Re: [Jmol-users] Jmol MediaWiki extension, works in preview but not on live page
Hi Joseph,
Can you give an URL to your wiki so that I can check myself ?
I have uploaded the latest version of JmolExtension.php on the Jmol
Wiki:
http://wiki.jmol.org:81/index.php/MediaWiki/JmolExtension.php
At the end of the mail, I have put a stripped version of my
LocalSettings.php file.
You can compare it with your own (for example, do you use MemCached ?)
If I have new ideas before monday, I will try to implement them.
Have a nice weekend
Nico
[EMAIL PROTECTED] wrote:
Regarding updating the argument list for
onBeforePageDisplay() to be just $out -- PHP was satisfied but
otherwise
no change.
Regarding your tests -- sorry I didn't
include
mention of purge tests from my end. But yes, our results matched:
edit/preview ok, normal/live nok, purge ok.
Now regarding your latest suggestion
regarding
disableCache() in wfJmolRender(), it's no dice on my end. I tried
it together with our earlier edits up to and including above, and then
I tried inserting the $wgParser-disableCache(); statement into a
stock
JmolExtension.php -- the results were the same (live nok).
That includes Firefox 2.0.0.3 and IE7
with
empty local caches, and after using the purge mode to clear MediaWiki's
cache. Touching or otherwise updating MediaWiki's LocalSettings.php
also forces MediaWiki to clear its cache, and I did so -- still nok on
the live page. I was beginning to think this was a cache issue within
MediaWiki and we could work around it with suitable tweaks to
LocalSettings.php,
now I don't know.
All the test pages on wiki.jmol.org do
work
for me -- I think before today only the uploaded XYZ example worked
properly,
now all three upload examples work, as does the "Inlined CML File"
example.
FYI, I'm heading home for the day and
won't
be able to revisit this until Monday. Thanks for your attention and
suggestions today,
--JRM
LocalSettings.php:
?php
# This file was automatically generated by the MediaWiki installer.
# If you make manual changes, please keep track in case you need to
# recreate them later.
#
# See includes/DefaultSettings.php for all configurable settings
# and their default values, but don't forget to make changes in _this_
# file, not there.
# If you customize your file layout, set $IP to the directory that
contains
# the other MediaWiki files. It will be used as a base to locate files.
if( defined( 'MW_INSTALL_PATH' ) ) {
$IP = MW_INSTALL_PATH;
} else {
$IP = dirname( __FILE__ );
}
$path = array( $IP, "$IP/includes", "$IP/languages" );
set_include_path( implode( PATH_SEPARATOR, $path ) . PATH_SEPARATOR .
get_include_path() );
require_once( "includes/DefaultSettings.php" );
# If PHP's memory limit is very low, some operations may fail.
# ini_set( 'memory_limit', '20M' );
if ( $wgCommandLineMode ) {
if ( isset( $_SERVER ) array_key_exists(
'REQUEST_METHOD', $_SERVER ) ) {
die( "This script must be run from the command line\n" );
}
} elseif ( empty( $wgNoOutputBuffer ) ) {
## Compress output if the browser supports it
if( !ini_get( 'zlib.output_compression' ) ) @ob_start(
'ob_gzhandler' );
}
$wgSitename = "Jmol";
$wgScriptPath = "";
$wgScript = "$wgScriptPath/index.php";
$wgRedirectScript = "$wgScriptPath/redirect.php";
## For more information on customizing the URLs please see:
## http://meta.wikimedia.org/wiki/Eliminating_index.php_from_the_url
## If using PHP as a CGI module, the ?title= style usually must be used.
$wgArticlePath = "$wgScript/$1";
# $wgArticlePath = "$wgScript?title=$1";
$wgStylePath = "$wgScriptPath/skins";
$wgStyleDirectory = "$IP/skins";
#$wgLogo = "$wgStylePath/common/images/wiki.png";
$wgLogo = "$wgScriptPath/Jmol_smallLogo.gif";
$wgUploadPath = "$wgScriptPath/images";
$wgUploadDirectory = "$IP/images";
$wgEnableEmail = true;
$wgEnableUserEmail = true;
## For a detailed description of the following switches see
## http://meta.wikimedia.org/Enotif and
http://meta.wikimedia.org/Eauthent
## There are many more options for fine tuning available see
## /includes/DefaultSettings.php
## UPO means: this is also a user preference option
$wgEnotifUserTalk = true; # UPO
$wgEnotifWatchlist = true; # UPO
$wgEmailAuthentication = true;
# Experimental charset support for MySQL 4.1/5.0.
$wgDBmysql5 = false;
## Shared memory settings
$wgMainCacheType = CACHE_NONE;
$wgMemCachedServers = array();
## To enable image uploads, make sure the 'images' directory
## is writable, then set this to true:
$wgEnableUploads = true;
$wgUseImageResize = true;
# $wgUseImageMagick = true;
# $wgImageMagickConvertCommand = "/usr/bin/convert";
## If you want to use image uploads under safe mode,
## create the directories images/archive, images/thumb and
## images/temp, and make them all writable. Then uncomment
## this, if it's not already uncommented:
$wgHashedUploadDirectory = false;
## If you have the appropriate support software installed
## you can enable inline LaTeX equations:
$wgUseTeX = false;
$wgMathPath =
Re: [Jmol-users] two more minor issues
Volker, nobody has worked on the Povray output for a long time. Not much is supported there. My guess is that the povray code has serious deficiencies at this point. Bob On 3/23/07, Volker Blum [EMAIL PROTECTED] wrote: Using jmol 11.1.25: * When rendering long thin structures in povray, jmol builds a gigantic empty boundary around the structure. This is not the case for direct jpg export. Somehow the boundary defaults for povray do not match the jmol window at all. I can provide an example if necessary. * With white background, displayed labels (e.g. atom numbers) for hydrogen are also white and hence unreadable by default. [I am sure this happens for other elements with other backgrounds]. Perhaps the default could be changed based on the current background color? best, VB - 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 - 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] save state
Frieda, can you verify that these are or are not fixed in 11.1.27, please. On 3/21/07, Frieda Reichsman [EMAIL PROTECTED] wrote: On Mar 21, 2007, at 2:21 PM, [EMAIL PROTECTED] wrote: 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! A couple of things that were not reproduced exactly with write state in Jmol 11.1.18: - background applet color was black instead of white. - incomplete rendering of hydrogen bonds created/modified with the connect command - backbone trace applied through most of the model was extended into an area where it had not been present, when the state script was called after a script that had the entire backbone in trace (i.e., it did not turn the trace off in that area. I don't know whether a state script is intended to work from a blank slate or whether it should be able to follow any other script.) - problem with isosurface, I think it did not appear. I know I wound up putting it in by hand. 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 - 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] save state
I will check this out. On 3/21/07, Volker Blum [EMAIL PROTECTED] wrote: On write state in jmol 11.1.25: using write state file.spt the quit application, reload structure, and script file.spt restored everything (including background color) but did not reproduce H bonds as H bonds, replacing them with regular bonds instead (see below). thanks! VB On Wednesday 21 March 2007 19:47, Frieda Reichsman wrote: On Mar 21, 2007, at 2:21 PM, [EMAIL PROTECTED] wrote: 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! A couple of things that were not reproduced exactly with write state in Jmol 11.1.18: - background applet color was black instead of white. - incomplete rendering of hydrogen bonds created/modified with the connect command - backbone trace applied through most of the model was extended into an area where it had not been present, when the state script was called after a script that had the entire backbone in trace (i.e., it did not turn the trace off in that area. I don't know whether a state script is intended to work from a blank slate or whether it should be able to follow any other script.) - problem with isosurface, I think it did not appear. I know I wound up putting it in by hand. Frieda /// Frieda Reichsman, PhD Molecules in Motion Interactive Molecular Structures http://www.moleculesinmotion.com /// -- Dr. Volker Blum Theory Department Fritz Haber Institute of the Max Planck Society Faradayweg 4-6 D-14195 Berlin Germany Phone: +49 30 8413-4846 Fax: +49 30 8413 4700 email [EMAIL PROTECTED] A physicist is the atoms' way of thinking about atoms. - 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 - 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] Jmol 11.1.25 and beyond
will be fixed in 11.1.28, thanks. On 3/21/07, William Reusch [EMAIL PROTECTED] wrote: Bob, You have done a fantastic job expanding Jmol capability. I have downloaded version 11.1.25 and am having great fun exploring with it. I have encountered a small problem with the dots command. All the parameters described on your site seem to be working, except the dots nn%, which I understand should display a percentage of the vanderwaals volume. Only the 100% vanderwaals display, equivalent to dots on, is shown, regardless of the value chosen. Congratulations on your fine work! Bill Bob Hanson wrote: I have finally brought http://www.stolaf.edu/academics/chemapps/jmol/docs/examples-11/new.htm up to date. I have also updated the JVXL file format information at: http://www.stolaf.edu/academics/chemapps/jmol/docs/misc/JVXL-format.pdf to reflect some of the newer capabilities of isosurfaces in Jmol. Bob - 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 - 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] Jmol 11.1.25 and beyond
fixed. On 3/21/07, C Anthony Lewis [EMAIL PROTECTED] wrote: Bob, I was looking through the examples and for number 37 I got the following on trying to load the file: script ERROR: java.io.FileNotFoundException: http://www.stolaf.edu/academics/chemapps/jmol/docs/examples-11/data/2by9 .pdb load 2by9.pdb Many thanks for your continued development, Jmol is great! Anthony -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Bob Hanson Sent: 21 March 2007 07:56 To: jmol-users@lists.sourceforge.net Subject: [Jmol-users] Jmol 11.1.25 and beyond I have finally brought http://www.stolaf.edu/academics/chemapps/jmol/docs/examples-11/new.htm up to date. I have also updated the JVXL file format information at: http://www.stolaf.edu/academics/chemapps/jmol/docs/misc/JVXL-format.pdf to reflect some of the newer capabilities of isosurfaces in Jmol. Bob - 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=DEVDE V ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users - 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 - 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
