Rotkit
Author
This pymol script is made by Troels Emtekær Linnet
Introduction
Example of use
The dye .pdb file
COMPND Atto590
AUTHOR GENERATED BY OPEN BABEL 2.2.3 an in Avogadro
HETATM 1 C LIG 1 -4.057 2.454 -1.838 1.00 0.00 C
HETATM 2 N LIG 1 -2.619 2.797 -1.904 1.00 0.00 N
HETATM 3 C LIG 1 -4.780 3.335 -0.830 1.00 0.00 C
HETATM 4 C LIG 1 -4.192 1.001 -1.344 1.00 0.00 C
HETATM 5 C LIG 1 -4.793 2.597 -3.193 1.00 0.00 C
HETATM 6 C LIG 1 -1.942 3.160 -0.686 1.00 0.00 C
HETATM 7 C LIG 1 -4.149 3.889 0.224 1.00 0.00 C
HETATM 8 C LIG 1 -2.678 3.711 0.383 1.00 0.00 C
HETATM 9 C LIG 1 -2.011 4.104 1.567 1.00 0.00 C
HETATM 10 C LIG 1 -0.555 2.983 -0.540 1.00 0.00 C
HETATM 11 C LIG 1 -0.625 3.896 1.713 1.00 0.00 C
HETATM 12 C LIG 1 0.087 3.328 0.645 1.00 0.00 C
HETATM 13 O LIG 1 1.412 3.104 0.756 1.00 0.00 O
HETATM 14 C LIG 1 0.146 4.247 2.961 1.00 0.00 C
HETATM 15 C LIG 1 1.477 3.899 3.020 1.00 0.00 C
HETATM 16 C LIG 1 2.103 3.331 1.896 1.00 0.00 C
HETATM 17 C LIG 1 3.458 3.002 1.923 1.00 0.00 C
HETATM 18 C LIG 1 2.254 4.083 4.182 1.00 0.00 C
HETATM 19 C LIG 1 4.257 3.179 3.087 1.00 0.00 C
HETATM 20 C LIG 1 3.617 3.727 4.231 1.00 0.00 C
HETATM 21 N LIG 1 5.544 2.857 3.105 1.00 0.00 N
HETATM 22 C LIG 1 4.377 3.930 5.483 1.00 0.00 C
HETATM 23 C LIG 1 6.402 3.070 4.308 1.00 0.00 C
HETATM 24 C LIG 1 5.668 3.624 5.509 1.00 0.00 C
HETATM 25 C LIG 1 7.010 1.725 4.768 1.00 0.00 C
HETATM 26 C LIG 1 7.526 4.086 3.998 1.00 0.00 C
HETATM 27 H LIG 1 -5.861 3.428 -0.908 1.00 0.00 H
HETATM 28 H LIG 1 -2.574 4.547 2.368 1.00 0.00 H
HETATM 29 H LIG 1 0.038 2.543 -1.329 1.00 0.00 H
HETATM 30 C LIG 1 -0.510 4.983 4.109 1.00 0.00 C
HETATM 31 H LIG 1 1.794 4.486 5.067 1.00 0.00 H
HETATM 32 H LIG 1 3.861 2.612 1.004 1.00 0.00 H
HETATM 33 H LIG 1 6.234 3.777 6.426 1.00 0.00 H
HETATM 34 C LIG 1 3.721 4.478 6.733 1.00 0.00 C
HETATM 35 H LIG 1 6.199 1.004 5.010 1.00 0.00 H
HETATM 36 H LIG 1 7.638 1.861 5.675 1.00 0.00 H
HETATM 37 H LIG 1 7.662 1.271 3.996 1.00 0.00 H
HETATM 38 H LIG 1 7.085 5.060 3.696 1.00 0.00 H
HETATM 39 H LIG 1 8.209 3.753 3.194 1.00 0.00 H
HETATM 40 H LIG 1 8.161 4.256 4.897 1.00 0.00 H
HETATM 41 C LIG 1 6.193 2.277 1.907 1.00 0.00 C
HETATM 42 H LIG 1 6.034 2.929 1.021 1.00 0.00 H
HETATM 43 C LIG 1 5.765 0.821 1.653 1.00 0.00 C
HETATM 44 H LIG 1 7.291 2.219 2.020 1.00 0.00 H
HETATM 45 H LIG 1 4.681 0.690 1.481 1.00 0.00 H
HETATM 46 H LIG 1 6.040 0.186 2.519 1.00 0.00 H
HETATM 47 H LIG 1 6.299 0.437 0.758 1.00 0.00 H
HETATM 48 C LIG 1 -1.890 2.833 -3.182 1.00 0.00 C
HETATM 49 H LIG 1 -2.440 3.435 -3.934 1.00 0.00 H
HETATM 50 C LIG 1 -1.575 1.431 -3.708 1.00 0.00 C
HETATM 51 H LIG 1 -0.922 3.362 -3.078 1.00 0.00 H
HETATM 52 H LIG 1 -2.484 0.841 -3.923 1.00 0.00 H
HETATM 53 H LIG 1 -0.963 0.879 -2.964 1.00 0.00 H
HETATM 54 H LIG 1 -0.995 1.515 -4.651 1.00 0.00 H
HETATM 55 H LIG 1 -4.746 3.648 -3.551 1.00 0.00 H
HETATM 56 H LIG 1 -5.866 2.324 -3.085 1.00 0.00 H
HETATM 57 H LIG 1 -4.381 1.935 -3.977 1.00 0.00 H
HETATM 58 H LIG 1 -3.709 0.878 -0.350 1.00 0.00 H
HETATM 59 H LIG 1 -3.705 0.294 -2.046 1.00 0.00 H
HETATM 60 H LIG 1 -5.261 0.709 -1.249 1.00 0.00 H
HETATM 61 C LIG 1 -4.954 4.653 1.250 1.00 0.00 C
HETATM 62 H LIG 1 -6.034 4.696 0.992 1.00 0.00 H
HETATM 63 H LIG 1 -4.575 5.694 1.319 1.00 0.00 H
HETATM 64 H LIG 1 -4.866 4.160 2.240 1.00 0.00 H
HETATM 65 H LIG 1 3.315 5.492 6.533 1.00 0.00 H
HETATM 66 H LIG 1 4.431 4.561 7.584 1.00 0.00 H
HETATM 67 H LIG 1 2.898 3.803 7.049 1.00 0.00 H
HETATM 68 C LIG 1 -1.636 4.418 4.750 1.00 0.00 C
HETATM 69 C LIG 1 -2.232 5.057 5.855 1.00 0.00 C
HETATM 70 C LIG 1 -1.685 6.253 6.329 1.00 0.00 C
HETATM 71 C LIG 1 -0.594 6.836 5.705 1.00 0.00 C
HETATM 72 C LIG 1 0.008 6.242 4.581 1.00 0.00 C
HETATM 73 H LIG 1 -2.038 3.477 4.395 1.00 0.00 H
HETATM 74 C LIG 1 -3.451 4.513 6.512 1.00 0.00 C
HETATM 75 H LIG 1 -2.125 6.763 7.177 1.00 0.00 H
HETATM 76 H LIG 1 -0.253 7.779 6.099 1.00 0.00 H
HETATM 77 C LIG 1 1.134 6.976 3.886 1.00 0.00 C
HETATM 78 O LIG 1 1.472 6.651 2.760 1.00 0.00 O
HETATM 79 O LIG 1 1.765 8.032 4.452 1.00 0.00 O
HETATM 80 H LIG 1 1.616 8.338 5.353 1.00 0.00 H
HETATM 81 O LIG 1 -3.939 5.126 7.450 1.00 0.00 O
HETATM 82 O LIG 1 -4.098 3.438 5.979 1.00 0.00 O
HETATM 83 N LIG 1 -5.268 2.966 6.406 1.00 0.00 N
HETATM 84 C LIG 1 -6.192 2.486 5.575 1.00 0.00 C
HETATM 85 C LIG 1 -5.710 2.891 7.675 1.00 0.00 C
HETATM 86 O LIG 1 -5.047 3.211 8.649 1.00 0.00 O
HETATM 87 C LIG 1 -7.100 2.339 7.770 1.00 0.00 C
HETATM 88 C LIG 1 -7.441 2.046 6.278 1.00 0.00 C
HETATM 89 H LIG 1 -7.617 0.963 6.107 1.00 0.00 H
HETATM 90 H LIG 1 -8.307 2.651 5.933 1.00 0.00 H
HETATM 91 H LIG 1 -7.781 3.103 8.204 1.00 0.00 H
HETATM 92 H LIG 1 -7.110 1.409 8.375 1.00 0.00 H
HETATM 93 O LIG 1 -6.033 2.434 4.365 1.00 0.00 O
END
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)