Modevectors

DESCRIPTION

modevectors.py is a PyMol script that was originally written to visualize results obtained from Normal Mode Analysis (NMA). However, this script can be used to visualize the direction of motion between two specified states. The strength of this script is that the arrows are highly customizable with numerous options to choose from (see script below).

USAGE

load the script using the run command

modevectors first_obj_frame, last_obj_frame[, outname=modevectors[, head=1.0[,tail=0.3[, head_length=1.5[, headrgb=(1.0,1.0,1.0)[,tailrgb=(1.0,1.0,1.0)[,cutoff=4.0[,skip=0[,cut=0.5[,atom=CA[,stat=show[,factor=1.0]]]]]]]]]]]

Please see the script comments for further custom options. Once the script completes, it will generate a new object called "modevectors" (which can be changed through the options).

EXAMPLES

modevectors 1E3M, 1W7A
modevectors 1E3M, 1W7A, outname="arrows"
modevectors 1E3M, 1W7A, atom="P"

PYMOL API

from pymol.cgo import * # get constants from math import * from pymol import cmd

def modevectors( first_obj_frame, last_obj_frame, outname="modevectors", head=1.0,tail=0.3, head_length=1.5, headrgb="1.0,1.0,1.0",tailrgb="1.0,1.0,1.0",cutoff=4.0,skip=0,cut=0.5,atom="CA",stat="show",factor=1.0): """ Authors Sean Law & Srinivasa Michigan State University slaw@msu.edu

Editor Sacha Yee

USAGE

While in PyMOL

load modevectors.py

modevectors( first_obj_frame, last_obj_frame, outname=modevectors, head=1.0,tail=0.3, head_length=1.5, headrgb=(1.0,1.0,1.0),tailrgb=(1.0,1.0,1.0),cutoff=4.0,skip=0,cut=0.5,atom=CA,stat=show,factor=1.0)

Parameter Preset Type Description first_obj_frame Undefined String Object name of the first structure. The mode vector will propagate from this structure. Defined by user. last_obj_frame Undefined String Object name of the last structure. The mode vector (arrow head) will end at this structure. Defined by user. outname modevectors String Name of object to store mode vectors in. head 1.0 Float Radius for the circular base of the arrow head (cone) tail 0.3 Float Radius for the cylinder of the arrow tail (cylinder) head_length 1.5 Float Length of the arrow head (from the base of the cone to the tip of cone) head_rgb 1.0,1.0,1.0 String RGB colour for the arrow head. tail_rgb 1.0,1.0,1.0 String RGB colour for the arrow tail. cutoff 4.0 Float Skips mode vectors that do not meet the cutoff distance (in Angstroms). skip 0 Integer Denotes how many atoms to skip. No arrows will be created for skipped atoms. cut 0.0 Float Truncates all arrow tail lengths (without disturbing the arrow head) (in Angstroms). atom CA String Designates the atom to derive mode vectors from. stat show String Keeps track and prints statistics (total modevectors, skipped, cutoff). factor 1.0 Float Multiplies each mode vector length by a specified factor. Values between 0 and 1 will decrease the relative mode vector length. Values greater than 1 will increase the relative mode vector length.

"""

framefirst=cmd.get_model(first_obj_frame) framelast=cmd.get_model(last_obj_frame) objectname=outname factor=float(factor) arrow_head_radius=float(head) arrow_tail_radius=float(tail) arrow_head_length=float(head_length) cutoff=float(cutoff) skip=int(skip) cut=float(cut) atomtype=atom.strip('"[]()')

headrgb=headrgb.strip('" []()') tailrgb=tailrgb.strip('" []()') hr,hg,hb=map(float,headrgb.split(',')) tr,tg,tb=map(float,tailrgb.split(','))

pi=4*atan2(1,1) arrow=[] arrowhead = [] arrowtail = [] x1 = [] y1 = [] z1 = [] x2 = [] y2 = [] z2 = [] exit_flag=0

2. #
3. Define an object called "tail" and store the tail and a #
4. circular base of the triangle in this object. #
5. #

       skipcount=0

skipcounter=0 keepcounter=0 atom_lookup={} for atom in framefirst.atom: if atom.name == atomtype: if skipcount == skip: x1.append(atom.coord[0]) y1.append(atom.coord[1]) z1.append(atom.coord[2])

########################################## # # # Set atom_lookup for a specific atom # # equal to ONE for the first input set. # # This dictionary will be used as a # # reference for the second set. # # # ##########################################

current_atom="CHAIN "+atom.chain+" RESID "\ +atom.resi+" RESTYPE "\ +atom.resn+\ " ATMNUM "+str(atom.index)

1. print current_atom

atom_lookup['current_atom']=1

skipcount=0 keepcounter=keepcounter+1 else:

1. print skipcount

skipcount=skipcount+1 skipcounter=skipcounter+1

       skipcount=0

for atom in framelast.atom: if atom.name == atomtype: if skipcount == skip: x2.append(atom.coord[0]) y2.append(atom.coord[1]) z2.append(atom.coord[2])

######################################### # # # Get atom information from second set # # and compare with first set. All # # atoms from this second set MUST be # # found in the first set! Otherwise, # # the script will exit with an error # # since modevectors can only be created # # by calculating values from identical # # sources. # # # #########################################

current_atom="CHAIN "+atom.chain+" RESID "\ +atom.resi+" RESTYPE "\ +atom.resn+\ " ATMNUM "+str(atom.index)

1. print current_atom

if atom_lookup.has_key('current_atom') != 1: print "\nError: "+current_atom+" from \""\ +last_obj_frame+\ " \"is not found in \""+first_obj_frame+"\"." print "\nPlease check your input and/or selections and try again." exit_flag=1 break

skipcount=0 else: skipcount=skipcount+1

if exit_flag == 1: ########################################### # # # Exit script because an atom cannot be # # found in both input files # # # ########################################### return

cutoff_counter=0 # Track number of atoms failing to meet the cutoff

################################################### # # # Check that the two selections/PDB files contain # # the same number of atoms. # # # ###################################################

if len(x2) != len(x1): print "\nError: \""+first_obj_frame+\ "\" and \""+last_obj_frame+\ "\" contain different number of residue/atoms." print "\nPlease check your input and/or selections and try again." return else: #Continue with representing modevectors! ######################################### # # # Delete old selection or object if it # # exists so that it can be overwritten # # # ######################################### save_view=cmd.get_view(output=1,quiet=1) cmd.delete(name=outname) cmd.hide(representation="everything",selection=first_obj_frame) cmd.hide(representation="everything",selection=last_obj_frame)

################################################### # # # Begin drawing arrow tails # # # ###################################################

arrowtail = [] for mv in range(len(x1)): vectorx=x2[mv]-x1[mv] vectory=y2[mv]-y1[mv] vectorz=z2[mv]-z1[mv] length=sqrt(vectorx**2+vectory**2+vectorz**2) if length < cutoff: cutoff_counter=cutoff_counter+1 continue t=1.0-(cut/length) x2[mv]=x1[mv]+factor*t*vectorx y2[mv]=y1[mv]+factor*t*vectory z2[mv]=z1[mv]+factor*t*vectorz vectorx=x2[mv]-x1[mv] vectory=y2[mv]-y1[mv] vectorz=z2[mv]-z1[mv] length=sqrt(vectorx**2+vectory**2+vectorz**2) d=arrow_head_length # Distance from arrow tip to arrow base t=1.0-(d/length) tail = [ # Tail of cylinder CYLINDER, x1[mv],y1[mv],z1[mv]\ ,x1[mv]+(t+0.01)*vectorx,y1[mv]+(t+0.01)*vectory,z1[mv]+(t+0.01)*vectorz\ ,arrow_tail_radius,tr,tg,tb,tr,tg,tb # Radius and RGB for each cylinder tail ] arrow.extend(tail)

x=x1[mv]+t*vectorx y=y1[mv]+t*vectory z=z1[mv]+t*vectorz dx=x2[mv]-x dy=y2[mv]-y dz=z2[mv]-z seg=d/100 intfactor=int(factor) for i in range (100,0,-1): t1=seg*i t2=seg*(i+1) radius=arrow_head_radius*(1.0-i/(100.0)) #Radius of each disc that forms cone head=[ CYLINDER, x+t2*dx,y+t2*dy,z+t2*dz\ ,x+t1*dx,y+t1*dy,z+t1*dz\ ,radius,hr,hg,hb,hr,hg,hb # Radius and RGB for slice of arrow head ] arrow.extend(head)

2. #
3. Load the entire object into PyMOL #
4. #
5. Print statistics if requested by user #
6. #

if stat == "show": natoms=skipcounter+keepcounter print "\nTotal number of atoms = "+str(natoms) print "Atoms skipped = "+str(skipcounter) if keepcounter-cutoff_counter > 0: print "Atoms counted = "+str(keepcounter-cutoff_counter)+" (see PyMOL object \""+outname+"\")" else: print "Atoms counted = "+str(keepcounter-cutoff_counter)+" (Empty CGO object not loaded)" print "Atoms cutoff = "+str(cutoff_counter) #Note that cutoff occurs AFTER skipping! if keepcounter-cutoff_counter > 0: cmd.load_cgo(arrow,objectname) #Ray tracing an empty object will cause a segmentation fault. No arrows = Do not display in PyMOL!!! cmd.show(representation="cartoon",selection=first_obj_frame) cmd.cartoon("tube") cmd.show(representation="cartoon",selection=last_obj_frame) cmd.hide(representation="cartoon",selection=last_obj_frame) cmd.bg_color(color="white") cmd.set_view(save_view) return

cmd.extend("modevectors",modevectors)