Editing Rotkit (section)

=== Functions available in PyMOL ===
* rotateline(Pos1,Pos2,degangle,molecule):
*: "Pos1->Pos2" define a line whereabout "molecule" will be rotated "degangle" degrees 
*: '''rotateline Pos1=P513C_CA, Pos2=P513C_CB, degangle=5, molecule=Atto590'''
*: '''rotateline Pos1=dyeatom87, Pos2=dyeatom85, degangle=10, molecule=Atto590'''
* mutate(molecule,chain,resi,target="CYS",mutframe="1"):
*: Mutate a /molecule//chain/resi into a target, and selecting most probable frame 1
*: '''mutate 1HP1, chain=A, resi=515, target=CYS, mutframe=1'''
* toline(Pos1,Pos2,atom,molecule,dist=1):
*: Translate molecule atom, 1 angstrom away in the same direction Pos1->Pos2 specify
*: '''toline Pos1=P513C_CA, Pos2=P513C_CB, atom=dyeatom87, molecule=Atto590, dist=3'''

'''Available through rotkit.functionname'''
* printMat(matrix):
*: prints the TTT matrix in a readable format. (4X4)
* getxyz(Sel):
*: output is a list [x,y,z] in float. The input can be a list, a string(list) or a selection.
* vector(Sel1,Sel2):
*: Finds the vector between points. Gets the xyz list from getxyz, so input can be anything.
* vectorstr(vector):
*: turn a vector in list format into string. No real function actually.
* transmat(vector,dist=1):
*: Makes a TTT translation matrix for according to the input vector. The vector is multiplied with dist.
* unitvector(vector):
*: Make a vector a unitvector. 
* radangle(angle):
*: Convert degree to radians. Not that all input are assumed to be in degrees, and are converted automatically.
* rotmat(angle,vectornorm,pointcoord):
*: This function is the most important. That makes the TTT matrix that rotates a molecule around a normalized vector, which goes through a coordinate point.
* crossprod(Vector1, Vector2):
*: Makes a crossproduct between two vectors
* crosspoint(Pos1, crossprod):
*: Returns the endpoint for the Position plus the crossproduct vector. Suitable if one would like to rotate around a crossvector.

<gallery heights="240px" widths="340px">
Image:Rotkitex1.png|Place your dye how you want. You always get same ending position.
Image:Rotkitex2.png|Mutate a residue through command line, and quickly put your dye there.
</gallery>