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== Example of use == | == Example of use == | ||
=== The dye .pdb file === | === The example dye Atto590.pdb file === | ||
To be able to follow the examples, you need the dye molecule. | |||
Can be downloaded here: [http://dl.dropbox.com/u/101911/pymol/Atto590.pdb Atto590.pdb] | |||
=== The testrotkit.pml file === | === The testrotkit.pml file === | ||
<source lang="python"> | <source lang="python"> | ||
Revision as of 18:13, 29 August 2011
Author
This pymol script is made by Troels Emtekær Linnet
Introduction
Example of use
The example dye Atto590.pdb file
To be able to follow the examples, you need the dye molecule.
Can be downloaded here: Atto590.pdb
The testrotkit.pml file
#-------------------------------------------------------------------------------
# Name: rotkit.py
# Purpose: To rotate molecules easier in pymol
#
# Author: tlinnet
#
# Created: 30/08/2011
# Copyright: (c) tlinnet 2011
# Licence: Free
#-------------------------------------------------------------------------------
cd C:\Users\tlinnet\Documents\My Dropbox\Speciale\5NT-project\Mutant-construct\Distance-Plot
import rotkit
#fetch 1HP1, async=0
load 1HP1.pdb
load Atto590.pdb
### Get the names of the loaded objects
protname = cmd.get_names()[0]
molname = cmd.get_names()[1]
### Make the names we are going to use
protselectCB="%s and resi 308 and name CB"%protname
protnameselectCB="K308CB"
protselectCA="%s and resi 308 and name CA"%protname
protnameselectCA="K308CA"
molselect87="%s and id 87"%molname
molnameselect87="dyeatom87"
molselect85="%s and id 85"%molname
molnameselect85="dyeatom85"
### Make some selections
cmd.select("%s"%protnameselectCB,"%s"%protselectCB)
cmd.select("%s"%protnameselectCA,"%s"%protselectCA)
cmd.select("%s"%molnameselect85,"%s"%molselect85)
cmd.select("%s"%molnameselect87,"%s"%molselect87)
### Make nice representations
cmd.show_as("cartoon","%s"%protname)
cmd.show("sticks","byres %s"%protnameselectCB)
##### PART I: Use of functions #####
### This view will take you to the first part
set_view (\
0.377224118, 0.880101919, -0.288305759,\
0.661396861, -0.473919988, -0.581338286,\
-0.648268998, 0.028612033, -0.760871351,\
0.000000000, 0.000000000, -56.408561707,\
19.480533600, 34.572898865, 6.978204727,\
46.615653992, 66.201446533, -20.000001907 )
#### Just unhash each part for itself, as you continue through
#### The python mini shell is important, to get the return values of the functions
### To print a objects TTT matrix in a readable format
python
rotkit.printMat(cmd.get_object_matrix(molname))
python end
##### We want to move the dye to a desired location, and rotate it to a view we desire
##### First get the vector bewteen the dyeatom and the protein atom
##python
##diffvector = rotkit.vector("%s"%molselect87,"%s"%protnameselectCB)
##python end
##
##### Then move the dye
##python
##move = rotkit.transmat(diffvector)
##### print the matrix for fun
##rotkit.printMat(move)
##### Move the dye
##cmd.transform_selection("%s"%molname,move)
##python end
##
##### Now we want to displace the dye in the CA-CB bond direction
##python
##### First find the vector/direction to displace it in. From A -> B
##diffvector = rotkit.vector("%s"%protnameselectCA,"%s"%protnameselectCB)
##### Make the vector so its lenth is equal 1
##uvector = rotkit.unitvector(diffvector)[0]
##### Make the move translation matrix, and we multiply the matrix with 3, so it moves 3 Angstrom
##move = rotkit.transmat(uvector,3)
##### Print the matrix
##rotkit.printMat(move)
##### Displace it in the CA-CB direction
##cmd.transform_selection("%s"%molname,move)
##python end
##
##### Now we want to rotate it a single time. We convert 40 degress to radians
##### The input is the angle, the line to rotate around, and a point where the line goes through
##python
##CBxyz = rotkit.getxyz("%s"%protnameselectCB)[0]
##rmat = rotkit.rotmat(rotkit.radangle(40),uvector,CBxyz)
##rotkit.printMat(rmat)
##### Copy paste this line into pymol to see it manually
##cmd.transform_selection("%s"%molname,rmat)
##python end
##
##### We are not quite satisfied, we want to rotate it around its own bond
##### So we rotate in around its own 87-85 bonds
##python
##diffvector = rotkit.vector("%s"%molnameselect87,"%s"%molnameselect85)
##uvector = rotkit.unitvector(diffvector)[0]
##xyz85 = rotkit.getxyz("%s"%molnameselect85)[0]
##rmat = rotkit.rotmat(rotkit.radangle(10),uvector,xyz85)
##### Copy paste this line into pymol to see it manually
##cmd.transform_selection("%s"%molname,rmat)
##python end
##
##### Now, lets make a function that collects all these call in one function
##### We only want to define two positions that defines the line, the angle and the object to rotate
##python
##rotkit.rotateline("%s"%molnameselect87,"%s"%molnameselect85,180,"%s"%molname)
##python end
##### This is made as a pymol command as well. I first print the names that we should write manually in the consol
##print("rotateline Pos1=%s, Pos2=%s, degangle=15, molecule=%s"%(molnameselect87, molnameselect85, molname))
##
##### To illustate best, we create som copies of the dye
##python
##anglerange = range(90,360,90)
##for angle in anglerange:
## ### Make a suitable name for the new molecule
## molanglename="%s%s"%(molname,angle)
## ### Now make a copy
## cmd.create(molanglename,molname)
## ### Rotate the copy
## rotkit.rotateline("%s"%molnameselect87,"%s"%molnameselect85,angle,"%s"%molanglename)
##python end
##
####### End of PART I ####
####### PART II: More advanced functions #####
##### This view will take you to the second part
##set_view (\
## 0.723298192, 0.467510879, 0.508201897,\
## 0.371686131, -0.883831143, 0.284063697,\
## 0.581970334, -0.016570913, -0.813038886,\
## 0.000000000, 0.000000000, -76.609786987,\
## 11.790571213, 64.992294312, 20.803859711,\
## -31.181428909, 184.401092529, -20.000001907 )
##
##### We can fast mutate a protein. frame 1 is the most probable mutation
##python
##rotkit.mutate(protname, chain="A", resi=513, target="CYS", mutframe=1)
##python end
##### This is made as a pymol command as well. I first print the names that we should write manually in the consol
##print("mutate %s, chain=%s, resi=%s, target=CYS, mutframe=1"%(protname, "A", 515))
##
##### We now make some selections for this mutation
##protselectCBcys="%s and resi 513 and name CB"%protname
##protnameselectCBcys="P513C_CB"
##protselectCAcys="%s and resi 513 and name CA"%protname
##protnameselectCAcys="P513C_CA"
##cmd.select("%s"%protnameselectCBcys,"%s"%protselectCBcys)
##cmd.select("%s"%protnameselectCAcys,"%s"%protselectCAcys)
##
##### Now, lets make a function that collects all the commands to put on an atom on the same line defined by two points
##### The input is the two points that define the line, the atom of a molecule to be put on the line, and the distance to move
##python
##rotkit.toline(protnameselectCAcys,protnameselectCBcys,molnameselect87,molname,3)
##rotkit.rotateline(protnameselectCAcys,protnameselectCBcys,5,molname)
##rotkit.rotateline(molnameselect87,molnameselect85,10,molname)
##python end
##print("toline Pos1=%s, Pos2=%s, atom=%s, molecule=%s, dist=%s"%(protnameselectCAcys,protnameselectCBcys,molnameselect87,molname,3))
##print("rotateline Pos1=%s, Pos2=%s, degangle=5, molecule=%s"%(protnameselectCAcys, protnameselectCBcys, molname))
##print("rotateline Pos1=%s, Pos2=%s, degangle=10, molecule=%s"%(molnameselect87, molnameselect85, molname))
##
####### End of PART II ####
rotkit.py
The code can be downloaded fast from here http://tinyurl.com/pymolrotkit
- wget http://tinyurl.com/pymolrotkit
- mv pymolrotkit rotkit.py
#-------------------------------------------------------------------------------
# Name: rotkit.py examples
# Purpose: To rotate molecules easier
#
# Author: tlinnet
#
# Created: 30/08/2011
# Copyright: (c) tlinnet 2011
# Licence: Free
#-------------------------------------------------------------------------------
from pymol import cmd
import math
def printMat(matrix):
print("%s %s %s %s \n%s %s %s %s \n%s %s %s %s \n%s %s %s %s"%(matrix[0],matrix[1],matrix[2],matrix[3],matrix[4],matrix[5],matrix[6],matrix[7],matrix[8],matrix[9],matrix[10],matrix[11],matrix[12],matrix[13],matrix[14],matrix[15]))
return None
def getxyz(Sel):
if type(Sel)==list and len(Sel)==3:
return Sel, "listXYZ"
if type(Sel)==str and Sel[0]=="[" and Sel[-1]=="]":
Selsplit = list(Sel[1:-1].split(","))
Selsplit = [float(x) for x in Selsplit]
return Selsplit, "strXYZ"
if type(Sel)==str:
pos = cmd.get_atom_coords(Sel)
return pos, "selXYZ"
def vector(Sel1,Sel2):
PosSel1 = getxyz(Sel1)[0]
PosSel2 = getxyz(Sel2)[0]
vectorcalc = [PosSel2[0]-PosSel1[0],PosSel2[1]-PosSel1[1],PosSel2[2]-PosSel1[2]]
return(vectorcalc)
def vectorstr(vector):
return("[%s,%s,%s]"%(vector[0],vector[1],vector[2]))
def transmat(vector,dist=1):
mat = [1,0,0,0,0,1,0,0,0,0,1,0,dist*vector[0],dist*vector[1],dist*vector[2],1]
return(mat)
def unitvector(vector):
vectorlen = math.sqrt(math.pow(vector[0],2)+math.pow(vector[1],2)+math.pow(vector[2],2))
vectordiv = [vector[0]/vectorlen, vector[1]/vectorlen, vector[2]/vectorlen]
return(vectordiv,vectorlen)
def radangle(angle):
return(math.radians(angle))
def rotmat(angle,vectornorm,pointcoord):
### From: http://inside.mines.edu/~gmurray/ArbitraryAxisRotation/ Section 6.2
u,v,w = vectornorm
a,b,c = pointcoord
makerotmat = [(math.pow(u,2)+(math.pow(v,2)+math.pow(w,2))*math.cos(angle)),
(u*v*(1-math.cos(angle))-w*math.sin(angle)),
(u*w*(1-math.cos(angle))+v*math.sin(angle)),
((a*(math.pow(v,2)+math.pow(w,2))-u*(b*v+c*w))*(1-math.cos(angle))+(b*w-c*v)*math.sin(angle)),
(u*v*(1-math.cos(angle))+w*math.sin(angle)),
(math.pow(v,2)+(math.pow(u,2)+math.pow(w,2))*math.cos(angle)),
(v*w*(1-math.cos(angle))-u*math.sin(angle)),
((b*(math.pow(u,2)+math.pow(w,2))-v*(a*u+c*w))*(1-math.cos(angle))+(c*u-a*w)*math.sin(angle)),
(u*w*(1-math.cos(angle))-v*math.sin(angle)),
(v*w*(1-math.cos(angle))+u*math.sin(angle)),
(math.pow(w,2)+(math.pow(u,2)+math.pow(v,2))*math.cos(angle)),
((c*(math.pow(u,2)+math.pow(v,2))-w*(a*u+b*v))*(1-math.cos(angle))+(a*v-b*u)*math.sin(angle)),
(0),(0),(0),(1),]
return(makerotmat)
def rotateline(Pos1,Pos2,degangle,molecule):
diffvector = vector(Pos1,Pos2)
uvector = unitvector(diffvector)[0]
xyz = getxyz(Pos2)[0]
rmat = rotmat(radangle(float(degangle)),uvector,xyz)
cmd.transform_selection(molecule,rmat)
return(None)
cmd.extend("rotateline",rotateline)
def mutate(molecule,chain,resi,target="CYS",mutframe="1"):
target = target.upper()
cmd.wizard("mutagenesis")
cmd.do("refresh_wizard")
cmd.get_wizard().set_mode("%s"%target)
selection="/%s//%s/%s"%(molecule,chain,resi)
cmd.get_wizard().do_select(selection)
cmd.frame(str(mutframe))
cmd.get_wizard().apply()
cmd.set_wizard("done")
cmd.select("%s%s%s_%s"%(molecule,chain,resi,target),"byres %s"%(selection))
cmd.extend("mutate",mutate)
def toline(Pos1,Pos2,atom,molecule,dist=1):
dist = float(dist)
diffvector = vector(atom,Pos2)
move = transmat(diffvector)
cmd.transform_selection("%s"%molecule,move)
diffvector = vector(Pos1,Pos2)
uvector = unitvector(diffvector)[0]
move = transmat(uvector,dist)
cmd.transform_selection("%s"%molecule,move)
return(None)
cmd.extend("toline",toline)