[Jmol-users] chains

2007-03-26 Thread stefanie neumann
hi, is their a possibillity to get the number and names of the chains of the 
protein besides the possibilty to parse it out of the pdb-file?? 
thanks, steffi
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Re: [Jmol-users] Jmol MediaWiki extension, works in preview but not on live page

2007-03-26 Thread joseph . r . moran
Hi folks.  It works now!  Details follow.

My group's wiki is behind a corporate proxy so it's unreachable from your 
ends.  Thanks Nico for providing the new JmolExtension.php on 
wiki.jmol.org and for your LocalSettings.php excerpts.  No significant 
differences between our LocalSettings.php files.  Regarding the 
JmolExtension.php diffs, they were as follows:

-bash-3.00$ diff JmolExtension.php.old JmolExtension.php
611a612
 $wgParser-disableCache();
637a639
 $wgParser-disableCache();

...one disableCache() call in wfJmolRender() as discussed on Friday, and 
another in wfJmolDevRender() which is new but may or may not be relevant 
for nondevelopment use.  That said, I did have to save the wiki page one 
more time after updating JmolExtension.php before it would work, perhaps 
to remove some cache data within the wiki that disableCache() couldn't 
reach.  I'm really not sure, and it's possible if I had done this on 
Friday it would have worked then.  At any rate, live/normal page views do 
work consistently now.

Thanks Nico and everyone for your help!

--JRM





Nicolas Vervelle [EMAIL PROTECTED] 
24-Mar-2007 06:22
 
To
jmol-users@lists.sourceforge.net
cc
[EMAIL PROTECTED]
Subject
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   

Re: [Jmol-users] two more minor issues

2007-03-26 Thread Volker Blum

Thanks for the update and changing the label colors - great!

About povray - it does work fine most of the time, just in some cases  
I do not understand how the boundaries are chosen, at all. I may look  
into it but it may take a while ...


One more minor issue:

I noticed that, on an Intel Mac (current software, particularly java  
version), jmol 11.1.27 happily crashes as soon as the isosurface  
command is launched (with filename and cutoff 0.05 specified)


exact same structure  isosurface (.cube format) worked fine under  
SUSE Linux 10.2 and 11.1.25 .


best
vb

On Mar 24, 2007, at 11:01 PM, Bob Hanson wrote:


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

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