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== New ==
 
== New ==
−
=== Hierarchy and Naming===
+
* 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.
−
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?
+
* 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)
  
−
[[User:Tree|Tree]] 22:21, 20 Feb 2005 (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 <nowiki>[[:Category:Software_Movies]]</nowiki> 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.
  
−
== Old ==
+
* 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)
−
== 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. (?)
+
== Some Thoughts For Discussion ==
−
<br>
+
* 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.
−
[[User:Tree|Tree]] 00:12, 17 Feb 2005 (CST)
 
  
 +
* We need to accurately document settings for PyMol.  This would greatly improve the value of the site.  We should also provide images and examples.
  
−
=== Nucleic Acids ===
+
* 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...
−
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?
 
  
−
[[User:Tree|Tree]]
+
==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.
  
−
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.
+
== Needed Editing ==
−
--TheDude
 
  
−
== Organizing PyMol Commands ==
+
Needed edits are the following:
  
−
=== Possibly Deprecated: Need Feedback ===
+
# 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.
−
NEW: Tell me what you guys want!
+
## 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.
  
−
Due to the inherent ambiguity of wiki naming, we have come up with a way to categorize the naming/sorting of PyMol commands.
+
== Searching ==
  
−
Since PyMol has two types of commands: command script as Warren calls it; and, the API we will separate the two by the following convention.
+
The default method for searching, eg hitting ENTER, should be the "Search" command not the "Go" command.
  
−
Command Script commands page names will be "CmdScript COMMANDNAME" and will be in the category called, "CmdScript".  The API naming will be similar, but we don't have to worry about namespace collisions b/c that's already been taken care of by Warren in that he has differen library names, viz "cmd" and "util" and whatnot. So an API command will be "LIBRARYNAME.COMMANDNAME" and will be in the category "API COMMANDS".
+
* 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)
  
−
Lastly, make sure you add the category text at the bottom of each page as needed.  If you're adding to the CmdScript then put this at the bottom
+
== New Format ==
−
<pre>
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Code for the new page
−
[[Category:CmdScript COMMANDNAME|COMMANDNAME]]
 
−
</pre>
 
−
If for some library put
 
−
<pre>
 
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[[Category:API|API]]
 
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[[Category:LIBRARYNAME|FUNCTIONAME]]
 
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</pre>
 
  
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This will allow us to keep track of all CmdScripts in one category, and also allow us to keep categories of individual Libraries and ALL API commands as well.  Very cool.
 
  
−
=== Examples ===
+
__NOTOC__
−
See [[CmdScript.center]]
 
  
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See [[Cmd.center]]
+
{| 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.
 +
|}
  
−
[[User:Tree|Tree]] 15:02, 19 Feb 2005 (CST)
+
{| 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;"
 +
|+ 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]]'''
 +
|}
  
  
−
For CmdScript, would it make more sense to mirror the API style and do
+
{| width="100%"
−
<pre> [[Category:CmdScript|Cmdscript]]
+
| style="vertical-align: top; width: 45%" |
−
[[Category:COMMANDNAME|COMMANDNAME]]</pre>
+
{| class="jtable" style="float: left; width: 90%;"
−
--[[User:Jcorn|Jcorn]] 18:20, 19 Feb 2005 (CST)
+
|+ style="font-size: 1.4em; font-weight: bold; text-align:left; border-bottom: 2px solid #6678b1;" | News &amp; Updates
−
 
+
|-
−
Yes, the CmdScript commands should all link back (be categorized in the CmdScript category.
+
! Warren
−
 
+
| News about Warren DeLano's passing may be read on [[Warren|Warren's memorial page]].
−
[[User:Tree|Tree]] 22:21, 20 Feb 2005 (CST)
+
|-
−
 
+
! PyMOLWiki
−
==Quote==
+
| Reformatted Main Page.
−
However, a good Wiki needs to be structured beforehand, rather than having
+
|-
−
everything grow by itself. Users will add things where aproppriate, anyway.
+
! PyMOLWiki
−
Thus, in a heavily used Wiki its definitely easy to get lost.
+
| New &mdash; Search the PyMOLWiki via [[GoogleSearch]]
−
 
+
|-
−
== Expanded Schema ==
+
! PyMOL
−
Proposal to incorporate more than just a manual into this site:
+
| 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]].
−
 
+
|-
−
# Manual
+
! PyMOL
−
## GUI
+
| PyMOL now has a [[Set]] command for basic settings, and a [[Set_bond]] command for bond-only settings.
−
## Command Script
+
|-
−
## Python API
+
! PyMOL
−
## Settings
+
| [[Space]]&mdash; new command to control PyMOL's usage of color spaces.
−
## Miscellaneous
+
|}
−
## Command Line
+
|style="vertical-align: top; width: 45%"|
−
# Meta Manual
+
{| class="jtable" style="float: right; width: 90%"
−
## Selections
+
|+ style="font-size: 1.4em; font-weight: bold; text-align:left; border-bottom: 2px solid #6678b1;" |Do you know this PyMOL command...
−
## Colors
+
|-
−
## Palettes
+
|<div class="didyouknow" >
−
## Writing/Running Scripts
+
<dpl>
−
## Customizing PyMOL
+
namespace=
−
# Discussions
+
category=Commands
−
## News
+
includepage=*
−
## Development
+
includemaxlength=300
−
## Questions
+
escapelinks=false
−
# Special Topics
+
resultsheader=__NOTOC__ __NOEDITSECTION__
−
## Movies and Animation
+
randomcount=1
−
## biochemical calculations
+
mode=userformat
−
## NMR
+
addpagecounter=true
−
## Crystallography
+
listseparators=,<h3>[[%PAGE%]]</h3>,,\n
−
## DNA
+
</dpl>
−
## Stereo 3D
+
</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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