[Jmol-users] Fwd: jmol-11.6 bug
Victor, Thanks for the picture. That's just an illusion. The 11.6.RC16 image has set perspectiveDepth OFF and the two balls are exactly the same size. The 11.4.6 image has set perspectiveDepth ON and something like set cameraFactor 0.1 showing a bizarrely distorted molecule. The default for Jmol is set perspectiveDepth ON but that will automatically be turned off if a crystal structure is loaded. Bob On Thu, Sep 25, 2008 at 12:54 PM, Victor Chest <[EMAIL PROTECTED]>wrote: > Hi, > > I found some error in visualization of bounded atoms in version 11.6 RC16 > (there is no this bug in version 11.4.6): atom on the back plan is bigger > then another one on the front. In case of short bond it is not recognizable > enough so I created some artificial example (see attachment "test.gif" > file). Left panel is Jmol 11.4.6, the right one is 11.6 RC16 > > Thanks, > Victor > > -- Robert M. Hanson Professor of Chemistry St. Olaf College 1520 St. Olaf Ave. Northfield, MN 55057 http://www.stolaf.edu/people/hansonr phone: 507-786-3107 If nature does not answer first what we want, it is better to take what answer we get. -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900 <>- This SF.Net email is sponsored by the Moblin Your Move Developer's challenge Build the coolest Linux based applications with Moblin SDK & win great prizes Grand prize is a trip for two to an Open Source event anywhere in the world http://moblin-contest.org/redirect.php?banner_id=100&url=/___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] jmol movie
I had no trouble watching the Jmol movie on my computer, running Windows XP.
-Jennifer
Message: 2
Date: Wed, 1 Oct 2008 12:25:34 -0500
From: "Robert Hanson" <[EMAIL PROTECTED]>
Subject: [Jmol-users] jmol movie
To: jmol-users@lists.sourceforge.net
Message-ID:
<[EMAIL PROTECTED]>
Content-Type: text/plain; charset="iso-8859-1"
Question: Can you watch this movie on your machine? If so, how's the
resolution?
http://www.stolaf.edu/people/hansonr/temp/rasraf.avi
It's supposed to be 145 frames of a molecular dynamics calculation. It was
created using the following Jmol script followed by running a program called
VideoMach:
function createFrame
var fname = "movie_"+_frameID[-2][0] + ".jpg"
write image 500 500 @fname
end function
function createMovie
var nframes = {*}.model.max
for (var i = 1; i <= nframes; i = i + 1)
frame @i
createFrame
end for
end function
createMovie
Bob
--
Robert M. Hanson
Professor of Chemistry
St. Olaf College
1520 St. Olaf Ave.
Northfield, MN 55057
http://www.stolaf.edu/people/hansonr
phone: 507-786-3107
If nature does not answer first what we want,
it is better to take what answer we get.
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Re: [Jmol-users] jmol movie
No problem seeing it here Bob (OSX 10.4.11, Camino 1.6.4 with QT 7.5.5 with the Xvid codec). I did re-export it as an image sequence (145 images) and created a new movie at 2 fps (using QT) to make it more easily watched. There are some rather odd H atoms wandering around/displayed which I'm assuming are the result of some strangeness in the MD calculations rather than coming from Jmol. Rich On 1-10-2008 13:25, Robert Hanson wrote: > Question: Can you watch this movie on your machine? If so, how's the > resolution? > > http://www.stolaf.edu/people/hansonr/temp/rasraf.avi > > It's supposed to be 145 frames of a molecular dynamics calculation. It was > created using the following Jmol script followed by running a program called > VideoMach: - This SF.Net email is sponsored by the Moblin Your Move Developer's challenge Build the coolest Linux based applications with Moblin SDK & win great prizes Grand prize is a trip for two to an Open Source event anywhere in the world http://moblin-contest.org/redirect.php?banner_id=100&url=/ ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] jmol movie
OK, then I think we have the capability now of creating Jmol video movies.
The addition to Jmol, to be in 11.7, not 11.6, is;
write frames {xxx} "movie.jpg"
{xxx} is some atom expression, such as {*} (all frames) or {1.0} (all models
in the first file) or {1.1,1.3,1.5} (three specific frames). Files will be
created by replacing "" with "0001" "0002" etc. as necessary, creating a
set of image files (JPEG in this case).
What you do with those files is up to you. I loaded them into VideoMach just
to see if it could handle them, which it did, apparently. I purposely set
the frame rate very high. But there are plenty of utilities out there that
can do this. Maybe someone with more experience can fill us in on a few of
the options.
Bob
On Sun, Oct 5, 2008 at 9:38 AM, Rich <[EMAIL PROTECTED]> wrote:
> No problem seeing it here Bob (OSX 10.4.11, Camino 1.6.4 with QT 7.5.5
> with the Xvid codec). I did re-export it as an image sequence (145
> images) and created a new movie at 2 fps (using QT) to make it more
> easily watched. There are some rather odd H atoms wandering
> around/displayed which I'm assuming are the result of some strangeness
> in the MD calculations rather than coming from Jmol
>
> Rich
>
> On 1-10-2008 13:25, Robert Hanson wrote:
> > Question: Can you watch this movie on your machine? If so, how's the
> > resolution?
> >
> > http://www.stolaf.edu/people/hansonr/temp/rasraf.avi
> >
> > It's supposed to be 145 frames of a molecular dynamics calculation. It
> was
> > created using the following Jmol script followed by running a program
> called
> > VideoMach:
>
> -
> This SF.Net email is sponsored by the Moblin Your Move Developer's
> challenge
> Build the coolest Linux based applications with Moblin SDK & win great
> prizes
> Grand prize is a trip for two to an Open Source event anywhere in the world
> http://moblin-contest.org/redirect.php?banner_id=100&url=/
> ___
> Jmol-users mailing list
> Jmol-users@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/jmol-users
>
--
Robert M. Hanson
Professor of Chemistry
St. Olaf College
1520 St. Olaf Ave.
Northfield, MN 55057
http://www.stolaf.edu/people/hansonr
phone: 507-786-3107
If nature does not answer first what we want,
it is better to take what answer we get.
-- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900
-
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Re: [Jmol-users] moving draw objects produces duplicates
OK, I'll not worry about it. You can force Jmol to create only one object using the FIXED keyword within the DRAW command. That makes the object appear in every frame. Unless you do that, if four files are displayed, you might get four separate points. Bob On Sat, Oct 4, 2008 at 6:21 PM, Angel Herráez <[EMAIL PROTECTED]> wrote: > > I'll need a state to work with. Is it possible you have 4 files? I don't > think it's cloning itself. I think > > there are really four objects all being displayed at the same place and > you are just picking up the > > top one and moving it, so it LOOKS like it's being replicated. > > You are probably on the right track, Bob. > Today I tried to reproduce the problem and could only do so in the original > situation; if I try > it on a clean Jmol (app or applet), it does not happen. > Yes, I have 4 files loaded and I'm drawing several objects by script > (applet). Then, when I > add a new one from the console (just trying to manually locate the right > position to put one > of the existing scripted ones), I found this. > But I'd say I had done it before, so have the feeling it's happening only > with this version. > > I'll try to get the state and send it to you, but it will be quite complex. > Don't worry too much > about it, as the intended (scripted) features are working OK. > Maybe I need to set on a specific frame before I do the drawings? > > Ok, after testing it's now clear --no need for the state--: > > I had all 4 frames shown. The draw command creates 4 objects, one on each > frame. > If I first do "frame 1.1", then draw, there's a single object. > > BTW, the scripted draws were being done on the first frame, then all 4 were > selected for > display. > > > - > This SF.Net email is sponsored by the Moblin Your Move Developer's > challenge > Build the coolest Linux based applications with Moblin SDK & win great > prizes > Grand prize is a trip for two to an Open Source event anywhere in the world > http://moblin-contest.org/redirect.php?banner_id=100&url=/ > ___ > Jmol-users mailing list > Jmol-users@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/jmol-users > -- Robert M. Hanson Professor of Chemistry St. Olaf College 1520 St. Olaf Ave. Northfield, MN 55057 http://www.stolaf.edu/people/hansonr phone: 507-786-3107 If nature does not answer first what we want, it is better to take what answer we get. -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900 - This SF.Net email is sponsored by the Moblin Your Move Developer's challenge Build the coolest Linux based applications with Moblin SDK & win great prizes Grand prize is a trip for two to an Open Source event anywhere in the world http://moblin-contest.org/redirect.php?banner_id=100&url=/___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Jmol 11.6 release -- delayed
On Thu, Oct 2, 2008 at 9:59 AM, Rolf Huehne <[EMAIL PROTECTED]> wrote: > Rolf Huehne wrote: > > 3) The "java.security.AccessControlException" problem still remains. I > > don't know if this is specific to our site because I can't check it > > with other sites. But it must be caused by changes introduced after > > 11.6.RC13 because the problem doesn't occur with this version or earlier > > ones. > > If I use the signed applet I get a "file not found" error instead. > > (Since the "file not found" error occurs before the > > "java.security.AccessControl" error I can't tell if the security problem > > doesn't occur there.) > > > When I use the signed applet without a server directly from a local HTML > file it works properly on Linux with Java 1.4.2_18: no "file not found" > error, no "java.security.AccessControlException" error. > > But on WinXP with Java 1.6.0_07 I can only open local files. When I try > to load a structure from a remote server by providing the full URL or > using for example "=1deh" I get a "java.security.AccessControlException" > error. (This time with the addition "connect,resolve" compared to > "permission denied" in the cases with a server described earlier.) In > this case the same error also occurs with Jmol 11.5.35. > Q: Is this the general behaviour of Java 1.6.x? > No --- WinXP/Java 1.6.0_10rc works fine for me for "load =1blu" using a local signed applet. Please try that update. Could just be a Java bug. There should be no such issue there. > > When I tried the "load/save" options from the popup menu with the signed > applet on Linux I could not enter any filename directly (as was > previously reported by someone else on MacOS). This is particularly bad > for the "save" option because one can't change the default name. The MacOS issue was resolved by not using the Mac "look and feel" (which doesn't include that file entry box). That was a change made in Jmol 11.6.RC15 on 9/15/2008. But if you can't enter a file name in that Linux box, what is it for? Sounds like a Linux/Java bug. Bob > > While working with the popup menu (which I rarely use) I found that "Set > picking" is not very clear if one hasn't read the documentation on "set > picking". I doubt that any newbie would recognize that this is related > to selection with the mouse. > So I would suggest to change it to "Mouse selection mode" (in german: > "Maus-Auswahlmodus"). Keept that thought -- no new translations for 11.6, please. > > > Regards, > Rolf > > - > This SF.Net email is sponsored by the Moblin Your Move Developer's > challenge > Build the coolest Linux based applications with Moblin SDK & win great > prizes > Grand prize is a trip for two to an Open Source event anywhere in the world > http://moblin-contest.org/redirect.php?banner_id=100&url=/ > ___ > Jmol-users mailing list > Jmol-users@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/jmol-users > -- Robert M. Hanson Professor of Chemistry St. Olaf College 1520 St. Olaf Ave. Northfield, MN 55057 http://www.stolaf.edu/people/hansonr phone: 507-786-3107 If nature does not answer first what we want, it is better to take what answer we get. -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900 - This SF.Net email is sponsored by the Moblin Your Move Developer's challenge Build the coolest Linux based applications with Moblin SDK & win great prizes Grand prize is a trip for two to an Open Source event anywhere in the world http://moblin-contest.org/redirect.php?banner_id=100&url=/___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
[Jmol-users] jmol movie
Fine on MacOS X 10.5.5/Safari/QT resolution clear but rather fast to actually see anything! While it was downloading, it played a bit then stopped and was pixelated. Fine once it was all downloaded though. All the best Nick -- 3D Organic Animations http://www.chemtube3d.com Tel: +44 (0)151-794-3506 (3500 secretary) On 5 Oct 2008, at 20:22, [EMAIL PROTECTED] wrote: Question: Can you watch this movie on your machine? If so, how's the resolution? http://www.stolaf.edu/people/hansonr/temp/rasraf.avi - This SF.Net email is sponsored by the Moblin Your Move Developer's challenge Build the coolest Linux based applications with Moblin SDK & win great prizes Grand prize is a trip for two to an Open Source event anywhere in the world http://moblin-contest.org/redirect.php?banner_id=100&url=/___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
[Jmol-users] en_GB translation ?
Recently an en_GB (United Kingdom) translation for Jmol was introduced. I'm fixing that a bit, but at the same time I'm wondering if people realize that this adds 200K to the size of the applet for all UK users. (That's a 30% increase in base size.) Questions: 1. Not that it isn't good to have this language variant, but is the trade-off in download size worth it? [Obviously it is for other languages, but I'd like to hear what our UK users think.] 2. Should then en_GB be the default for en_XX -- a country other than US but not GB? 3. Should we perhaps package the languages classes separately or in separate groups so that the entire translation package isn't downloaded with any particular language switch? Bob -- Robert M. Hanson Professor of Chemistry St. Olaf College 1520 St. Olaf Ave. Northfield, MN 55057 http://www.stolaf.edu/people/hansonr phone: 507-786-3107 If nature does not answer first what we want, it is better to take what answer we get. -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900 - This SF.Net email is sponsored by the Moblin Your Move Developer's challenge Build the coolest Linux based applications with Moblin SDK & win great prizes Grand prize is a trip for two to an Open Source event anywhere in the world http://moblin-contest.org/redirect.php?banner_id=100&url=/___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] ff3 vs safari.. again.. load
Angel has it exactly. Just to be clear, for ANY browser: 1) Never use jmolScript() during page loading. The applet won't be there. 2) Never run a Jmol script from the body onload event. On most browsers the applet won't be loaded yet. 3) If possible, put whatever start-up script you want to use in the jmolApplet() call itself. 4) If that is not possible for some reason, you have to set up the applet with a callback and have the script in the jmolApplet() notify JavaScript that it is working or done. That's generally unnecessary, though. Bob -- Robert M. Hanson Professor of Chemistry St. Olaf College 1520 St. Olaf Ave. Northfield, MN 55057 http://www.stolaf.edu/people/hansonr phone: 507-786-3107 If nature does not answer first what we want, it is better to take what answer we get. -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900 - This SF.Net email is sponsored by the Moblin Your Move Developer's challenge Build the coolest Linux based applications with Moblin SDK & win great prizes Grand prize is a trip for two to an Open Source event anywhere in the world http://moblin-contest.org/redirect.php?banner_id=100&url=/___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Translucent cylinder disappears when viewed edge on
this is fixed for Jmol 11.6
On Sat, Oct 4, 2008 at 12:20 AM, Dean Johnston <[EMAIL PROTECTED]>wrote:
> Here's an odd one. My (very short) translucent cylinders disappear when
> viewed within a few degrees of edge-on. To be more exact, the center
> disappears while the edge remains visible. These are the same type of
> cylinders that are generated by the draw pointgroup command. I've only
> started to notice this with the most recent version (11.6.RC19).
>
> Here's the command.
>
> draw plane1_disk width 6.2001 cylinder {-0.0300 0. 0.} {0.0300
> 0. 0.} color translucent orange fixed;
>
> Dean
>
> P.S. If it's any help, the angle at which it disappears gets smaller if
> you turn on antialiasDisplay.
>
>
>
> -
> This SF.Net email is sponsored by the Moblin Your Move Developer's
> challenge
> Build the coolest Linux based applications with Moblin SDK & win great
> prizes
> Grand prize is a trip for two to an Open Source event anywhere in the world
> http://moblin-contest.org/redirect.php?banner_id=100&url=/
> ___
> Jmol-users mailing list
> Jmol-users@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/jmol-users
>
>
--
Robert M. Hanson
Professor of Chemistry
St. Olaf College
1520 St. Olaf Ave.
Northfield, MN 55057
http://www.stolaf.edu/people/hansonr
phone: 507-786-3107
If nature does not answer first what we want,
it is better to take what answer we get.
-- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900
-
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Re: [Jmol-users] Jmol 11.6 release -- delayed
I have tentatively modified Jmol to make load "/xxx/xxx" for the application and the SIGNED applet default to load "file:/xxx/xxx" and for the UNSIGNED applet default to load "http://whatever.server/xxx/xxx"; when the applet is on a server or load "file:/xxx/xxx" when it is local. Rationale: --The remote unsigned applet couldn't load file:/xxx anyway. --No change then for unsigned applet behavior relative to 11.4 --Unlikely anyone has been using the signed applet to read files via root of webserver I'm not totally happy with this, because it allows two different behaviors between the signed and unsigned applets, but I think it will let us proceed with 11.6, since it represents no change in the unsigned applet, and almost certainly the desired behavior with the signed applet and application. Comments requested. Bob On Sun, Oct 5, 2008 at 2:22 PM, Robert Hanson <[EMAIL PROTECTED]> wrote: > > > On Thu, Oct 2, 2008 at 9:59 AM, Rolf Huehne <[EMAIL PROTECTED]>wrote: > >> Rolf Huehne wrote: >> > 3) The "java.security.AccessControlException" problem still remains. I >> > don't know if this is specific to our site because I can't check it >> > with other sites. But it must be caused by changes introduced after >> > 11.6.RC13 because the problem doesn't occur with this version or earlier >> > ones. >> > If I use the signed applet I get a "file not found" error instead. >> > (Since the "file not found" error occurs before the >> > "java.security.AccessControl" error I can't tell if the security problem >> > doesn't occur there.) >> > >> When I use the signed applet without a server directly from a local HTML >> file it works properly on Linux with Java 1.4.2_18: no "file not found" >> error, no "java.security.AccessControlException" error. >> >> But on WinXP with Java 1.6.0_07 I can only open local files. When I try >> to load a structure from a remote server by providing the full URL or >> using for example "=1deh" I get a "java.security.AccessControlException" >> error. (This time with the addition "connect,resolve" compared to >> "permission denied" in the cases with a server described earlier.) In >> this case the same error also occurs with Jmol 11.5.35. > > >> Q: Is this the general behaviour of Java 1.6.x? >> > > No --- WinXP/Java 1.6.0_10rc works fine for me for "load =1blu" using a > local signed applet. Please try that update. Could just be a Java bug. There > should be no such issue there. > > >> >> When I tried the "load/save" options from the popup menu with the signed >> applet on Linux I could not enter any filename directly (as was >> previously reported by someone else on MacOS). This is particularly bad >> for the "save" option because one can't change the default name. > > > The MacOS issue was resolved by not using the Mac "look and feel" (which > doesn't include that file entry box). That was a change made in Jmol > 11.6.RC15 on 9/15/2008. But if you can't enter a file name in that Linux > box, what is it for? Sounds like a Linux/Java bug. > > Bob > > > >> >> While working with the popup menu (which I rarely use) I found that "Set >> picking" is not very clear if one hasn't read the documentation on "set >> picking". I doubt that any newbie would recognize that this is related >> to selection with the mouse. >> So I would suggest to change it to "Mouse selection mode" (in german: >> "Maus-Auswahlmodus"). > > > Keept that thought -- no new translations for 11.6, please. > >> >> >> Regards, >> Rolf >> >> - >> This SF.Net email is sponsored by the Moblin Your Move Developer's >> challenge >> Build the coolest Linux based applications with Moblin SDK & win great >> prizes >> Grand prize is a trip for two to an Open Source event anywhere in the >> world >> http://moblin-contest.org/redirect.php?banner_id=100&url=/ >> ___ >> Jmol-users mailing list >> Jmol-users@lists.sourceforge.net >> https://lists.sourceforge.net/lists/listinfo/jmol-users >> > > > > -- > Robert M. Hanson > Professor of Chemistry > St. Olaf College > 1520 St. Olaf Ave. > Northfield, MN 55057 > http://www.stolaf.edu/people/hansonr > phone: 507-786-3107 > > > If nature does not answer first what we want, > it is better to take what answer we get. > > -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900 > -- Robert M. Hanson Professor of Chemistry St. Olaf College 1520 St. Olaf Ave. Northfield, MN 55057 http://www.stolaf.edu/people/hansonr phone: 507-786-3107 If nature does not answer first what we want, it is better to take what answer we get. -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900 - This SF.Net email is sponsored by the Moblin Your Move Developer's challenge Build the coolest Linux based applications with Moblin SDK & win great prizes Grand prize is a trip for two to an Open Source even
Re: [Jmol-users] Translucent cylinder disappears when viewed edge on
Just confirming that the fix works for me. Thanks Bob.
Dean
On Sun, Oct 5, 2008 at 8:20 PM, Robert Hanson <[EMAIL PROTECTED]> wrote:
> this is fixed for Jmol 11.6
>
> On Sat, Oct 4, 2008 at 12:20 AM, Dean Johnston <[EMAIL PROTECTED]>wrote:
>
>> Here's an odd one. My (very short) translucent cylinders disappear when
>> viewed within a few degrees of edge-on. To be more exact, the center
>> disappears while the edge remains visible. These are the same type of
>> cylinders that are generated by the draw pointgroup command. I've only
>> started to notice this with the most recent version (11.6.RC19).
>>
>> Here's the command.
>>
>> draw plane1_disk width 6.2001 cylinder {-0.0300 0. 0.} {0.0300
>> 0. 0.} color translucent orange fixed;
>>
>> Dean
>>
>> P.S. If it's any help, the angle at which it disappears gets smaller if
>> you turn on antialiasDisplay.
>>
>>
>>
>> -
>> This SF.Net email is sponsored by the Moblin Your Move Developer's
>> challenge
>> Build the coolest Linux based applications with Moblin SDK & win great
>> prizes
>> Grand prize is a trip for two to an Open Source event anywhere in the
>> world
>> http://moblin-contest.org/redirect.php?banner_id=100&url=/
>> ___
>> Jmol-users mailing list
>> Jmol-users@lists.sourceforge.net
>> https://lists.sourceforge.net/lists/listinfo/jmol-users
>>
>>
>
>
> --
> Robert M. Hanson
> Professor of Chemistry
> St. Olaf College
> 1520 St. Olaf Ave.
> Northfield, MN 55057
> http://www.stolaf.edu/people/hansonr
> phone: 507-786-3107
>
>
> If nature does not answer first what we want,
> it is better to take what answer we get.
>
> -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900
>
> -
> This SF.Net email is sponsored by the Moblin Your Move Developer's
> challenge
> Build the coolest Linux based applications with Moblin SDK & win great
> prizes
> Grand prize is a trip for two to an Open Source event anywhere in the world
> http://moblin-contest.org/redirect.php?banner_id=100&url=/
> ___
> Jmol-users mailing list
> Jmol-users@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/jmol-users
>
>
-
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Build the coolest Linux based applications with Moblin SDK & win great prizes
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