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?
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".
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)
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.
Please add content! Sorry for not removing that text!
Tree 00:47, 18 Feb 2005 (CST)
Proposal to incorporate more than just a manual into this site:
- Command Script
- Python API
- Command Line
- Meta Manual
- Writing/Running Scripts
- Customizing PyMOL
- Special Topics
- Movies and Animation
- biochemical calculations
- Stereo 3D