The MandarWeb Website: Tone and Accent marks page
Section 6. Tone and Accent marks
In Mandarin Chinese, each character can have one of four tones, or a short unaccented pronunciation essentially without tone. Here we are concerned with how these tones are figured in standard Pinyin and in the MandarWeb files.
Below is shown a sample page from a small Collins Chinese dictionary , which includes characters for "shan". It's a pocket-size dictionary intended for travellers, so it has only more common words.
The extract is from the Chinese-English section of the dictionary. Like virtually all such dictionaries in modern times, it is alphabetical by Pinyin, from "a" to "zuo". So to use this dictionary, you need to know or find out the Pinyin (pronunciation) for a character.
The dictionary page lists words which start off with the sound "shan". The dictionary includes 9 different variations, as follows.
Page with "shan" characters from a dictionary 
The first 4 of the 9 are pronounced with Mandarin "First Tone", a high level tone. In MandarWeb they are listed as "shan1". Each of these characters (syllables) is pronounced the same.
Note 6-1. In Mandarin, about 80% of words are made up of two or more characters (syllables). Under the first "shan1", meaning mountain, are listed the words for cave, peak, valley, etc, each of which has two syllables, while the English meanings have only one. All variations are possible.
Pinyin with tone marks for "shan" characters
The fifth character listed is shan3, with Mandarin "Third Tone" a falling then rising pronunciation. The last 4 characters are shan4, with "Fourth Tone", a short falling tone.
Notice also that the 4th and 6th characters are exactly the same, though in their Pinyin the tone marks are different. It's quite common in Mandarin for characters to have different meanings according to their tones.
There are no "shan2" characters, with the rising "Second Tone". Second Tone is found in the second syllable of shan1-lin2, the Mandarin word for a wooded hill. You can almost see the mountain shape plus the two trees of lin2, a forest.
Characters for shan1-lin2 (wooded hill)
As well as the 4 tones, Mandarin contains short unstressed pronunciations of syllables which are said to be without tone. On the top left of the dictionary page you can see the characters and Pinyin for "dice", with 3rd-tone "shai" and no-tone "zi". In MandarWeb this word is written shai3-zi0. Writing tones as following digits makes it simpler to represent tones with keyboard input, and also easier to remember.
In MandarWeb, the Pinyin of characters in a phrase are separated by hyphens for easier recognition. The second main entry on the dictionary page contains characters and Pinyin for "She was sunbathing on the beach". In Mandarweb, the Pinyin would be ta1-zai4-sha1-tan1-shang4-shai4-tai4-yang0.
OK, this is quite a mouthful, but it's easier to comprehend and remember than the standard Pinyin you would get from writing down the Pinyin equivalents of each of the characters. The dictionary gives you extra information by grouping together characters forming part of a word, as sha1-tan1 and tai4-yang0. You don't know this from the characters, which are all run together. Other groupings are possible, zai-sha, tan-shang, and shang-shai are all good Mandarin words. You have to work out which characters are to be grouped together to form words yourself.
As well the tone marks, standard Pinyin-using dictionaries use an accent mark on some syllables, to denote a "U" sound which is preceded by a "Y" sound. If you look at the English and American pronunciations of "new", the English will say "nyu", while Americans usually say "noo".
In standard Pinyin, a syllable written with 2 dots over it has this "YU" sound. It will normally have a tone mark as well. A common character like this in Mandarin is the one meaning "female" or "woman", and is common in multi-syllable words. It looks as follows:
女 . nǚ . (female / woman)
In the following example, the characters and Pinyin are for 'female king', hence, "queen".
女王 . nǚ wáng . (queen)
You can have "nu" characters without the preceding "Y" sound, which are like "noo".
砮 . nǔ . (flint)
And you can have characters with the "Y" sound, and other tones.
恧 . nǜ . (ashamed)
In section 7, we'll see how the "nyu" sound is handled for phone or computer input -- essentially, "nv" is substituted for it. This is a non-intuitive fix or kludge, and can be used only because the letter "V" is not used elsewhere in standard Pinyin.
In MandarWeb, this sound is written as "nyu", so the character for female is written "nyu3".
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(previous version 1.04, on Web 2008 Oct 22, see http://www.aoi.com.au/mandarin/ ).
Version 2.01, 2015 Mar 5.