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== New ==
 
== New ==
 +
* Due to wiki code (or my inability) I couldn't get images to float left/right in the table w/o it looking really ugly.  So, if someone can get say the Colorama example to float right and look good, please do.
  
−
=== Some Thoughts For Discussion ===
+
* Let me know if you like the updates to the main page.  I like it because it utilizes more of the screen real estate.  Thus, no scrolling (for me).  If you can clean it up, and make it prettier, feel free. [[User:Inchoate|Tree]] 17:08, 9 December 2007 (CST)
  
−
* Would it be helpful to get rid of display of the somewhat awkward "Cmd" prefix for commands, and simply do a better job of separating the sections that cover concepts and ideas from those that discuss specific commands? 
+
*So, I found out, finally, why it's been hard to find things.  Category pages aren't scanned for keywords for searching.  So, we'll need to move our category pages' text to new pages and make the links.  For example, searching for "mencoder" didn't work before today.  Since I moved <nowiki>[[:Category:Software_Movies]]</nowiki> to '''Making_Movies''' we can now search for the keywords in that page.
  
−
* Empty links discourage.  Could we eliminate them sooner rather than later?  Yes, they are helpful initially for maintaining some structure, but people do get bummed out when they follow a link for an interesting topic and end up with nothing. If there are too many of these, then they may quit and go home before finding the real content -- and that would be a shame since there is now plenty of real content.
+
*Well, one idiot/spammer made it through the new system. If there's an influx of the idiots, we may go back to the old registration method, as that seemed pretty secure.
  
−
* For those coming into the Wiki for the first time, we should insure that the most useful content is out front and on top. Right now the TOC has an awful lot of blank links, so having it on top isn't so helpful as a starting point for nagivation. In contrast, the Categories, Script Library, and PyMOL Commands sections all seem like pretty good starting points.
+
* Feature Request: Support for 3D DLP and plasma HDTVs. These require a different stereo output format (checkerboard.) Feel free to contact me for details. --[[User:Martyholloway|Martyholloway]] 17:46, 30 May 2008 (CDT)
  
−
* For people (like me) who don't know the first thing about Wiki's, more "newbies click here to learn" links would help ease the transition...
+
== Some Thoughts For Discussion ==
 +
* Folks, please check out the section [http://www.mediawiki.org/wiki/Help:Images#Gallery_of_images MediaWiki Image Galleries] for cleaning up the code for  inserting more than one image.  This fixes the problem of having to insert tons of blank lines to cleanly offset the following text. So, if you have some time, please head back to old pages and help clean this up.
  
−
* Categories & subcategories confuse me.  The resulting titles baffle.  For example, '''Category: Using Pymol Objects and Selections Working with Objects'''. Shouldn't there be another colon in there? '''Category: Using Pymol Objects and Selections: Working with Objects'''  Is this just a Wiki thing?
+
* We need to accurately document settings for PyMol.  This would greatly improve the value of the site.  We should also provide images and examples.
  
−
[[User:Warren|Warren]] (BTW: Please don't weight what I write too heavily here.  With respect to PyMolWiki, I am just another user -- and a clueless one at that).
+
* For people (like me) who don't know the first thing about Wiki's, more "newbies click here to learn" links would help ease the transition...
−
 
 
−
=== Hierarchy and Naming===
 
−
Ok, the hierarchy is good, however the naming convention is foolish. Since the only hierarchy is based on how categories link to each other let's make all salient points in the hierarchy below it's own category and make the less prominent its own page. Yes/No?
 
  
−
I'm new at this and just want the best layout.  I think I was wrong in my first design,  I think began to realize it when I was typing the same thing over and over: in CS whenver you're doing that, you're doing something wrong.  So, following others' suggestions, keep the page names short.  I'll try to clean up the CmdScrip and API stuff tonight.  I think the CmdScript stuff and API stuff should all be on page as Warren has them in the documentation.  Maybe we need a chatroom and a time to meet so we can hash this out w/folks.  Ideas, comments?
 
  
−
[[User:Tree|Tree]] 22:21, 20 Feb 2005 (CST)
+
==Where is the anti-spam mechanism/strategy?==
 +
Manual removing spam contents really sucks.
 +
----
 +
Edit by AdShea
 +
One good strategy is to search all namespaces for 'http' (without the quotes).  This will show links containing that string, which should catch any spam links.
  
−
=== Organizing PyMol Commands ===
+
== Needed Editing ==
  
−
==== New Simpler Rules ====
+
Needed edits are the following:
−
Our naming idea was stupid, too.  All commands are easily found under [[:Category:Commands|PyMol Commands]].  We have something like 60 commands or so already documented!  All we require is that if you make a PyMol command page that you
 
−
* try to keep it simple like the ones we have up so far
 
−
* link it to the main PyMol Commands category by adding the text
 
−
<pre>[[Category:Commands|command_name_here]]</pre> Obviously replacing command_name_here with your command name.
 
−
* Make the see also's links as well.  It's real simple.  Just wrap the command in
 
−
<pre>[[Cmd command_name]]</pre> and that's it.  So, "center" becomes, <pre>[[Cmd center]]</pre>.
 
  
−
==== Examples ====
+
# We need more thorough "See Also" sections on each page.  [[Mesh]] shows what each page should look like.  People need to be able to find their content easily.
−
See [[Cmd center|center]]
+
## After some playing with this, I think we should create categories for each SET of settings.  Like, "surface_settings" and then just put all the surface settings in there.  Then, we can simply link out to this page and it'll change dynamically with the settings.
 +
# We need to continue linking categories to their respective pages.
 +
# More images should be uploaded for the settings changes so people can ''see'' what the settings do as well as read how to control them.
  
−
[[User:Tree|Tree]] 15:02, 19 Feb 2005 (CST)
+
== Searching ==
  
−
== Old ==
+
The default method for searching, eg hitting ENTER, should be the "Search" command not the "Go" command.
−
=== User Comments ===
 
−
Should content from the User's and Reference manual be incorporated into this site? Then in the content pages, one could reference a section of Walter's manuals.
 
−
--[[User:Saper|Saper]] 22:54, 16 Feb 2005 (CST)
 
  
−
Saper, I had considered that. I was going to strip out all the commands from PyMol and make a "commands" page where people could flush in some content. Maybe we'd be better off starting with page-by-page inserting PyMol commands into the wiki. (?)
+
* The search function is abysmal. If I type in "shadow" I get nothing. If I go to google and type in "site:pymolwiki.org shadow" I get both of the pages for ray-trace shadows which is what I wanted ("Ray Shadow" and "Ray Shadows"). I assume that there are two entries because of the poor search function. Just do what Wikipedia does and offer a google search of the site if the search function comes up empty-handed (Wikipedia does search the text of it's articles correctly but the google offer includes all languages). [[User:MortenGroftehauge|MortenGroftehauge]] ([[User talk:MortenGroftehauge|talk]]) 14:53, 24 March 2016 (UTC)
−
<br>
 
−
[[User:Tree|Tree]] 00:12, 17 Feb 2005 (CST)
 
  
 +
== New Format ==
 +
Code for the new page
  
−
=== Nucleic Acids ===
 
−
From Luca Jovine:
 
−
I apologize for being late, but... how about a section about nucleic acids? As in any other related program, they always end up being the poor siblings of proteins (I can't believe PyMOL's  cartoon command still does not recognise the most common 5' and 3' nucleotides!), and I'm pretty sure people who work with them would benefit from such a section in the Wiki.
 
−
Thanks,
 
  
−
Where should we put the Nucleic Acids Stuff?
+
__NOTOC__
  
−
[[User:Tree|Tree]]
+
{| align="center" style="padding-bottom: 4em;"
 +
|+ style="font-size:210%; font-weight: bold; color:#032d45; text-align:center; padding: 5px; margin-bottom: 7px" | Welcome to the PyMOL Wiki!
 +
|- style="text-align:center; font-weight:bold; color: #6d6003; font-size: 140%; font-style: italic; font-family: serif;"
 +
| The community-run support site for the [http://pymol.org PyMOL] molecular viewer.
 +
|}
  
−
For NA's - at the moment, the most appropriate location seems to be "Modeling and Editing". But perhaps we should add a special section devoted to types of molecules? ie/small molecules (like fatty acids, ligands, etc), nucleic acids, proteins, nucleic-acid/protein complexes, large macromolecules (ie/ribosome). I'm sure people have tips on how best to represent and work with each. Scale always seems to be an important factor when thinking of display details.
+
{| align="center" width="45%" style="background: #EDEBD5; margin-bottom: 4em; border-bottom: 1px solid #AFB29E; border-left: 1px solid #AFB29E; border-right: 1px solid #AFB29E;"
−
--TheDude
+
|+ style="font-size: 1.4em; font-weight: bold; color: #032d45; text-align:center; background: #5F7F96; padding-top:0.5em; padding-bottom: 0.25em; border-top: 2px solid #AFB29E; border-bottom: 1px solid #fff;" |Quick Links
 +
|-
 +
| style="font-size: 1.1em; color #61021F; padding: 0.5em 1em 0.5em 3em;"|'''[[:Category:Tutorials|Tutorials]]''' || '''[[TOPTOC|Table of Contents]]''' || '''[[:Category:Commands|Commands]]'''
 +
|-
 +
| style="font-size: 1.1em; color #61021F; padding: 0.5em 1em 0.5em 3em;"|'''[[:Category:Script_Library|Script Library]]''' || '''[[:Category:Plugins|Plugins]]''' || '''[[:Category:FAQ|FAQ]]'''
 +
|-
 +
| style="font-size: 1.1em; color #61021F; padding: 0.5em 1em 0.5em 3em;"|'''[[Gallery]]''' | '''[[Covers]]'''
 +
||'''[[CheatSheet|PyMOL Cheat Sheet]]''' (''[[Media:PymolRef.pdf|PDF]]'')
 +
||'''[[GoogleSearch]]'''
 +
|}
  
−
=== Expanded Schema ===
 
−
Proposal to incorporate more than just a manual into this site:
 
  
−
# Manual
+
{| width="100%"
−
## GUI
+
| style="vertical-align: top; width: 45%" |
−
## Command Script
+
{| class="jtable" style="float: left; width: 90%;"
−
## Python API
+
|+ style="font-size: 1.4em; font-weight: bold; text-align:left; border-bottom: 2px solid #6678b1;" | News &amp; Updates
−
## Settings
+
|-
−
## Miscellaneous
+
! Warren
−
## Command Line
+
| News about Warren DeLano's passing may be read on [[Warren|Warren's memorial page]].
−
# Meta Manual
+
|-
−
## Selections
+
! PyMOLWiki
−
## Colors
+
| Reformatted Main Page.
−
## Palettes
+
|-
−
## Writing/Running Scripts
+
! PyMOLWiki
−
## Customizing PyMOL
+
| New &mdash; Search the PyMOLWiki via [[GoogleSearch]]
−
# Discussions
+
|-
−
## News
+
! PyMOL
−
## Development
+
| PyMOL is known to work under Mac OS X 10+ (Snow Leopard) using the new Fink and incentive builds.  See [[MAC_Install#PyMOL_Install_from_Source.2C_Using_Fink|Installing PyMOL under Fink]].
−
## Questions
+
|-
−
# Special Topics
+
! PyMOL
−
## Movies and Animation
+
| PyMOL now has a [[Set]] command for basic settings, and a [[Set_bond]] command for bond-only settings.
−
## biochemical calculations
+
|-
−
## NMR
+
! PyMOL
−
## Crystallography
+
| [[Space]]&mdash; new command to control PyMOL's usage of color spaces.
−
## DNA
+
|}
−
## Stereo 3D
+
|style="vertical-align: top; width: 45%"|
 +
{| class="jtable" style="float: right; width: 90%"
 +
|+ style="font-size: 1.4em; font-weight: bold; text-align:left; border-bottom: 2px solid #6678b1;" |Do you know this PyMOL command...
 +
|-
 +
|<div class="didyouknow" >
 +
<dpl>
 +
namespace=
 +
category=Commands
 +
includepage=*
 +
includemaxlength=300
 +
escapelinks=false
 +
resultsheader=__NOTOC__ __NOEDITSECTION__
 +
randomcount=1
 +
mode=userformat
 +
addpagecounter=true
 +
listseparators=,<h3>[[%PAGE%]]</h3>,,\n
 +
</dpl>
 +
</div>
 +
<div style="clear: both;"></div>
 +
|}
 +
|}

Latest revision as of 00:36, 4 April 2016

New

  • Due to wiki code (or my inability) I couldn't get images to float left/right in the table w/o it looking really ugly. So, if someone can get say the Colorama example to float right and look good, please do.
  • Let me know if you like the updates to the main page. I like it because it utilizes more of the screen real estate. Thus, no scrolling (for me). If you can clean it up, and make it prettier, feel free. Tree 17:08, 9 December 2007 (CST)
  • So, I found out, finally, why it's been hard to find things. Category pages aren't scanned for keywords for searching. So, we'll need to move our category pages' text to new pages and make the links. For example, searching for "mencoder" didn't work before today. Since I moved [[:Category:Software_Movies]] to Making_Movies we can now search for the keywords in that page.
  • Well, one idiot/spammer made it through the new system. If there's an influx of the idiots, we may go back to the old registration method, as that seemed pretty secure.
  • Feature Request: Support for 3D DLP and plasma HDTVs. These require a different stereo output format (checkerboard.) Feel free to contact me for details. --Martyholloway 17:46, 30 May 2008 (CDT)

Some Thoughts For Discussion

  • Folks, please check out the section MediaWiki Image Galleries for cleaning up the code for inserting more than one image. This fixes the problem of having to insert tons of blank lines to cleanly offset the following text. So, if you have some time, please head back to old pages and help clean this up.
  • We need to accurately document settings for PyMol. This would greatly improve the value of the site. We should also provide images and examples.
  • For people (like me) who don't know the first thing about Wiki's, more "newbies click here to learn" links would help ease the transition...


Where is the anti-spam mechanism/strategy?

Manual removing spam contents really sucks.

Edit by AdShea One good strategy is to search all namespaces for 'http' (without the quotes). This will show links containing that string, which should catch any spam links.

Needed Editing

Needed edits are the following:

  1. We need more thorough "See Also" sections on each page. Mesh shows what each page should look like. People need to be able to find their content easily.
    1. After some playing with this, I think we should create categories for each SET of settings. Like, "surface_settings" and then just put all the surface settings in there. Then, we can simply link out to this page and it'll change dynamically with the settings.
  2. We need to continue linking categories to their respective pages.
  3. More images should be uploaded for the settings changes so people can see what the settings do as well as read how to control them.

Searching

The default method for searching, eg hitting ENTER, should be the "Search" command not the "Go" command.

  • The search function is abysmal. If I type in "shadow" I get nothing. If I go to google and type in "site:pymolwiki.org shadow" I get both of the pages for ray-trace shadows which is what I wanted ("Ray Shadow" and "Ray Shadows"). I assume that there are two entries because of the poor search function. Just do what Wikipedia does and offer a google search of the site if the search function comes up empty-handed (Wikipedia does search the text of it's articles correctly but the google offer includes all languages). MortenGroftehauge (talk) 14:53, 24 March 2016 (UTC)

New Format

Code for the new page



Welcome to the PyMOL Wiki!
The community-run support site for the PyMOL molecular viewer.
Quick Links
Tutorials Table of Contents Commands
Script Library Plugins FAQ
Gallery | Covers PyMOL Cheat Sheet (PDF) GoogleSearch


News & Updates
Warren News about Warren DeLano's passing may be read on Warren's memorial page.
PyMOLWiki Reformatted Main Page.
PyMOLWiki New — Search the PyMOLWiki via GoogleSearch
PyMOL PyMOL is known to work under Mac OS X 10+ (Snow Leopard) using the new Fink and incentive builds. See Installing PyMOL under Fink.
PyMOL PyMOL now has a Set command for basic settings, and a Set_bond command for bond-only settings.
PyMOL Space— new command to control PyMOL's usage of color spaces.
Do you know this PyMOL command...

The DPL extension (version 2.3.0) produced a SQL statement which lead to a Database error.
The reason may be an internal error of DPL or an error which you made,
especially when using DPL options like titleregexp.
Query text is:
SELECT DISTINCT `page`.page_namespace AS page_namespace,`page`.page_title AS page_title,`page`.page_id AS page_id, `page`.page_title AS sortkey, `page`.page_counter AS page_counter FROM `page` INNER JOIN `categorylinks` AS cl0 ON `page`.page_id=cl0.cl_from AND (cl0.cl_to='Commands') WHERE 1=1 AND `page`.page_namespace IN (0) AND `page`.page_is_redirect=0 ORDER BY page_title ASC LIMIT 500 OFFSET 0

Error message is:
Unknown column 'page.page_counter' in 'field list' (data01-pymol.chw7f2hgrkps.us-west-2.rds.amazonaws.com)


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