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Creating your wand
To get started in Thaumcraft 3 you will need to craft your first wand. To do this you need to go on a short venture out into the world and find an Infused Stone, and break it apart to gather the shards within. It doesn't matter what kind of shard you receive, you just need to gather at least one. Next you will need some gold, because what wand is complete without a little bit of the stuff of kings? Oh, you will also need a stick.
After you have gathered the necessary ingredients make your way to the nearest (or any other) Crafting Table. Upon the table, place a gold nugget in one of the bottom corners, the stick in the center, and a single shard in one of the top corners opposite the gold nugget. You are looking for the rough shape of a diagonal line. Concentrate your mind, and grab your very own Wand of the Apprentice.
Now that you have your first magic wand, you will need arguably the most important item in your life, a Thaumonomicon. But this isn't just any book, this book requires the magical fusing of all the knowledge of at least three books, what better place to do that than in a bookshelf. Either acquire one for yourself, or craft one if you have the means to do so. Once you have one, simply place it on the ground and point your wand at it (Right-Click). The knowledge will be fused together and present itself to you in the form of your very own Thaumonomicon.
By this point you may have noticed that your Thaumonomicon is a bit perplexingly empty. I would highly suggest you read any of the topics in the top left area of your Thaumonomicon as they give basic, but usually very helpful advice and hidden tips about advanced alchemy. Looking slightly below and to the right of the basic info section will show you a lot of things that you may have heard hints about during your travels, but never learned enough about to fully understand. Attempting to read these entries will show foreign symbols that will most likely just hurt your head at this point. To better grip these concepts you will need to begin Researching them. You can only research certain aspects of this pantheon of knowledge at a time, requiring you to work your way from more basic concepts into more advanced one, lest you explode your mind with the vast knowledge of advanced concepts.
You are only able to work the concepts in the book that are "highlighted" and have a solid line pointing to them. Sometimes however you will discover concepts in the book you have never heard of, and will mostly likely only accidentally stumble upon these. To start out at this point is craft a Research Table, which is crafted when you use Scribing Tools on two Tables (you remember how to make those right?) placed side-by-side. To create Scribing Tools, you just need to acquire a feather, a glass jar, and a sac of ink. Place these items in your Arcane Workbench to receive what any good scholar should keep with them at all times (really). Once you have your Research Table decorated the way you want (I usually put a Skeleton Skull on mine), pull up a chair and familiarize yourself with the layout.
Once you have the two basic tools of any good thaumaturge, you will need to begin your ascent to magical kingship. But first, where to start? Generally the best place to start is with an Arcane Worktable. To do this, you first need to create a table to infuse a bit of your arcane power. To craft a table simply make your way to another crafting table with a bit of wooden planks. Place three horizontally in a row to craft some wooden slabs. Then place those slabs back onto the Crafting Table along the middle row, then place two more wooden planks in the bottom corners, roughly in the shape of... a table. Now place the table in a warm corner of your abode, and point your wand at it. And now you have received a place to craft many magical items you may need on your journey.
Now that you have your paper in the correct spot, your items placed ready for study, simply start looking them over (click the magnifying glass icon). If there is a concept you are able to understand that uses one of the aspects you have at your disposal, you will notice that a discovery will appear just above the paper spot. If one does not appear, choose another item, there is no reason to use the same one twice at this point. Once you discover a concept, keep looking the item over until you identify the aspect related to it. This aspect will appear eventually on the right side of the table. As you understand how that aspect plays a part in your concept it will move further and further to the edge of your transmutation circle. During this period you may also notice that some of the aspects on the item may darken, this means that during your study your have realized that those aspects don't play any part in this concept and should be excluded if possible from future study of the discovery.
As you delve deeper and deeper into whatever discovery you have found you will reach a few noteworthy checkpoints. The first is when you name your discovery, this will be added to your notes when you feel you have around 25% of the discovery completed. The second is when you realize how many aspects are needed in the discovery, this will happen around 50% of completion. The third is when you realize what those aspects are, and this will happen around 75% of completion. At the second checkpoint you will also finally be able to read about the concept's basic theory on the paper to the top left of your transmutation circle, this will usually give some insight into what the discovery may actually do.
After you are finished with one item and all of its aspects you will need to begin study on another. Repeating this until you have either finished the discovery, or more likely you have realized that the item does not hold any aspects that can be used on the discovery. Simply keep up your review of items until you have found an item that contains the necessary aspects for you to complete your discovery. Once that is finished place the discovery in your hand and transcribe your notes into your Thaumonomicon (right click). Now open your Thaumonomicon and review your notes. You will have most likely found a full description of your discovery, what it can do, and how to craft it.
To craft something you have discovered you will need one of three different vessels, your notes should tell you which needs to be used.
The first being the most simplistic, and one we have already crafted, the Arcane Workbench. To use the Workbench just place the necessary items in their place, set your wand onto the table in the bottom right corner of the workspace and begin your construction.
The second and more advanced vessel is a Crucible. To create this iron juggernaut is quite simple if you are familiar with basic crafting; simply place an ordinary cauldron on the floor and infuse it with your magical essence (use your wand). Now that you have a Crucible, there are a few more things that need to be done before it is usable. Any apprentice chef will tell you hot water dissolves things faster than cold, so we need some heat. Either place some fire under the Crucible, or some lava. It doesn't matter which, it just needs to burn hot and burn long. Now that the Crucible is heated, simply displace some water from a local reservoir or pond into the Crucible. After a few seconds you will notice that the water begins to boil. Now that it's prepared for crafting, all you need to do at this point is toss some items into the boiling water and they will be broken down into its contained Essentia, or magical aspects. Once you feel you have enough magical energy for crafting just use your wand on the Crucible and you will craft an item, if one exists from the magical energies you have gathered. Be warned however, any unused Essentia in the Crucible after crafting will dissipate into the atmosphere, large amounts of this energy can begin to clump together and sometimes have nasty effects on the surrounding environment, or EVEN YOU!
The third and most advanced vessel for crafting is an Infusion Altar. One of these may only be crafted once you have mastered some basic concepts however so refer back to your notes to see if you are able to make one of these. For those of you that forgot to keep notes around, you will need to create four magical stone blocks, and place them in a 2x2 square in your laboratory, then infuse them once more with your magical energy. The Infusion Altar is a complex object that requires the co-operation of the Crucible in order to function, therefore you should place them relatively close together (no more than 10 blocks away). To craft items on the Infusion Altar you will need both physical items, and latent Essentia from the Crucible. Anything you may need for crafting should be listed on your notes. Simply put items into the Crucible to break them down into Essentia, then place the physical materials onto the Infusion Altar with your wand. Before crafting, back up and look at the Infusion Altar, you should notice the Essentia being gathered and pulled into the Infusion Altar. Once you have all the necessary ingredients for final construction the Essentia will be pulled out of the Crucible and the rest will dissipate into the air.
Once you have reached this point you should have a basic understanding of everything you will need to complete your journey to becoming a Master Thaumaturge, however there are a few other notes you may need in your travels.
First - Anytime you use the Crucible, always try to keep a set of Scribing wood and paper on hand. You never know what you may discover from the resulting Essentia.
Second - Not all things are shown in the Thaumonomicon. You may need to make full discoveries on your own. Usually these profound ancient concepts can be hinted at by Knowledge Fragments. You can find these from other Master Thaumaturges that tend to reside in villages, or in old forsaken laboratories around the world. Beware however, most of these old locations have been overrun with monsters and sealed up with iron bars, do not enter unprepared.