Re: [Jmol-users] jmol demo on sourceforge
On Wed, Oct 1, 2008 at 10:08 PM, Robert Hanson <[EMAIL PROTECTED]> wrote:
> So what's this port 81 thing? leaving that off changes it to the standard
> http port 80; I don't know of any system that allows you to use port 81 if
> port 80 is the right port.
>
The problem is with the hosting company on which the wiki is setup.
To be able to provide both PHP4 and PHP5 on shared computers, they have
decided that PHP4 will be available on port 80 (standard HTTP port) and PHP5
on port 81.
Since MediaWiki requires PHP5, all access are done through port 81 on the
wiki.
I have added a .htaccess file (contents below) to automatically redirect
request on port 80 to port 81, so that people accessing the wiki without
specifying the port will still have access to the wiki.
If anyone knows how to do this is an more cleaner way, please help :)
RewriteEngine on
RewriteCond %{SERVER_PORT} ^80$
RewriteRule ^(.*)$ http://%{HTTP_HOST}:81%{REQUEST_URI} [QSA,P]
Nico
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[Jmol-users] Jmol 11.6 release -- delayed
A few additional bugs were found just today; Nico has released 11.6.RC18 -- those who found these bugs please check that they are fixed there, and we will give it a few more days and release 11.6 this weekend. Thanks, 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] jmol demo on sourceforge
So what's this port 81 thing? leaving that off changes it to the standard http port 80; I don't know of any system that allows you to use port 81 if port 80 is the right port. On Wed, Oct 1, 2008 at 1:17 PM, Jennifer L. Muzyka < [EMAIL PROTECTED]> wrote: > Tom- > THANKS for the suggestion about stripping out the port number on the wiki > URL. I did that and the page loaded in a jiffy! > -Jennifer > > > > Message: 5 > Date: Wed, 1 Oct 2008 10:58:10 -0700 > From: "Thomas Stout" <[EMAIL PROTECTED]> > Subject: Re: [Jmol-users] jmol demo on sourceforge > To: jmol-users@lists.sourceforge.net > Message-ID: > <[EMAIL PROTECTED]> > Content-Type: text/plain; charset="iso-8859-1" > > One thought about the wiki not loading: I have the same problem for any > link to the wiki that uses the "port number". > > For example: > http://wiki.jmol.org:81/index.php/Solving_Java_Problems#Java_cache > will never load for me due to the ":81" and our local firewall denying > access. If I cut-and-paste the link into my browser's address box and then > strip the port number out (so that it looks like: > http://wiki.jmol.org/index.php/Solving_Java_Problems#Java_cache ), then > the > wiki pages load just fine... > > I'm not certain that is your problem as well, but it sounds very similar to > my experience... > -Tom > > > > - > 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 demo on sourceforge
Tom- THANKS for the suggestion about stripping out the port number on the wiki URL. I did that and the page loaded in a jiffy! -Jennifer Message: 5 Date: Wed, 1 Oct 2008 10:58:10 -0700 From: "Thomas Stout" <[EMAIL PROTECTED]> Subject: Re: [Jmol-users] jmol demo on sourceforge To: jmol-users@lists.sourceforge.net Message-ID: <[EMAIL PROTECTED]> Content-Type: text/plain; charset="iso-8859-1" One thought about the wiki not loading: I have the same problem for any link to the wiki that uses the "port number". For example: http://wiki.jmol.org:81/index.php/Solving_Java_Problems#Java_cache will never load for me due to the ":81" and our local firewall denying access. If I cut-and-paste the link into my browser's address box and then strip the port number out (so that it looks like: http://wiki.jmol.org/index.php/Solving_Java_Problems#Java_cache ), then the wiki pages load just fine... I'm not certain that is your problem as well, but it sounds very similar to my experience... -Tom - 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] final testing appreciated
same problem
On Wed, Oct 1, 2008 at 8:47 AM, Rolf Huehne <[EMAIL PROTECTED]> wrote:
> Robert Hanson wrote:
> > Final testing appreciated for Jmol 11.6. Anything you can do to try to
> break
> > it would be great.
> >
>
> The following commands that used to work at least until 11.5.35 give an
> error message in 11.6.RC17:
>
> bound_box = getProperty("boundboxInfo", "vector");
> vector_x = bound_box.x;
>
> script ERROR: unexpected end of script command
> line 1 command 1 of file null:
> vector_x = bound_box . >> x <<
>
> 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
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> ___
> 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] final testing appreciated
yeah, I know what that is thanks.
On Wed, Oct 1, 2008 at 8:47 AM, Rolf Huehne <[EMAIL PROTECTED]> wrote:
> Robert Hanson wrote:
> > Final testing appreciated for Jmol 11.6. Anything you can do to try to
> break
> > it would be great.
> >
>
> The following commands that used to work at least until 11.5.35 give an
> error message in 11.6.RC17:
>
> bound_box = getProperty("boundboxInfo", "vector");
> vector_x = bound_box.x;
>
> script ERROR: unexpected end of script command
> line 1 command 1 of file null:
> vector_x = bound_box . >> x <<
>
> 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
-
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Re: [Jmol-users] jmol demo on sourceforge
One thought about the wiki not loading: I have the same problem for any link to the wiki that uses the "port number". For example: http://wiki.jmol.org:81/index.php/Solving_Java_Problems#Java_cache will never load for me due to the ":81" and our local firewall denying access. If I cut-and-paste the link into my browser's address box and then strip the port number out (so that it looks like: http://wiki.jmol.org/index.php/Solving_Java_Problems#Java_cache ), then the wiki pages load just fine... I'm not certain that is your problem as well, but it sounds very similar to my experience... -Tom On Wed, Oct 1, 2008 at 10:19 AM, Jennifer L. Muzyka < [EMAIL PROTECTED]> wrote: > Angel- > Thanks for the additional information about the protein cavities / > isosurfaces. > > I tried following your advice about clearing my Java cache in order to get > the Jmol applet on the front page to work, but my browser keeps getting a > Page Load Error for the jmol wiki. I was having the same problem last week > as well. Other websites work okay for me, so I can't figure out what the > problem might be. On the other hand, I went back to the demo and this time > it loaded just fine! (Last time it failed with both IE and Firefox..) > -Jennifer > > > > Message: 10 > Date: Wed, 01 Oct 2008 17:31:37 +0200 > From: "Angel Herraez" <[EMAIL PROTECTED]> > Subject: Re: [Jmol-users] jmol demo on sourceforge > To: jmol-users@lists.sourceforge.net > Message-ID: <[EMAIL PROTECTED]> > Content-Type: text/plain; charset=US-ASCII > > Hi Jennifer > > Thanks for reporting this. However, I am seeing no problem. > Please, > 1.- Clear your Java cache > (procedure described at > http://wiki.jmol.org:81/index.php/Solving_Java_Problems#Java_cache > > 2. Clear your browser cache. Quit your browser and reopen it > > 3. Try the page. If the problem still persists, please report > details: your browser, OS and Java versions, and any > messages in the Java console. > > I assume that you mean the Jmol applet in the front page, not in the > "demo" sections, right? > > > > > > - > 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 > - 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 demo on sourceforge
I think problems like this have to do with domain issues. We see this sometimes with different web domain providers, but we haven't seen it at sourceForge. On Wed, Oct 1, 2008 at 12:28 PM, Robert Hanson <[EMAIL PROTECTED]> wrote: > Hmm, I don't see that... could be a one-time event? > > > On Wed, Oct 1, 2008 at 9:56 AM, Jennifer L. Muzyka < > [EMAIL PROTECTED]> wrote: > >> I just tried the demo on the jmol.sourceforge.net page, and I get a an >> error instead of the demo. The error says: >> java:security.AccessControlException. >> -Jennifer >> >> >> >> >> Jennifer Muzyka >> Professor of Chemistry >> On sabbatical at University of Kentucky College of Pharmacy >> Centre College >> Danville, KY 40422 >> >> [EMAIL PROTECTED] >> http://web.centre.edu/muzyka >> >> - >> 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 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 demo on sourceforge
Hmm, I don't see that... could be a one-time event? On Wed, Oct 1, 2008 at 9:56 AM, Jennifer L. Muzyka < [EMAIL PROTECTED]> wrote: > I just tried the demo on the jmol.sourceforge.net page, and I get a an > error instead of the demo. The error says: > java:security.AccessControlException. > -Jennifer > > > > > Jennifer Muzyka > Professor of Chemistry > On sabbatical at University of Kentucky College of Pharmacy > Centre College > Danville, KY 40422 > > [EMAIL PROTECTED] > http://web.centre.edu/muzyka > > - > 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 demo on sourceforge
Angel- Thanks for the additional information about the protein cavities / isosurfaces. I tried following your advice about clearing my Java cache in order to get the Jmol applet on the front page to work, but my browser keeps getting a Page Load Error for the jmol wiki. I was having the same problem last week as well. Other websites work okay for me, so I can't figure out what the problem might be. On the other hand, I went back to the demo and this time it loaded just fine! (Last time it failed with both IE and Firefox..) -Jennifer Message: 10 Date: Wed, 01 Oct 2008 17:31:37 +0200 From: "Angel Herraez" <[EMAIL PROTECTED]> Subject: Re: [Jmol-users] jmol demo on sourceforge To: jmol-users@lists.sourceforge.net Message-ID: <[EMAIL PROTECTED]> Content-Type: text/plain; charset=US-ASCII Hi Jennifer Thanks for reporting this. However, I am seeing no problem. Please, 1.- Clear your Java cache (procedure described at http://wiki.jmol.org:81/index.php/Solving_Java_Problems#Java_cache 2. Clear your browser cache. Quit your browser and reopen it 3. Try the page. If the problem still persists, please report details: your browser, OS and Java versions, and any messages in the Java console. I assume that you mean the Jmol applet in the front page, not in the "demo" sections, right? - 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] final testing appreciated
Using 11.6.RC17 I get this error:
eval ERROR: el argumento no es válido
line 1 command 64 of file null:
{ selected } . >> y << = 0
The offending script is
select 2.0; spacefill off; wireframe 0.04; color [xFF00FF];
{selected}.y = 0;
It worked in 11.5.41 at least
(I seem to recall having problems with this before)
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Re: [Jmol-users] jmol demo on sourceforge
Hi Jennifer Thanks for reporting this. However, I am seeing no problem. Please, 1.- Clear your Java cache (procedure described at http://wiki.jmol.org:81/index.php/Solving_Java_Problems#Java_cache 2. Clear your browser cache. Quit your browser and reopen it 3. Try the page. If the problem still persists, please report details: your browser, OS and Java versions, and any messages in the Java console. I assume that you mean the Jmol applet in the front page, not in the "demo" sections, right? - 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 demo on sourceforge
I just tried the demo on the jmol.sourceforge.net page, and I get a an error instead of the demo. The error says: java:security.AccessControlException. -Jennifer Jennifer Muzyka Professor of Chemistry On sabbatical at University of Kentucky College of Pharmacy Centre College Danville, KY 40422 [EMAIL PROTECTED] http://web.centre.edu/muzyka - 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] final testing appreciated
Rolf Huehne wrote:
> Robert Hanson wrote:
>> Hmm. This could be a mix of signed applet versions. Try using
>>
>> jmolInitialize(".","JmolAppletSigned.jar")
>>
>> so that it is definitely picking up just the one JAR file.
>>
>> I'll try
>>
>> jmolInitialize(".","JmolAppletSigned0.jar")
>>
>> and see if I forgot to include something in one of the Jar files. Could be
>> -- those were reorganized recently.
>>
>
> I tried this already. All 4 possible applet names show the same error:
>
> JmolApplet.jar
> JmolApplet0.jar
> JmolAppletSigned.jar
> JmolAppletSigned0.jar
>
> You can try it yourself with the unsigned applet at this URL:
>
> http://www.imb-jena.de/cgi-bin/3d_mapping.pl?CODE=2arc&JMOLVERSION=11.6.RC16
>
> When I try this URL on WinXP (Java 1.6.0_07, Firefox 2.0.0.14, IE
> 7.0.5730.11) I get a "java.security.AccessControlException" instead of
> the error reported for Java 1.4 on Linux.
>
With Jmol 11.6.RC17 the reported specific error on Linux vanished but
now I get the "java.security.AccessControlException" on all systems.
It occurs when using the 'script' or 'load' command if a server absolute
path is provided, e.g.:
load /ImgLibPDB/tmp/pdb2arc.ent.gz
It doesn't occur if a complete URL is provided instead in the 'load'
command (which apparantly isn't possible with 'script'):
load http://www.imb-jena.de/ImgLibPDB/tmp/pdb2arc.ent.gz
With Jmol 11.6.RC13 and earlier the problem doesn't exist.
Regards,
Rolf
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Re: [Jmol-users] final testing appreciated
Robert Hanson wrote:
> Final testing appreciated for Jmol 11.6. Anything you can do to try to break
> it would be great.
>
The following commands that used to work at least until 11.5.35 give an
error message in 11.6.RC17:
bound_box = getProperty("boundboxInfo", "vector");
vector_x = bound_box.x;
script ERROR: unexpected end of script command
line 1 command 1 of file null:
vector_x = bound_box . >> x <<
Regards,
Rolf
-
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Re: [Jmol-users] volume of cavities inside proteins?
Bob- You're right that that I'm having a lot of fun learning about proteins and ligands and calculations involving their interactions on my sabbatical. I'm at the University of Kentucky College of Pharmacy working with Chang-Guo Zhan, a physical chemist. The group does structure based drug design. Thanks for the suggestions about navigating through the cavities as well as the description of how to make the pdb animations. The animations sound easier than I had hoped, and the navigation through the cavities sounds like an interesting travel experience that I can't wait to try. -Jennifer - 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
