Help:Contents

From MolWiki
Jump to: navigation, search

Editing pages

The most detailed explanation is given on the corresponding page of MediaWiki. In MolWiki.org the most important principles are:

  • Please follow the general practice of good scientific writing.
  • Prove your statements by including references to peer reviewed journals.
  • Use preview functionality as much as possible! Try not to save changes just for testing purposes.

Molecule-related pages

MolWiki.org among other information also contains pages related to particular molecules. The naming convention for such pages is based on the Hill system. The total name for a molecule-related page should be constructed as a chemical formula according to the Hill system and an index number, which makes this page unique. Example: C10H17B-1.
Index numbers are used for distinguishing different structural isomers. Different conformers belonging to the same structural isomer are described in one article.
It is also reasonable to create an additional page with human-readable name corresponding to the compound, which redirects to the main page of the molecule. Example: 3-Methyl-1-boraadamantane.
You can find a 'copy/paste' template for your new article here: Help:MolTemplate

Source code

To publish source code with highlighted syntax use code tags with indication of the language type:

<syntaxhighlight lang="your_language">
Your source code goes here...
</syntaxhighlight>

The following example is for Fortran:

<syntaxhighlight lang="fortran">
C     A Simple program
      program hello
         print *, "Hello World!"
      end program hello
</syntaxhighlight>

The result is

C     A Simple program
      program hello
         print *, "Hello World!"
      end program hello

Mathematical formulae

You can include formulae by using
<math></math>
tags and LaTeX syntax. The example
<math>
  \operatorname{erfc}(x) =
  \frac{2}{\sqrt{\pi}} \int_x^{\infty} e^{-t^2}\,dt =
  \frac{e^{-x^2}}{x\sqrt{\pi}}\sum_{n=0}^\infty (-1)^n \frac{(2n)!}{n!(2x)^{2n}}
</math>

produces the following output:
$ \operatorname{erfc}(x) = \frac{2}{\sqrt{\pi}} \int_x^{\infty} e^{-t^2}\,dt = \frac{e^{-x^2}}{x\sqrt{\pi}}\sum_{n=0}^\infty (-1)^n \frac{(2n)!}{n!(2x)^{2n}} $

You can click on the formula to enlarge it.

Molecular structures

MolWiki.org has a Jmol extension, which can be used to show molecular structures interactively. To create a link to a molecular structure upload a XYZ file and use the jmolFile tag:

<jmolFile  text="An example of molecular structure">C26NH28.xyz</jmolFile>

The example produces the following link:
An example of molecular structure
You can also create a window with structure. The following example

<jmol>
 <jmolApplet>
  <inlineContents>
   11
   test
   F  0.000000000000 -0.000000000000 -1.685455090782
   C  0.000000000000 -0.000000000000 -0.385040888542
   N -1.006202819407  1.006202819407  0.139899574177
   O -1.068429240123  2.026449428610 -0.506881519565
   O -1.600251840223  0.695487106176  1.148009747048
   N -0.368295793263 -1.374498612670  0.139899574177
   O -1.220742064599 -1.938511578398 -0.506881519565
   O  0.197816418158 -1.733602299174  1.148009747048
   N  1.374498612670  0.368295793263  0.139899574177
   O  2.289171304722 -0.087937850212 -0.506881519565
   O  1.402435422065  1.038115192997  1.148009747048
  </inlineContents>
 </jmolApplet>
</jmol>

creates the window with structure:


Sometimes structures defined in XYZ format like in examples above are visualized by Jmol with some missing bonds. In this case it is better to define structure in MOL format like this:

<jmol>
 <jmolApplet>
  <inlineContents>
1
 OpenBabel06141312083D

 13 12  0  0  0  0  0  0  0  0999 V2000
    0.0001    0.0000   -0.6042 P   0  0  0  0  0  0  0  0  0  0  0  0
    1.6159   -0.3009    0.2804 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0189   -1.2740   -0.0163 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.3421    0.4621   -0.0161 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.5107   -0.2814    1.3713 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0685   -1.2489    0.2803 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1129   -1.1107   -0.0158 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7715   -2.2593   -0.0167 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9986   -1.1680    1.3712 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5474    1.5497    0.2804 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0941    2.3852   -0.0159 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5711    1.7973   -0.0165 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5121    1.4486    1.3712 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  6  1  0  0  0  0
  1 10  1  0  0  0  0
  1  2  1  0  0  0  0
  2  5  1  0  0  0  0
  3  2  1  0  0  0  0
  4  2  1  0  0  0  0
  6  9  1  0  0  0  0
  7  6  1  0  0  0  0
  8  6  1  0  0  0  0
 10 13  1  0  0  0  0
 11 10  1  0  0  0  0
 12 10  1  0  0  0  0
  </inlineContents>
 </jmolApplet>
</jmol>

The structure is then visualized with all explicitly defined bonds:


Conversion from XYZ to MOL format can be easily done by using the OpenBabel program:

$ babel file.xyz file.mol

Participating in discussion

Each article has a dedicated discussion page where you can ask questions, find more information on the topic and talk to other people. More information about discussion pages is on MediaWiki site.

Bibliography

MolWiki.org has a central repository for references. You can find it in Special:SpecialPages in category BibManager. Whenever you want to cite an article check first the repository if it contains already the corresponding entry. If not, then you have to add a new entry manually or import it as BibTeX string automatically. Note, that only registered users can add new or edit existing entries. Each entry has its own unique id called Citation, which is then used for making automatic references in articles of MolWiki.org. This id should be defined manually upon creation of a new entry. The ids are written as a composition of the name of first author of an article, the capital letters of journal (or book, ...) name and the year of publication. For example BergerZFN2009. More examples can be found in overview of BibManager entries.

When you want to cite a paper in text use bib tag as in example:

<bib id="BergerZFN2009" />

which automatically produces a link like [BergerZFN2009]Author: Berger, Raphael J. F.; Hoffmann, Manfred; Hayes, Stuart A.; Mitzel, Norbert W.
Journal: Z. Naturforsch B
Number: 11
Pages: 1259-1268
Title: An Improved Gas Electron Diffractometer -- The Instrument, Data Collection, Reduction and Structure Refinement Procedures
Volume: 64
Year: 2009
Link to Google Scholar
.