The Scid analysis window shows the analysis by a chess program (known as an engine) of the current board position. Whenever the board changes, Scid sends the new position to the engine and it shows its assessment of that position.
The score shown in the analysis window is always from the perspective of White, so a negative score indicates Black is better. The lower frame in the window (with the scrollbar) shows the history of evaluations produced by the engine for the current position, so you can see how the assessment has changed.
To add the best move chosen by the engine as a new move in the current game, press the Add move button.
Scid maintains a list of the engines you have used, along with an estimated Elo rating (if you guess one) and the date when each engine was last used. You can sort the engine list by name, Elo rating, or date. Select the New or Edit buttons to add a new engine to the list or edit the details for an existing entry.
For each engine, you must specify the executable file to run and which directory Scid should run it in.
The most likely cause of engine starting problems is the choice of which directory the engine should run in. Some engines require an initialization or opening book file in their start directory to run properly. Other engines (like Crafty) write log files to the directory they start in, so you will need to run them in a directory where you have write access. If the directory setting for an engine is ".", Scid will just start the engine in the current directory.
So if an engine that should work fine in Scid does not start, try changing its directory setting. To avoid engines creating log files in many different directories, I recommend starting engines in the directory of the Scid User files (this is where the scid.exe file is located on Windows, or ~/.scid/ on Unix); there is a button in the dialog box for editing engine details marked scid.exe dir on Windows or ~/.scid on Unix that lets you set the engine to start in this directory.
With the Training button, you can play moves against the analysis engine. The time for each move is fixed, and the analysis results are not shown when training mode is on.
The Add variation button in the analysis window adds the current score and best line of play as a new variation in the game.
You can do this automatically for a number of moves (annotating the game) by pressing the Annotate button. This prompts you for some annotation options and then turns on autoplay mode. When autoplay mode is used and the analysis window is open, a variation containing the score and best line of play is automatically added for each position as autoplay mode moves through the game. Only positions from the current position until the end of the game (or until you exit autoplay mode) are annotated, so you can skip annotation of opening moves by moving to a middlegame position before starting autoplay.
To cancel annotation at any time, just turn off autoplay mode, for example by pressing the Escape key in the main window.
Note that for simplicity, the Annotate button is only available in the window opened as analysis engine 1. If you open an engine as analysis engine 2, you cannot use it to annotate the game.
To use the analysis window, you will need a chess program that supports the WinBoard/Xboard protocol.
Scid sends he xboard, post and protover 2 to an engine when it starts, and will use the setboard and analyze commands for more efficient communication if the engine responds indicating that it supports them. If an engine does not support the setboard command, it will not be able to provide analysis in any game that begins with a non-standard start position.
For programs that do not support the analyze command, Scid sends the following commands every time the position changes: new and force, then the moves in the game to the current position, then go.
Bob Hyatt's excellent free chess program Crafty is what I use and recommend for the Scid analysis window, but many other WinBoard or XBoard compatible programs have been successfully used with Scid. Some download sites for a few engines are listed below.
Crafty: ftp://ftp.cis.uab.edu/pub/hyatt/
Yace: http://home1.stofanet.dk/moq/
Phalanx: ftp://ftp.math.muni.cz/pub/math/people/Dobes/
Comet: http://members.aol.com/utuerke/comet/
Gnuchess: http://www.gnu.org/software/chess/chess.html
The Crazy Bishop: http://remi.coulom.free.fr/