Talk:Main Page: Difference between revisions

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--TheDude
--TheDude


== collapsing simple and advanced topics ==
== Organizing PyMol Commands ==


"Simple" vs "advanced" tasks are currently separated out, so that there are multiple places to find information on each topic, (eg - atom selections). I believe that all information about each topic should be kept together, but with many logical subheadings to separate them (and organized from simple->complex). That way a user only need look in one area to find the solution to their problem, rather than hunting around the wiki to find whether their answer is in the simple or advanced sections of each topic.
Due to the inherent ambiguity of wiki naming, we have come up with a way to categorize the naming/sorting of PyMol commands.
--[[User:Jcorn|Jcorn]] 14:51, 17 Feb 2005 (CST)


Jcorn, I agree, but I didn't/don't know the appropriate layout. It seems to be a 2x2 matrix
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.
Ex:


* Topic A
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".
** Simple Usage
** Advanced Usage


* Topic B
=== Examples ===
** Simple Usage
See [[CmdScript center]]
** Advanced Usage


Or,
See [[Cmd.center center]]


* Simple Usage
[[User:Tree|Tree]] 15:02, 19 Feb 2005 (CST)
** Topic A
** Topic B
 
* Advanced Usage
** Topic A
** Topic B
 
See?  I do agree and think that the better organization is to keep all the commands grouped as tightly as possible and put simple/medium/advanced on each page.
 
[[User:Tree|Tree]] 17:51, 17 Feb 2005 (CST)
 
 
Personally, I think the former organization scheme is more useful for both experienced and novice users. Since it organizes based on task/topic, rather than trying to relate the task to how skilled one thinks a user would have to be to attempt it. Anyway, it looks like the topic list has sorted itself out pretty nicely.
 
--[[User:Jcorn|Jcorn]] 00:39, 18 Feb 2005 (CST)


==Quote==
==Quote==

Revision as of 16:02, 19 February 2005

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. --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. (?)
Tree 00:12, 17 Feb 2005 (CST)

"" 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?

Tree

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. --TheDude

Organizing PyMol Commands

Due to the inherent ambiguity of wiki naming, we have come up with a way to categorize the naming/sorting of PyMol commands.

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.

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".

Examples

See CmdScript center

See Cmd.center center

Tree 15:02, 19 Feb 2005 (CST)

Quote

However, a good Wiki needs to be structured beforehand, rather than having everything grow by itself. Users will add things where aproppriate, anyway. Thus, in a heavily used Wiki its definitely easy to get lost.

Go!

Please add content! Sorry for not removing that text!

Tree 00:47, 18 Feb 2005 (CST)

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