourceForge.net's Techsay panel and you'll get the chance to share your opinions on IT business topics through brief surveys-and earn cash http://www.techsay.com/default.php?page=join.phpp=sourceforgeCID=DEVDEV ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Mac: copying from script window of Jmol application?
Bob, Would it be possible to have the show script output written into a file, similarly to the write iso myfile.jvxl command? Frieda On Mar 6, 2007, at 9:07 AM, Frieda Reichsman wrote: Hi all, On a Mac it seems impossible to get the wonderful show state text out of the script window of the Jmol application. Copy/paste is disabled, and drag drop is impossible because after selecting the text, the click inside the script window de-selects the text. (In terms of how other windows work on Mac, this second click should not de-select the text, if the click is held down and the mouse is dragged - it should carry the text and drop it into your waiting shiny new empty text file window. IOW, it is the difference between a mouse-down event and a mouse-up.) I dug up an old post on the list because I remembered someone saying that I could get the output from the Mac OSX Console.app's console.log. But the info does not appear in the log. Anyone solve this mystery already? Frieda /// Frieda Reichsman, PhD Molecules in Motion Interactive Molecular Structures http://www.moleculesinmotion.com /// -- --- Take Surveys. Earn Cash. Influence the Future of IT Join SourceForge.net's Techsay panel and you'll get the chance to share your opinions on IT business topics through brief surveys-and earn cash http://www.techsay.com/default.php? page=join.phpp=sourceforgeCID=DEVDEV ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users /// Frieda Reichsman, PhD Molecules in Motion Interactive Molecular Structures http://www.moleculesinmotion.com /// - Take Surveys. Earn Cash. Influence the Future of IT Join SourceForge.net's Techsay panel and you'll get the chance to share your opinions on IT business topics through brief surveys-and earn cash http://www.techsay.com/default.php?page=join.phpp=sourceforgeCID=DEVDEV___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
[Jmol-users] Bond lengths valence sum calculation with Jmol?
At 15:47 06/03/2007, Bob Hanson [EMAIL PROTECTED] wrote: Alan, the latest incarnation of Jmol, 11.1.17, includes just the sort of thing you want, although not sorted. (Come now, you can do that on your own, right? :) ) Thanks Bob. I thought that it might already be possible with all the new things you have implemented. Yes, I should be able to sort the bonds if I have them in a nice javascript array, and probably I can also calculate the valence sum from them (though I am more familiar with calculations server side than client side). BTW I was since told that CDC's Mercury CIF molecular viewer http://www.ccdc.cam.ac.uk/products/mercury/ although much less powerful than Jmol for structure visualisation, especially for inorganics, has bond-lengths built in under the MoreInfo menu. It even has powder pattern visualisation, which one day I would like to see in Java. Alan (still catching up on all the new Jmol features). _ 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/ _ - Take Surveys. Earn Cash. Influence the Future of IT Join SourceForge.net's Techsay panel and you'll get the chance to share your opinions on IT business topics through brief surveys-and earn cash http://www.techsay.com/default.php?page=join.phpp=sourceforgeCID=DEVDEV ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] New Window with resizable applet command?
OK, how about this in Jmol.js: jmolResize(w,h) w or h = 1 implies a percent; h missing defaults to w: jmolResize(500,500) jmolResize(400) jmolResize(0.95,0.60) jmolResize(0.95) Ah, and here is the nicest part: I've modified Jmol.js to allow for percentages as well in the jmolApplet command itself: jmolApplet(95%) or jmolApplet(0.95) Then the applet automatically resizes, far as I can tell -- tested in Firefox, Opera, and IE on a PC. Looks like the browsers properly send the information to the applet indicating resizes if the applet width/height are given as percentages. In playing with this, I notice that if the applet is in a DIV, then that percent applies only to that div. What's interesting is that with the capability of saving and restoring the state now, we really could do just this -- have a button (on the webpage, I think) that captures the state of the applet, designs a new window with the appropriate resize functions, and inserts applet code into the new window such that the state script is run. OK, I have that now in http://www.stolaf.edu/academics/chemapps/jmol/docs/examples-11/new.htm Just click on new applet window under the applet. Let me know if this does not work. Bob Nick Greeves wrote: I agree this works well and made me think about how it could be used more widely. In ordinary web pages I often use the Open Link in New Window(Frame) feature of my browser (Safari) to create a new window of the content I want to scrutinise in more detail without losing the initial page. Or when you click on thumbnail image to see the full size picture So how about a command for Jmol (and in the menu) that creates a New Window with a resizable Jmol frame. That way we can keep small windows as embedded items in web pages but have the capability to blow them up if required. All the best Nick -- WWW Pages: http://www.liv.ac.uk/Chemistrywww/Staff/greeves.html Tel: +44 (0)151-794-3506 (3500 secretary) On 6 Mar 2007, at 13:28, [EMAIL PROTECTED] mailto:[EMAIL PROTECTED] wrote: From: Frieda Reichsman [EMAIL PROTECTED] mailto:[EMAIL PROTECTED] Subject: Re: [Jmol-users] resize applet with window (was: Mol-graphics: Jmol VB ?) To: jmol-users@lists.sourceforge.net mailto:jmol-users@lists.sourceforge.net Cc: Bob Hanson [EMAIL PROTECTED] mailto:[EMAIL PROTECTED] Message-ID: [EMAIL PROTECTED] mailto:[EMAIL PROTECTED] Content-Type: text/plain; charset=us-ascii I changed the subject line to make this a bit easier to find in future, if someone is looking on the archives - and wow, it works beautifully-- what a great enhansonment! ;^) - Take Surveys. Earn Cash. Influence the Future of IT Join SourceForge.net's Techsay panel and you'll get the chance to share your opinions on IT business topics through brief surveys-and earn cash http://www.techsay.com/default.php?page=join.phpp=sourceforgeCID=DEVDEV ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Mac: copying from script window of Jmol application?
It should appear in the log (along with all sorts of other stuff) if you use set loglevel 5 But I wonder what the issue is with Macs. Anyway, with the WRITE command, you shouldn't have to fool with any of this. But I see that I haven't fully realized the CLIPBOARD functionality of that command. Right now we only have: write image clipboard (Does that work for you, frieda?) I guess we can have write isosurface clipboard write mo clipboard write state clipboard write var x clipboard etc. ... OK, these are all part of Jmol 11.1.18. the code checkin system (SVN) is not working for me, so this is to be found at http://www.stolaf.edu/academics/jmol/docs/examples-11/Jmol.jar Bob Frieda Reichsman wrote: Hi all, On a Mac it seems impossible to get the wonderful show state text out of the script window of the Jmol application. Copy/paste is disabled, and drag drop is impossible because after selecting the text, the click inside the script window de-selects the text. (In terms of how other windows work on Mac, this second click should not de-select the text, if the click is held down and the mouse is dragged - it should carry the text and drop it into your waiting shiny new empty text file window. IOW, it is the difference between a mouse-down event and a mouse-up.) I dug up an old post on the list because I remembered someone saying that I could get the output from the Mac OSX Console.app's console.log. But the info does not appear in the log. Anyone solve this mystery already? Frieda /// Frieda Reichsman, PhD Molecules in Motion Interactive Molecular Structures http://www.moleculesinmotion.com /// - Take Surveys. Earn Cash. Influence the Future of IT Join SourceForge.net's Techsay panel and you'll get the chance to share your opinions on IT business topics through brief surveys-and earn cash http://www.techsay.com/default.php?page=join.phpp=sourceforgeCID=DEVDEV ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Mac: copying from script window of Jmol application?
It should appear in the log (along with all sorts of other stuff) if you use set loglevel 5 But I wonder what the issue is with Macs. Anyway, with the WRITE command, you shouldn't have to fool with any of this. But I see that I haven't fully realized the CLIPBOARD functionality of that command. Right now we only have: write image clipboard (Does that work for you, frieda?) I guess we can have write isosurface clipboard write mo clipboard write state clipboard write var x clipboard etc. ... OK, these are all part of Jmol 11.1.18. the code checkin system (SVN) is not working for me, so this is to be found at http://www.stolaf.edu/academics/chemapps/jmol/docs/examples-11/Jmol.jar Bob Frieda Reichsman wrote: Hi all, On a Mac it seems impossible to get the wonderful show state text out of the script window of the Jmol application. Copy/paste is disabled, and drag drop is impossible because after selecting the text, the click inside the script window de-selects the text. (In terms of how other windows work on Mac, this second click should not de-select the text, if the click is held down and the mouse is dragged - it should carry the text and drop it into your waiting shiny new empty text file window. IOW, it is the difference between a mouse-down event and a mouse-up.) I dug up an old post on the list because I remembered someone saying that I could get the output from the Mac OSX Console.app's console.log. But the info does not appear in the log. Anyone solve this mystery already? Frieda /// Frieda Reichsman, PhD Molecules in Motion Interactive Molecular Structures http://www.moleculesinmotion.com /// - Take Surveys. Earn Cash. Influence the Future of IT Join SourceForge.net's Techsay panel and you'll get the chance to share your opinions on IT business topics through brief surveys-and earn cash http://www.techsay.com/default.php?page=join.phpp=sourceforgeCID=DEVDEV ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] New Window with resizable applet command?
Bob Hanson wrote:
[snip]
OK, I have that now in
http://www.stolaf.edu/academics/chemapps/jmol/docs/examples-11/new.htm
Amazing and delightful!
Works fine in WinXP:
Firefox 1.5
Opera 9.0
Netscape 7.0
Mozilla 1.7.12
but
IE 7 and 5.5: new window is empty -no applet-
As for the source of trouble, I try to guess:
1) Some Microsoft security -protect you from yourself? ;-)
2) Bob, I had a look at Jmol.js, and think that in
_jmolGetAppletSize()
you are adding px even if size is in percent?
IE says runtime error - object was expected (cannot find in which
point, since all is in one line and MS Script Editor doesn't give
more clues -or I don't know how to)
Firefox javascript console -although it basically works- says:
Error: an end of value was expected for the property, but 'px' was
found. Error while reading the value for the property 'width'.
Declaration rejected.
Source file:
http://www.stolaf.edu/academics/chemapps/jmol/docs/examples-
11/new.htm
Line: 0
and same for 'height'
I would say my observation above is right, and some browsers forgive
the error while others don't.
Specifically:
http://www.stolaf.edu/academics/chemapps/jmol/docs/examples-
11/Jmol.js
/* Jmol 11.0 script library Jmol.js (aka Jmol-11.js) 9:53 AM 3/6/2007
line 773:
function _jmolGetAppletSize(size) {
lines 781-792:
if (typeof width == number) {
if(! (width = 25 width = 2000))
width = (width 1 width 0 ? (width * 100)+%:300)
width += px
}
if (typeof height == number) {
if(! (height = 25 height = 2000))
height = (height 1 height 0? (height * 100)+%:300);
height += px
}
I think they should be:
if (typeof width == number) {
if(width = 25 width = 2000)
width += px
else
width = (width 1 width 0 ? (width * 100)+%:300px)
}
if (typeof height == number) {
if(height = 25 height = 2000)
width += px
else
height = (height 1 height 0? (height * 100)+%:300px);
}
Right?
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Re: [Jmol-users] Mac: copying from script window of Jmol application?
On Mar 6, 2007, at 12:31 PM, Bob Hanson wrote: Anyway, with the WRITE command, you shouldn't have to fool with any of this. But I see that I haven't fully realized the CLIPBOARD functionality of that command. Right now we only have: write image clipboard (Does that work for you, frieda?) LOL! when I tried it, the word image is what gets pasted from the clipboard into a new document. I will check out Jmol 11.1.18 with the new write commands... Frieda /// Frieda Reichsman, PhD Molecules in Motion Interactive Molecular Structures http://www.moleculesinmotion.com /// - Take Surveys. Earn Cash. Influence the Future of IT Join SourceForge.net's Techsay panel and you'll get the chance to share your opinions on IT business topics through brief surveys-and earn cash http://www.techsay.com/default.php?page=join.phpp=sourceforgeCID=DEVDEV___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Mac: copying from script window of Jmol application?
On Mar 6, 2007, at 12:31 PM, Bob Hanson wrote: ... OK, these are all part of Jmol 11.1.18. the code checkin system (SVN) is not working for me, so this is to be found at http://www.stolaf.edu/academics/jmol/docs/examples-11/Jmol.jar ...File not found... I believe the correct URL is: http://www.stolaf.edu/academics/chemapps/jmol/docs/examples-11/Jmol.jar Frieda /// Frieda Reichsman, PhD Molecules in Motion Interactive Molecular Structures http://www.moleculesinmotion.com /// - Take Surveys. Earn Cash. Influence the Future of IT Join SourceForge.net's Techsay panel and you'll get the chance to share your opinions on IT business topics through brief surveys-and earn cash http://www.techsay.com/default.php?page=join.phpp=sourceforgeCID=DEVDEV___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Mac: copying from script window of Jmol application?
On Mar 6, 2007, at 12:31 PM, Bob Hanson wrote: It should appear in the log (along with all sorts of other stuff) if you use set loglevel 5 After setting loglevel to 5, then saying 'show script' there is nothing in Java console.log, as accessed through Console.app. But there are other possible solutions to try at this point... Frieda /// Frieda Reichsman, PhD Molecules in Motion Interactive Molecular Structures http://www.moleculesinmotion.com /// - Take Surveys. Earn Cash. Influence the Future of IT Join SourceForge.net's Techsay panel and you'll get the chance to share your opinions on IT business topics through brief surveys-and earn cash http://www.techsay.com/default.php?page=join.phpp=sourceforgeCID=DEVDEV___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Mac: copying from script window of Jmol application?
OK, in Jmol 11.1.18, write state myfile.spt and write state clipboard both work to produce a script that reproduces the state. Hurrah! The only parameter I find that is not faithfully reproduced (so far) is background color of the applet. Is this intentional, since it might be specified in the code that creates the applet? Frieda On Mar 6, 2007, at 12:32 PM, Bob Hanson wrote: I guess we can have write isosurface clipboard write mo clipboard write state clipboard write var x clipboard etc. ... OK, these are all part of Jmol 11.1.18. /// Frieda Reichsman, PhD Molecules in Motion Interactive Molecular Structures http://www.moleculesinmotion.com /// - Take Surveys. Earn Cash. Influence the Future of IT Join SourceForge.net's Techsay panel and you'll get the chance to share your opinions on IT business topics through brief surveys-and earn cash http://www.techsay.com/default.php?page=join.phpp=sourceforgeCID=DEVDEV___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
[Jmol-users] Is there a simple way to create an ellipse?
Jmol users, I¹d like to create a representation of a plane that is an ellipse rather than a rectangle. Is there a simple way to create a representation of an ellipse in Jmol? Thanks for any pointers / suggestions. Dean Johnston - Take Surveys. Earn Cash. Influence the Future of IT Join SourceForge.net's Techsay panel and you'll get the chance to share your opinions on IT business topics through brief surveys-and earn cash http://www.techsay.com/default.php?page=join.phpp=sourceforgeCID=DEVDEV___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] .dx files available
Michael, thank you very much for the DX files. That was just what I needed. Frieda, by the time you read this I will have uploaded a new 11.1.18 version of Jmol that reads these DX files in the form: ISOSURFACE sasurface map 1dry.dx Then from the application write isosurface 1dry.jvxl saves the Jvxl file. To read that back in, just: load 1dry.pdb isosurface 1dry.jvxl That does it. Jmol can now map this APBS data onto any molecular surface. I'm happy to report that the resultant JVXL surface WITH the mapped colors comes in at 64K (this for 1dry.pdb). That's the expected 300:1 compression, considering that only 2/3 of the JVXL file is color data (40K). Basically that means we see a compression from 12900 KB to 40 KB. I can live with that! Michael, if you don't have a clue what I'm talking about, check out http://www.stolaf.edu/academics/chemapps/jmol/docs/misc/JVXL-format.pdf Basically what I have created is a very compact file format that Jmol can read and write (in command-line batch mode if desired, by the way). These Jmol Voxel files incorporate ONE full surface or planar slice with color mapping. The savings is due to the fact that we can't arbitrarily map the resultant data onto any data set. The mapping is done -- this is now effectively a 2-D selection from the 3D data -- 2D in the sense that all surfaces, no matter how curved, are still two dimensional, not three. So we see this incredible compression. Frieda, I'm compiling now, and Nico will be updating the SourceForge site sometime Wednesday, I expect. Bob Hanson Michael Lerner wrote: Hi, I'm uploading things right now. I compressed the rest of the files so that they would transfer more quickly. They should be done soon, but some of the .dx and .wrl files are large. Let me know if you need anything else, -Michael - Take Surveys. Earn Cash. Influence the Future of IT Join SourceForge.net's Techsay panel and you'll get the chance to share your opinions on IT business topics through brief surveys-and earn cash http://www.techsay.com/default.php?page=join.phpp=sourceforgeCID=DEVDEV ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
[Jmol-users] [Fwd: Re: New Window with resizable applet command?]
OK, this is good news. The basic story is that if you want your applet to resize automatically, just use the latest Jmol.js and instead of 300 or 400 for a size, use 0.6 or 0.95. This tells Jmol to use percent instead of pixels for the size in the object tag. That does the trick. If you have special need for other sorts of resizing -- a how about a bigger applet? button for example -- then tie that button to jmolResize(w,h) where w and h are the width and height you want. Bob Original Message Subject:Re: New Window with resizable applet command? Date: Tue, 6 Mar 2007 19:36:40 + From: Nick Greeves [EMAIL PROTECTED] To: Bob Hanson [EMAIL PROTECTED] References: [EMAIL PROTECTED] [EMAIL PROTECTED] [EMAIL PROTECTED] Hi Bob, Works nicely on Mac OS X Safari and Firefox. I know you only wanted to here about failures but this looks great! All the best Nick -- WWW Pages: http://www.liv.ac.uk/Chemistrywww/Staff/greeves.html Tel: +44 (0)151-794-3506 (3500 secretary) On 6 Mar 2007, at 16:48, Bob Hanson wrote: OK, how about this in Jmol.js: jmolResize(w,h) w or h = 1 implies a percent; h missing defaults to w: jmolResize(500,500) jmolResize(400) jmolResize(0.95,0.60) jmolResize(0.95) Ah, and here is the nicest part: I've modified Jmol.js to allow for percentages as well in the jmolApplet command itself: jmolApplet(95%) or jmolApplet(0.95) Then the applet automatically resizes, far as I can tell -- tested in Firefox, Opera, and IE on a PC. Looks like the browsers properly send the information to the applet indicating resizes if the applet width/height are given as percentages. In playing with this, I notice that if the applet is in a DIV, then that percent applies only to that div. What's interesting is that with the capability of saving and restoring the state now, we really could do just this -- have a button (on the webpage, I think) that captures the state of the applet, designs a new window with the appropriate resize functions, and inserts applet code into the new window such that the state script is run. OK, I have that now in http://www.stolaf.edu/academics/chemapps/jmol/docs/examples-11/new.htm Just click on new applet window under the applet. Let me know if this does not work. Bob Nick Greeves wrote: I agree this works well and made me think about how it could be used more widely. In ordinary web pages I often use the Open Link in New Window(Frame) feature of my browser (Safari) to create a new window of the content I want to scrutinise in more detail without losing the initial page. Or when you click on thumbnail image to see the full size picture So how about a command for Jmol (and in the menu) that creates a New Window with a resizable Jmol frame. That way we can keep small windows as embedded items in web pages but have the capability to blow them up if required. All the best Nick -- WWW Pages: http://www.liv.ac.uk/Chemistrywww/Staff/greeves.html Tel: +44 (0)151-794-3506 (3500 secretary) On 6 Mar 2007, at 13:28, [EMAIL PROTECTED] mailto:[EMAIL PROTECTED] wrote: From: Frieda Reichsman [EMAIL PROTECTED] mailto:[EMAIL PROTECTED] Subject: Re: [Jmol-users] resize applet with window (was: Mol-graphics: Jmol VB ?) To: jmol-users@lists.sourceforge.net mailto:jmol-users@lists.sourceforge.net Cc: Bob Hanson [EMAIL PROTECTED] mailto:[EMAIL PROTECTED] Message-ID: [EMAIL PROTECTED] mailto:[EMAIL PROTECTED] Content-Type: text/plain; charset=us-ascii I changed the subject line to make this a bit easier to find in future, if someone is looking on the archives - and wow, it works beautifully-- what a great enhansonment! ;^) - Take Surveys. Earn Cash. Influence the Future of IT Join SourceForge.net's Techsay panel and you'll get the chance to share your opinions on IT business topics through brief surveys-and earn cash http://www.techsay.com/default.php?page=join.phpp=sourceforgeCID=DEVDEV ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] New Window with resizable applet command?
Angel Herraez wrote:
Bob Hanson wrote:
[snip]
OK, I have that now in
http://www.stolaf.edu/academics/chemapps/jmol/docs/examples-11/new.htm
Amazing and delightful!
Works fine in WinXP:
Firefox 1.5
Opera 9.0
Netscape 7.0
Mozilla 1.7.12
but
IE 7 and 5.5: new window is empty -no applet-
As for the source of trouble, I try to guess:
1) Some Microsoft security -protect you from yourself? ;-)
2) Bob, I had a look at Jmol.js, and think that in
_jmolGetAppletSize()
you are adding px even if size is in percent?
function _jmolGetAppletSize(size) {
...
oops!
right! I got mixed up in all the negatives. This is better:
function _jmolGetAppletSize(size) {
var width, height;
var type = typeof size;
if (type == object size != null) {
width = size[0]; height = size[1];
} else {
width = height = size;
}
if (typeof width == number) {
width = (width = 25 width = 2000 ? width + px
: width 1 width 0 ? (width * 100)+%:300px)
}
if (typeof height == number) {
height = (height = 25 height = 2000 ? height + px
: height 1 height 0 ? (height * 100)+%:300px)
}
return [width, height];
}
Don't you love the way you can completely mess with variable types in
JavaScript!!!
IE says runtime error - object was expected (cannot find in which
point, since all is in one line and MS Script Editor doesn't give
more clues -or I don't know how to)
Hmm. I had trouble with MSIE 5.whatever but it went away when I took out
the body onresize... business.
Firefox javascript console -although it basically works- says:
Error: an end of value was expected for the property, but 'px' was
found. Error while reading the value for the property 'width'.
Declaration rejected.
Source file:
http://www.stolaf.edu/academics/chemapps/jmol/docs/examples-
11/new.htm
Line: 0
and same for 'height'
Right?
right. But I doubt that's the problem with MSIE 7. Would be nice if it
were only that.
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