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Revision as of 04:50, 21 February 2005 by Tree (talk | contribs)
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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?

Tree 22:21, 20 Feb 2005 (CST)


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. --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)

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?


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

Possibly Deprecated: Need Feedback

NEW: Tell me what you guys want!

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".

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


If for some library put


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.




Tree 15:02, 19 Feb 2005 (CST)

For CmdScript, would it make more sense to mirror the API style and do


--Jcorn 18:20, 19 Feb 2005 (CST)

Yes, the CmdScript commands should all link back (be categorized in the CmdScript category.

Tree 22:21, 20 Feb 2005 (CST)

Expanded Schema

Proposal to incorporate more than just a manual into this site:

  1. Manual
    1. GUI
    2. Command Script
    3. Python API
    4. Settings
    5. Miscellaneous
    6. Command Line
  2. Meta Manual
    1. Selections
    2. Colors
    3. Palettes
    4. Writing/Running Scripts
    5. Customizing PyMOL
  3. Discussions
    1. News
    2. Development
    3. Questions
  4. Special Topics
    1. Movies and Animation
    2. biochemical calculations
    3. NMR
    4. Crystallography
    5. DNA
    6. Stereo 3D