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#FragmentDB Plugin

#Fragment Chooser ##Selection Clicking on one of the list names selects a new fragment.

##Searching Do an unsharp search with a partial name and hit enter key. For example a search for cf3 finds all the fragments containing cf3 in their name and similar.

The search results in a shortened drop down menue.

##Reset The reset button restores the full fragment list after a search.

##User Defined Database The main database is write protected, but you can add and change as many fragments you like. They will be stored in a separate database in
[Datadir()/db/user-fragment-database.sqlite](shell DataDir()/db). The user database will never be overwritten by plugin updates!
Fragments created or changed by the user will get a *user* at the end of their names.

#Picture #Picture
Displays a picture of the fragment.
Click on the picture to display a magnified version of the picture.
User defined fragments only have pictures if the user provided one.

##Fit! The button Fit! starts the fit of the Fragment into the structure.

##Edit Edit the currenty selected or create new fragments.

##Editor Options ###Change Picture Select a picture for the fragment. Use at least 600dpi pictures.

###Drawstyle Save a style file for chemdraw to draw molecular pictures that look the same as the predefined.

###Name Name of the fragment

###Unit cell Cell parameters of the structure, where the fragment comes from. Use 1 1 1 90 90 90 for cartesian coordinates. The cell constants and the coordinates are converted into Cartesian coordinates during the adding to the database.

###Use selected atoms Uses the selected atoms for the Atoms field and creates a picture from the fragment.

###Atoms insert atoms here like O2 8 1.3984 -0.3778 0.4922. You can also directly copy atoms from SHELX files or copy coordiinates from Avogadro. URL[http://avogadro.cc/, http://avogadro.cc]

###Restraints Type any SHELX compatible restraint here (except SAME). The length of a line is unlimited.

###Residue Define the residue class of the fragment (up to four characters, the first has to be a letter).

#Properies #Properies Define PART, free variables (FVAR) and the occupancy here.

A free variable of 3 and an occupancy of 1 means 31.0 in SHELXL notation. -31.0 On the other hand is set with a free variable of -3. The corresponding free variable is assigned automatically.
All parameters will be displayed simultaneously through atomic labels.

#Properies 2 ##Use a residue Disable or enable putting the fitted fragment into a residue. The residue class has to start with a letter and can be up to four
characters. Usually, the class provided by the database is sufficient.

##Invert Inverts the coordinates of the fragment. Useful to fit the inverted geometry
of the fragment.

##Calculate DFIX The supplied fragment normally has predefined restraints like SADI, FLAT and others.
DFIX Generates DFIX/DANG restraints from the geometry of the fragment and replaces the predefined restraints.

#Properies 3

##Replace Mode If enabled, all atoms inside PART 0 lying in a radius of 1.22 A around the atoms of the fitted fragment will be deleted. This is particular useful to replace atoms of a disordered structure just solved using SHELXT.
It will not delete atoms in different PARTs than PART 0.

##No Restraints No restraints will be applied to the fitting fragment.

##Rigid group Keeps the fitted fragment rigid during refinement.

##Revert Fit Goes back in the history just before the last fragment fit.

#Results #Results This table shows the list of the most disagreeable restraints (in case there are some).
A click on the respective line opens the editor window to adjust the restraints values.
The long list shows ALL restraints and the short list only the most disargreeable ones.
The error of a parameter should generally not be higher than 3sigma. A higher value means that the assumption of the target value originating from general observations is not met. The reason for this can be either, for example, a distorted molecular geometry like a bend aromatic ring or systematic errors in the data.
Disagreeable restraints will be highlighted in yellow if the error is above 2.5sigma. They will be highlighted in red if the error is above 3.5sigma.