Difference between revisions of "Rotkit"
(3 intermediate revisions by the same user not shown) | |||
Line 2: | Line 2: | ||
|type = script | |type = script | ||
|filename = rotkit.py | |filename = rotkit.py | ||
− | |author = Troels E. Linnet | + | |author = [[User:Tlinnet|Troels E. Linnet]] |
− | |license = | + | |license = BSD |
}} | }} | ||
Line 55: | Line 55: | ||
</gallery> | </gallery> | ||
− | = Example of use = | + | == Example of use == |
− | == Example 1 - Make a rotation of domain == | + | === Example 1 - Make a rotation of domain === |
{{Template:PymolScriptRepoDownload|examples/rotkit_1.pml}} | {{Template:PymolScriptRepoDownload|examples/rotkit_1.pml}} | ||
<include src="https://raw.github.com/Pymol-Scripts/Pymol-script-repo/master/examples/rotkit_1.pml" highlight="python" /> | <include src="https://raw.github.com/Pymol-Scripts/Pymol-script-repo/master/examples/rotkit_1.pml" highlight="python" /> | ||
Line 67: | Line 67: | ||
{{Template:PymolScriptRepoDownload|examples/rotkit_3.pml}} | {{Template:PymolScriptRepoDownload|examples/rotkit_3.pml}} | ||
<include src="https://raw.github.com/Pymol-Scripts/Pymol-script-repo/master/examples/rotkit_3.pml" highlight="python" /> | <include src="https://raw.github.com/Pymol-Scripts/Pymol-script-repo/master/examples/rotkit_3.pml" highlight="python" /> | ||
− | |||
=== Example 4 - A tutorial file === | === Example 4 - A tutorial file === | ||
Line 75: | Line 74: | ||
{{Template:PymolScriptRepoDownload|examples/rotkit_4.pml}} | {{Template:PymolScriptRepoDownload|examples/rotkit_4.pml}} | ||
<include src="https://raw.github.com/Pymol-Scripts/Pymol-script-repo/master/examples/rotkit_4.pml" highlight="python" /> | <include src="https://raw.github.com/Pymol-Scripts/Pymol-script-repo/master/examples/rotkit_4.pml" highlight="python" /> | ||
− | |||
[[Category:Script_Library]] | [[Category:Script_Library]] | ||
[[Category:ObjSel_Scripts]] | [[Category:ObjSel_Scripts]] | ||
+ | [[Category:Pymol-script-repo]] |
Latest revision as of 11:05, 15 January 2012
Type | Python Script |
---|---|
Download | rotkit.py |
Author(s) | Troels E. Linnet |
License | BSD |
This code has been put under version control in the project Pymol-script-repo |
Introduction
This script-kit is a collection of small script to be able to precisely to put a molecule (like a dye) where you want in relation to a protein.
You can also create rotational states of a domain or simulate a dye freedom.
It simply makes the PyMOL TTT matrixes, in a easy and user friendly way. The calls to the functions available in PyMOL, takes care of all the conversion of input and such.
If you are interested in this, you might also want to check out the PyMOL Chempy module that is included in PyMOL. It provides handy vector and matrix functions.
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.
Example of use
Example 1 - Make a rotation of domain
Download: examples/rotkit_1.pml | |
This code has been put under version control in the project Pymol-script-repo |
reinitialize import rotkit fetch 1HP1, async=0 show_as cartoon, 1HP1 show_as sticks, 1HP1 and resn ATP ###################### Make rotation axis ################# pseudoatom axisA, vdw=1.0 pseudoatom axisB, vdw=1.0 rotkit.toline("/1HP1//A/477/C","/1HP1//A/423/CG1","axisA","axisA",20) rotkit.toline("/1HP1//A/423/CG1","/1HP1//A/477/C","axisB","axisB",5) show spheres, axisA or axisB label axisA, "axisA" label axisB, "axisB" dist rotaxis, axisA, axisB color green, rotaxis set dash_width, 5 set dash_gap, 0 hide label, rotaxis ## Create rotate states of 1HP1 create 1HP1_rot, 1HP1, 1, 1 python ang_incr = 1 anglerange = range(2,98,ang_incr) nrstates = len(anglerange)+1 states = 1 for angle in anglerange: states += 1 rot_1HP1 = "1HP1_rot_%s"%angle cmd.create(rot_1HP1,"(1HP1 and resi 363-550) or (1HP1 and resn ATP)") rotkit.rotateline("axisA","axisB",-(angle-1),rot_1HP1) cmd.create("1HP1_rot",rot_1HP1,1,states) cmd.create("1HP1_rot",rot_1HP1,1,2*nrstates-states) cmd.delete(rot_1HP1) python end hide cartoon, (1HP1 and resi 363-550) hide sticks, (1HP1 and resn ATP) mplay
Example 2 - Simulate dye freedom
Download: examples/rotkit_2.pml | |
This code has been put under version control in the project Pymol-script-repo |
reinitialize import rotkit fetch 1HP1, async=0 show_as cartoon, 1HP1 show_as sticks, 1HP1 and resn ATP set auto_zoom, off ###################### Make rotation axis ################# pseudoatom axisA, vdw=1.0 pseudoatom axisB, vdw=1.0 rotkit.toline("/1HP1//A/477/C","/1HP1//A/423/CG1","axisA","axisA",20) rotkit.toline("/1HP1//A/423/CG1","/1HP1//A/477/C","axisB","axisB",5) show spheres, axisA or axisB label axisA, "axisA" label axisB, "axisB" dist rotaxis, axisA, axisB color green, rotaxis set dash_width, 5 set dash_gap, 0 hide label, rotaxis ####################### Create rotate states of dye atoms ################### ##### First mutate, the mutate functions take 0.2 seconds, so we put in a refesh command to wait for everything is done rotkit.mutate("1HP1", chain="A", resi=308, target="CYS", mutframe=1) cmd.refresh() rotkit.mutate("1HP1", chain="A", resi=513, target="CYS", mutframe=1) cmd.refresh() ##### Create simulated dye movement atoms pseudoatom Donor, vdw=0.5 pseudoatom Acceptor, vdw=0.5 show spheres, Donor or Acceptor rotkit.toline("1HP1 and resi 308 and name CA","1HP1 and resi 308 and name SG","Donor","Donor",15.0) rotkit.toline("1HP1 and resi 513 and name CA","1HP1 and resi 513 and name SG","Acceptor","Acceptor",15.0) python Dye_ang_incr = 6 Donor_angle_range = range(0,359,Dye_ang_incr) Acceptor_angle_range = range(0,359,Dye_ang_incr) nrstates = len(Donor_angle_range)+1 Donor_states = 1 Acceptor_states = 1 for Donor_angle in Donor_angle_range: Donor_states += 1 Donor_angle_name="Donor_%s"%(Donor_angle) cmd.create(Donor_angle_name,"Donor") rotkit.rotateline("1HP1 and resi 308 and name CA","1HP1 and resi 308 and name CB",Donor_angle,Donor_angle_name) # Save it as states in Donor cmd.create("Donor",Donor_angle_name,1,Donor_states) cmd.create("Donor",Donor_angle_name,1,2*nrstates-Donor_states) cmd.group("All_Donors",Donor_angle_name) for Acceptor_angle in Acceptor_angle_range: Acceptor_states += 1 Acceptor_angle_name="Acceptor_%s"%(Acceptor_angle) cmd.create(Acceptor_angle_name,"Acceptor") rotkit.rotateline("1HP1 and resi 513 and name CA","1HP1 and resi 513 and name CB",Acceptor_angle,Acceptor_angle_name) # Save it as states in Acceptor cmd.create("Acceptor",Acceptor_angle_name,1,Acceptor_states) cmd.create("Acceptor",Acceptor_angle_name,1,2*nrstates-Acceptor_states) cmd.group("All_Acceptors",Acceptor_angle_name) python end disable All_Donors disable All_Acceptors cmd.create("Donor","All_Donors",1,1) cmd.create("Acceptor","All_Acceptors",1,1) mplay
Example 3 - Create distance distribution histogram
Download: examples/rotkit_3.pml | |
This code has been put under version control in the project Pymol-script-repo |
reinitialize import rotkit fetch 1HP1, async=0 show_as cartoon, 1HP1 show_as sticks, 1HP1 and resn ATP set auto_zoom, off ####################### Create rotate states of dye atoms ################### ##### First mutate, the mutate functions take 0.2 seconds, so we put in a refesh command to wait for everything is done rotkit.mutate("1HP1", chain="A", resi=308, target="CYS", mutframe=1) cmd.refresh() rotkit.mutate("1HP1", chain="A", resi=513, target="CYS", mutframe=1) cmd.refresh() ##### Create simulated dye movement atoms pseudoatom Donor, vdw=0.5 pseudoatom Acceptor, vdw=0.5 show spheres, Donor or Acceptor rotkit.toline("1HP1 and resi 308 and name CA","1HP1 and resi 308 and name SG","Donor","Donor",15.0) rotkit.toline("1HP1 and resi 513 and name CA","1HP1 and resi 513 and name SG","Acceptor","Acceptor",15.0) python Dye_ang_incr = 6 Donor_angle_range = range(0,359,Dye_ang_incr) Acceptor_angle_range = range(0,359,Dye_ang_incr) Donor_names = [] Acceptor_names = [] for Donor_angle in Donor_angle_range: Donor_angle_name="Donor_%s"%(Donor_angle) Donor_names.append([Donor_angle,Donor_angle_name]) cmd.create(Donor_angle_name,"Donor") rotkit.rotateline("1HP1 and resi 308 and name CA","1HP1 and resi 308 and name CB",Donor_angle,Donor_angle_name) cmd.group("All_Donors",Donor_angle_name) for Acceptor_angle in Acceptor_angle_range: Acceptor_angle_name="Acceptor_%s"%(Acceptor_angle) Acceptor_names.append([Acceptor_angle,Acceptor_angle_name]) cmd.create(Acceptor_angle_name,"Acceptor") rotkit.rotateline("1HP1 and resi 513 and name CA","1HP1 and resi 513 and name CB",Acceptor_angle,Acceptor_angle_name) cmd.group("All_Acceptors",Acceptor_angle_name) python end disable All_Donors disable All_Acceptors cmd.create("Donor","All_Donors") cmd.create("Acceptor","All_Acceptors") cmd.refresh() # Make a distribution for the Open case Don_Acc_distribution = [] python for Don in Donor_names: for Acc in Acceptor_names: distname = "%s_%s"%(Don[1],Acc[1]) distance = cmd.dist(distname,Don[1],Acc[1]) Don_Acc_distribution.append([Don[0], Acc[1], distance]) cmd.delete(distname) python end Newdir=rotkit.createdirs("results_rotkit") os.chdir(Newdir) rotkit.makehistogram(Don_Acc_distribution,dataname="Don_Acc_Open",datalistindex=2,nrbins=100,binrange=[0,0]) # Make a distribution for angle range cmd.create("Acceptor_rot","All_Acceptors") python ang_incr = 1 anglerange = range(2,98,ang_incr) nrstates = len(anglerange)+1 states = 1 for angle in anglerange: states += 1 rot_Acceptor = "Acceptor_rot_%s"%angle cmd.create(rot_Acceptor,"Acceptor_rot") rotkit.rotateline("/1HP1//A/423/CG1","/1HP1//A/477/C",-(angle-1),rot_Acceptor) cmd.create("Acceptor_rot",rot_Acceptor,1,states) cmd.create("Acceptor_rot",rot_Acceptor,1,2*nrstates-states) cmd.delete(rot_Acceptor) for Acc in Acceptor_names: rotkit.rotateline("/1HP1//A/423/CG1","/1HP1//A/477/C",(angle-1),Acc[1]) python end mplay
Example 4 - A tutorial file
To understand how the functions works, read through the tutorial. Hash/Unhash "##" each step at the time to see the effect. To be able to follow the tutorial, you need the dye molecule, which is loaded from the Pymol-script-repository.
Download: examples/rotkit_4.pml | |
This code has been put under version control in the project Pymol-script-repo |
reinitialize import rotkit fetch 1HP1, async=0 python if 'PYMOL_GIT_MOD' in os.environ: example_dir = os.path.join(os.path.split(os.environ['PYMOL_GIT_MOD'])[0],"files_for_examples") cmd.load(os.path.join(example_dir,"Atto590.pdb")) else: cmd.load("Atto590.pdb") python end # Make sure everything is loaded before we continue cmd.refresh() ### 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" molselect13="%s and id 13"%molname molnameselect13="dyeatom13" molselect12="%s and id 12"%molname molnameselect12="dyeatom12" ### Make some selections cmd.select("%s"%protnameselectCB,"%s"%protselectCB) cmd.select("%s"%protnameselectCA,"%s"%protselectCA) cmd.select("%s"%molnameselect13,"%s"%molselect13) cmd.label("%s"%molnameselect13,"13") cmd.select("%s"%molnameselect12,"%s"%molselect12) cmd.label("%s"%molnameselect12,"12") ### 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 ### To print a objects TTT matrix in a readable format rotkit.printMat(cmd.get_object_matrix(molname)) ##### 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 diffvector = rotkit.vector("%s"%molselect13,"%s"%protnameselectCB) ##### Then move the dye move = rotkit.transmat(diffvector) ##### print the matrix for fun rotkit.printMat(move) ##### Move the dye cmd.transform_selection("%s"%molname,move) ##### Now we want to displace the dye in the CA-CB bond direction ##### 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) ##### 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 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) ##### We are not quite satisfied, we want to rotate it around its own bond ##### So we rotate in around its own 13 -> 12 bonds diffvector = rotkit.vector("%s"%molnameselect13,"%s"%molnameselect12) uvector = rotkit.unitvector(diffvector)[0] xyz12 = rotkit.getxyz("%s"%molnameselect12)[0] rmat = rotkit.rotmat(rotkit.radangle(10),uvector,xyz12) ##### Copy paste this line into pymol to see it manually cmd.transform_selection("%s"%molname,rmat) ##### 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 rotkit.rotateline("%s"%molnameselect13,"%s"%molnameselect12,180,"%s"%molname) ##### 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"%(molnameselect13, molnameselect12, 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) cmd.label("%s and id 12"%molanglename,"12") cmd.label("%s and id 13"%molanglename,"13") ### Rotate the copy rotkit.rotateline("%s"%protnameselectCB,"%s"%molnameselect13,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 rotkit.mutate(protname, chain="A", resi=513, target="CYS", mutframe=1) ##### The mutate functions take 0.2 seconds, so we put in a refesh command to wait for everything is done cmd.refresh() ##### 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 rotkit.toline(protnameselectCAcys,protnameselectCBcys,molnameselect13,molname,3) rotkit.rotateline(protnameselectCAcys,protnameselectCBcys,180,molname) rotkit.rotateline(molnameselect13,molnameselect12,10,molname) print("toline Pos1=%s, Pos2=%s, atom=%s, molecule=%s, dist=%s"%(protnameselectCAcys,protnameselectCBcys,molnameselect13,molname,3)) print("rotateline Pos1=%s, Pos2=%s, degangle=180, molecule=%s"%(protnameselectCAcys, protnameselectCBcys, molname)) print("rotateline Pos1=%s, Pos2=%s, degangle=10, molecule=%s"%(molnameselect13, molnameselect12, molname)) cmd.refresh() ####### End of PART II #### ####### Now we make a cross product #### molselect14="%s and id 14"%molname molnameselect14="dyeatom14" cmd.select("%s"%molnameselect14,"%s"%molselect14) cmd.label("%s"%molnameselect14,"14") cross = rotkit.crossprod(rotkit.vector(molselect13,molselect12),rotkit.vector(molselect13,molselect14)) unity_cross = rotkit.unitvector(cross)[0] point_cross = rotkit.crosspoint(molselect13,cross) rotkit.rotateline(molnameselect13,point_cross,180,molname) print("rotateline Pos1=%s, Pos2=%s, degangle=10, molecule=%s"%(molnameselect13, point_cross, molname))