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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? 
 
  
−
* 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.
+
*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.
  
−
* 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.
+
*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. --[[User:Martyholloway|Martyholloway]] 17:46, 30 May 2008 (CDT)
 +
 
 +
== 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.
 +
 
 +
* 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...
 
* 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...
  
−
* 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?
 
  
−
[[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).
+
==Where is the anti-spam mechanism/strategy?==
 +
Manual removing spam contents really sucks.
 
----
 
----
−
=====Begin Inchoate's Comments To Warren=====
+
Edit by AdShea
−
First off, thanks for the post.  I always welcome better ways to work and organize information.  I don't claim to know any more than anyone else, I just took the initiative for PyMolWiki.
+
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.
  
−
Warren, you're completely right.  Something needs to change, to make this more usable for people.  I tried to organize the PyMol information via the user manual and user comments.  Imposing a hierarchy on a system that doesn't really want one, isn't such a good idea, or my imposition was implemented incorrectly.  The link names need to be MUCH shorter: take a look at http://wikipedia.org.  They have 500,000+ pages and they have short link names. I tried to make a hierarchy so that if three such people come in and look up "rotate" that they go to the right page.  That is, there's "rotate," "cmd.rotate," and camera independent rotations and whatnot.  We have name ambiguitities.  Do we just make one big page with "rotate" and include all its information there, or do we make "rotate" a category and dole out the pages to the category?
+
== Needed Editing ==
  
−
I'm ambivalent towards empty links.  They remind me of what basic concepts that need filling, but are annoying if you're searching for info. and there's nothing there.
+
Needed edits are the following:
  
−
As far as the comments on categories and subcategories, as I understand it, you can't use double ":"s in names.  You have categories and then something is made a subcategory by claiming that is'a  category of a category. Kinda' strange.
+
# 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.
 +
## 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.
  
−
I do think organization is good.  My way was seemingly obfuscated.  Don't you think PyMol commands should somehow be lumped into available categories?
+
== Searching ==
−
Changes to be made from my POV:
 
−
* Much shorter link names
 
−
* Kill the hierarchy?
 
−
* How to use the Wiki Intro
 
  
−
======Part 2======
+
The default method for searching, eg hitting ENTER, should be the "Search" command not the "Go" command.
−
I tihnk I found the problem, and I might be able to solve it.  I just made things hard by including the hierarchy <u>in</u> the naming scheme, when that's not appropriate.  I think the hierarchy's still very important; however, I think the name-ambiguity problem is not solved via this method.
 
  
−
======Part 3======
+
* 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)
−
I've made lots of changes:
 
−
* I actually took Warren's suggestion on epmty links. I sifted through the TOPTOC and made empty links normal text -- but left them there in case anyone wants to make them links by adding content.
 
−
* Also, I've gone through all the commands and removed the Cmd prefix. The commands, and all commands buried in modules should be easy to create by simply making a new page as, for example, "Editing.Get_Dihedral" or whatever.
 
−
* The names of the links should be MUCH easier to handle, and are far less obfuscated.
 
  
−
MediaWiki-style organization is starting to make sense.  :-)
+
== New Format ==
 +
Code for the new page
  
−
[[User:Inchoate|Inchoate]] 00:48, 6 May 2005 (CDT)
 
−
----
 
  
−
=====A singular vote from TStout=====
+
__NOTOC__
 +
 
 +
{| 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.
 +
|}
  
−
One thing that I think has been missing from the manuals and the Wiki (and manuals for many other programs, I might add) are copious EXAMPLES of how to actually use a command. Speaking as an advanced-dummy, I find it terribly imposing to be presented with something like '''"cmd.select(string name, string selection)"''' as an explanation for how a command works.  "How does that translate into what I should type?" is the polite version of how I end up reading such things....  :)  Recently, I have noticed more "real" examples being entered into the Wiki: THANK YOU!  The example given just now also comes complete with an Examples entry with things like:  
+
{| 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;"
−
              select near , (ll expand 8)
+
|+ 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
−
              select near , (ll expand 8)
+
|-  
−
              select bb, (name ca,n,c,o )
+
| style="font-size: 1.1em; color #61021F; padding: 0.5em 1em 0.5em 3em;"|'''[[:Category:Tutorials|Tutorials]]''' || '''[[TOPTOC|Table of Contents]]''' || '''[[:Category:Commands|Commands]]'''
−
For beginning users, such entries are invaluable. In fact, I would extend that to say that an inverted approach to manual/Wiki writing would be even better for the beginning PyMOL user: organize around how to accomplish the usual tasks, not around a glossary of all the possible commands......That said, a HUGE thank you to all who are putting in so much time building, maintaining and getting this to critical mass so that it becomes the invaluable resource it clearly is headed toward!  -Tom
+
|-
 +
| 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]]'''
 +
|}
  
−
----
 
  
−
=====Where is the anti-spam mechanism/strategy?=====
+
{| width="100%"
−
Manual removing spam contents really sucks.
+
| style="vertical-align: top; width: 45%" |
−
----
+
{| class="jtable" style="float: left; width: 90%;"
 +
|+ style="font-size: 1.4em; font-weight: bold; text-align:left; border-bottom: 2px solid #6678b1;" | News &amp; Updates
 +
|-
 +
! Warren
 +
| News about Warren DeLano's passing may be read on [[Warren|Warren's memorial page]].
 +
|-
 +
! PyMOLWiki
 +
| Reformatted Main Page.
 +
|-
 +
! PyMOLWiki
 +
| New &mdash; 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 [[MAC_Install#PyMOL_Install_from_Source.2C_Using_Fink|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]]&mdash; new command to control PyMOL's usage of color spaces.
 +
|}
 +
|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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