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Some Thoughts For Discussion

  • 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.
  • 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.
  • 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?

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).

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)

Organizing PyMol Commands

New Simpler Rules

Our naming idea was stupid, too. All commands are easily found under 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

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
[[Cmd command_name]]

and that's it. So, "center" becomes,

[[Cmd center]]



See center

Tree 15:02, 19 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

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