def rmsUpdateB(objA, alnAri, objB, alnBri):
for x in range(len(alnAri)):
s1 = objA + " and n. CA and i. " + alnAri[x]
s2 = objB + " and n. CA and i. " + alnBri[x]
rmsd = cmd.rms_cur(s1, s2, matchmaker=4)
cmd.alter( s1, "b = " + str(rmsd))
cmd.alter( s2, "b = " + str(rmsd))
cmd.sort(objA); cmd.sort(objB)
def rmsUpdateB(objA, alnAri, objB, alnBri):
for x in range(len(alnAri)):
s1 = objA + " and n. CA and i. " + alnAri[x]
s2 = objB + " and n. CA and i. " + alnBri[x]
rmsd = cmd.rms_cur(s1, s2, matchmaker=4)
cmd.alter( s1, "b = " + str(rmsd))
cmd.alter( s2, "b = " + str(rmsd))
cmd.sort(objA); cmd.sort(objB)
def b2vdw(*arg,**kw):
_self = kw.get('_self',cmd)
pymol=_self._pymol
cmd=_self
if not len(arg):
sele = 'all'
else:
sele = arg[0]
# use B values to create RMS VDW spheres
# rms = sqrt(b/(8*(PI^2)))
cmd.alter("(%s)"%sele,"vdw=math.sqrt(b/78.9568352087)")
def ff_copy(src,dst,_self=cmd):
pymol=_self._pymol
cmd=_self # NOT THREAD SAFE
pymol._rcopy = pymol.Scratch_Storage()
pymol._rcopy.pc={}
pymol._rcopy.tt={}
cmd.iterate("(%s)"%src,"_rcopy.pc[name]=partial_charge")
cmd.alter("(%s)"%dst,"partial_charge=_rcopy.pc[name]")
cmd.iterate("(%s)"%src,"_rcopy.tt[name]=text_type")
cmd.alter("(%s)"%dst,"text_type=_rcopy.tt[name]")
del pymol._rcopy
def protein_assign_charges_and_radii(obj_name,_self=cmd):
pymol=_self._pymol
cmd=_self
from chempy.champ import assign
# apply a few kludges
# convent Seleno-methionine to methionine
cmd.alter(obj_name+"///MSE/SE","elem='S';name='SD'",quiet=1)
cmd.alter(obj_name+"///MSE/","resn='MET'",quiet=1)
cmd.flag("ignore",obj_name,"clear")
# remove alternate conformers
cmd.remove(obj_name+" and not alt ''+A")
cmd.alter(obj_name,"alt=''")
cmd.sort(obj_name)
cmd.fix_chemistry(obj_name,obj_name,1)
# make sure all atoms are included...
cmd.alter(obj_name,"q=1.0",quiet=1)
print " Util: Fixing termini and assigning formal charges..."
assign.missing_c_termini(obj_name,quiet=1,_self=_self)
while not assign.formal_charges(obj_name,quiet=1,_self=_self):
print " WARNING: unrecognized or incomplete residues are being deleted:"
cmd.iterate("(byres ("+obj_name+" and flag 23)) and flag 31",
'print " "+model+"/"+segi+"/"+chain+"/"+resn+"`"+resi+"/"',quiet=1)
cmd.remove("byres ("+obj_name+" and flag 23)") # get rid of residues that weren't assigned
assign.missing_c_termini(obj_name,quiet=1,_self=_self)
print " Util: Assigning Amber 99 charges and radii..."
cmd.h_add(obj_name)
if not assign.amber99(obj_name,quiet=1,_self=_self):
print " WARNING: some unassigned atoms are being deleted:"
cmd.iterate("byres ("+obj_name+" and flag 23)",
'print " "+model+"/"+segi+"/"+chain+"/"+resn+"`"+resi+"/"+name+"? ["+elem+"]"',quiet=1)
cmd.remove(obj_name+" and flag 23") # get rid of any atoms that weren't assigned
# show the user what the net charges are...
formal = sum_formal_charges(obj_name,quiet=0,_self=_self)
partial = sum_partial_charges(obj_name,quiet=0,_self=_self)
if round(formal)!=round(partial):
print " WARNING: formal and partial charge sums don't match -- there is a problem!"
def displacementUpdateB(objA, alnAri, objB, alnBri):
### If residue is unassigned in one of the pdb files, we reset its value
for x in range(len(alnAri)):
s1 = objA + " and name CA and resi " + alnAri[x]
cmd.alter( s1, "b = " + str(-0.01))
for x in range(len(alnBri)):
s2 = objB + " and name CA and resi " + alnBri[x]
cmd.alter( s2, "b = " + str(-0.01))
cmd.sort(objA); cmd.sort(objB)
for x in range(len(alnAri)):
s1 = objA + " and name CA and resi " + alnAri[x]
s2 = objB + " and name CA and resi " + alnAri[x]
### Names starting with __ (underscores) are normally hidden by PyMOL
tempObject = "__tempObject"
Displacement = cmd.distance(tempObject, s1, s2)
cmd.alter( s1, "b = " + str(Displacement))
cmd.alter( s2, "b = " + str(Displacement))
cmd.delete(tempObject)
cmd.sort(objA); cmd.sort(objB)
def displacementUpdateBAll(objA, alnAri, objB, alnBri):
print "This will take a while to go through the for loops. Give me around 3-5 minutes..."
### If residue is unassigned in one of the pdb files, we reset its value
for x in range(len(alnAri)):
s1 = objA + " and resi " + alnAri[x][0] + " and name " + str(alnAri[x][1])
cmd.alter( s1, "b = " + str(-0.01))
for x in range(len(alnBri)):
s2 = objB + " and resi " + alnBri[x][0] + " and name " + alnBri[x][1]
cmd.alter( s2, "b = " + str(-0.01))
cmd.sort(objA); cmd.sort(objB)
for x in range(len(alnAri)):
s1 = objA + " and resi " + alnAri[x][0] + " and name " + alnAri[x][1]
s2 = objB + " and resi " + alnAri[x][0] + " and name " + alnAri[x][1]
### Names starting with __ (underscores) are normally hidden by PyMOL
tempObject = "__tempObject"
Displacement = cmd.distance(tempObject, s1, s2)
cmd.alter( s1, "b = " + str(Displacement))
cmd.alter( s2, "b = " + str(Displacement))
cmd.delete(tempObject)
cmd.sort(objA); cmd.sort(objB)
def ss(selection="(name ca and alt '',A)",state=1,_self=cmd):
pymol=_self._pymol
cmd=_self # NOT THREAD SAFE
print ' util.ss: WARNING: This is not a "correct" secondary structure'
print ' util.ss: assignment algorithm! Please use only as a last resort.'
cmd.feedback("push")
cmd.feedback("disable","executive","actions")
ss_pref = "_sss"
sss1 = ss_pref+"1"
cnt = cmd.select(sss1,"((byres ("+selection+")) and name ca and not het)")
print " util.ss: initiating secondary structure assignment on %d residues."%cnt
cas = cmd.index(sss1)
if not len(cas):
return
# set cartoon mode to auto over the selection
cmd.cartoon("auto",sss1)
print " util.ss: extracting sequence and relationships..."
# get CA list
res_list = []
pymol._ss = pymol.Scratch_Storage()
pymol._ss.res_list = res_list
cmd.iterate(sss1,'_ss.res_list.append((model,index))')
# generate atom-to-residue conversion dictionaries
ca_dict = {}
n_dict = {}
o_dict = {}
scr_dict = {} # scr = segment,chain,resi
pymol._ss.n_dict = n_dict
pymol._ss.o_dict = o_dict
pymol._ss.scr_dict = scr_dict
pymol._ss.ca_dict = ca_dict
cmd.iterate(sss1,
'_ss.scr_dict[(model,index)]=(segi,chain,resi)') # CA's
cmd.iterate("((byres "+sss1+") and n;n)"
,'_ss.scr_dict[(model,index)]=(segi,chain,resi)') # N's
cmd.iterate("((byres "+sss1+") and n;o)",
'_ss.scr_dict[(model,index)]=(segi,chain,resi)') # O's
cmd.iterate(sss1,
'_ss.ca_dict[(segi,chain,resi)] = (model,index)')
cmd.iterate("((byres "+sss1+") and n;n)",
'_ss.n_dict[(segi,chain,resi)] = (model,index)')
cmd.iterate("((byres "+sss1+") and n;o)",
'_ss.o_dict[(segi,chain,resi)] = (model,index)')
scr_dict[None]=None
o_dict[None]=None
n_dict[None]=None
ca_dict[None]=None
# create special version of cas with gaps
gap = [None,None,None,None]
# gap large enough to distinguish i+4 interations from gaps
last = None
for a in res_list:
if last!=None:
if(cmd.count_atoms(
"((neighbor(neighbor(neighbor (%s`%d)))) and (%s`%d))"%
(last[0],last[1],a[0],a[1]),quiet=1)==0):
gap.extend([None,None,None,None])
gap.append(a)
last = a
gap.extend([None,None,None,None])
print " util.ss: analyzing phi/psi angles (slow)..."
# generate reverse-lookup for gap indices
ss = {}
c = 0
gap_idx = {}
for a in gap:
gap_idx[a] = c
c = c + 1
# secondary structure database...
ss = {}
ss[None]=None
# make decisions based on phi/psi
for a in cas:
ss[a] = 'L' # default
phipsi = cmd.get_phipsi(sss1,state)
for a in phipsi.keys():
(phi,psi) = phipsi[a]
# print scr_dict[a],(phi,psi)
if (phi!=None) and (psi!=None):
if ((phi<-45) and (phi>-160) and
(psi<-170) or (psi>10)): # beta?
ss[a] = 's'
elif ((phi<-45) and (phi>-160) and
(psi>-80) and (psi<-25)): # helix?
ss[a] = 'H'
print " util.ss: finding hydrogen bonds..."
# find all pairwise hydrogen bonds and make note of them in dict
hb = cmd.find_pairs("((byres "+sss1+") and n;n)",
"((byres "+sss1+") and n;o)",mode=1,
cutoff=3.7,angle=55,
state1=state,state2=state)
hb_dict = {} # [((N-atom) (O-atom))] = 1
n_hb_dict = {} # [(N-atom)] = [(O-atom),...]
o_hb_dict = {} # [(O-atom)] = [(N-atom),...]
for a in hb:
# cmd.dist("(%s`%d)"%a[0],"(%s`%d)"%a[1])
hb_dict[a] = 1
n = a[0]
o = a[1]
if not n_hb_dict.has_key(n): n_hb_dict[n]=[]
if not o_hb_dict.has_key(o): o_hb_dict[o]=[]
n_hb_dict[n].append(o)
o_hb_dict[o].append(n)
# check to insure that all helical residues have at least an i +/- 4
# hydrogen bond
for c in xrange(4,len(gap)-4):
a = gap[c]
if ss[a]=='H':
aN = n_dict[scr_dict[a]]
aO = o_dict[scr_dict[a]]
am4O = o_dict[scr_dict[gap[c-4]]]
ap4N = n_dict[scr_dict[gap[c+4]]]
if not hb_dict.has_key((aN,am4O)):
if not hb_dict.has_key((ap4N,aO)):
ss[a]='L'
print " util.ss: verifying beta sheets..."
# check to insure that all beta residues have proper interactions
rep_dict = {}
repeat = 1
while repeat:
repeat = 0
c = 4
cc = len(gap)-4
while c<cc:
a1 = gap[c]
if (ss[a1] in ['s','S']) and not rep_dict.has_key(a1):
rep_dict[a1] = 1
valid = 0
scr_a1 = scr_dict[a1]
# look for antiparallel 2:2 H-bonds (NH-O=C + C=O-HN)
n_a1_atom = n_dict[scr_a1]
o_a1_atom = o_dict[scr_a1]
if (n_hb_dict.has_key(n_a1_atom) and
o_hb_dict.has_key(o_a1_atom)):
for n_hb_atom in n_hb_dict[n_a1_atom]:
for o_hb_atom in o_hb_dict[o_a1_atom]:
n_hb_scr = scr_dict[n_hb_atom]
o_hb_scr = scr_dict[o_hb_atom]
if o_hb_scr == n_hb_scr:
b1 = ca_dict[o_hb_scr]
if abs(c-gap_idx[b1])>2:
ss[b1] = 'S'
ss[a1] = 'S'
valid = 1
# look for antiparallel offset HB (i,i+2,j,j-2)
a3 = gap[c+2]
if (a3!=None):
scr_a3 = scr_dict[a3]
o_a1_atom = o_dict[scr_a1]
n_a3_atom = n_dict[scr_a3]
if (n_hb_dict.has_key(n_a3_atom) and
o_hb_dict.has_key(o_a1_atom)):
for n_hb_atom in n_hb_dict[n_a3_atom]:
for o_hb_atom in o_hb_dict[o_a1_atom]:
n_hb_scr = scr_dict[n_hb_atom]
o_hb_scr = scr_dict[o_hb_atom]
b1 = ca_dict[o_hb_scr]
if b1!=None:
b1_i = gap_idx[b1]
if abs(c-b1_i)>2: # no turns!
b3 = gap[b1_i-2]
if b3!=None:
b3_scr = scr_dict[b3]
if b3_scr == n_hb_scr:
a2 = gap[c+1]
b2 = gap[gap_idx[b1]-1]
ss[b1] = 'S'
ss[b3] = 'S'
ss[a1] = 'S'
ss[a3] = 'S'
if ss[a2]=='L': ss[a2] = 's'
if ss[b2]=='L': ss[b2] = 's'
valid = 1
# look for antiparallel offset HB (i,i-2,j,j+2)
a3 = gap[c-2]
if (a3!=None):
scr_a3 = scr_dict[a3]
n_a1_atom = n_dict[scr_a1]
o_a3_atom = o_dict[scr_a3]
if (n_hb_dict.has_key(n_a1_atom) and
o_hb_dict.has_key(o_a3_atom)):
for n_hb_atom in n_hb_dict[n_a1_atom]:
for o_hb_atom in o_hb_dict[o_a3_atom]:
n_hb_scr = scr_dict[n_hb_atom]
o_hb_scr = scr_dict[o_hb_atom]
b1 = ca_dict[o_hb_scr]
if b1!=None:
b1_i = gap_idx[b1]
if abs(c-b1_i)>2: # no turns!
b3 = gap[b1_i-2]
if b3!=None:
b3_scr = scr_dict[b3]
if b3_scr == n_hb_scr:
a2 = gap[c-1]
b2 = gap[gap_idx[b1]-1]
ss[b1] = 'S'
ss[b3] = 'S'
ss[a1] = 'S'
ss[a3] = 'S'
if ss[a2]=='L': ss[a2] = 's'
if ss[b2]=='L': ss[b2] = 's'
valid = 1
# look for parallel 1:3 HB (i,j-1,j+1)
n_a1_atom = n_dict[scr_a1]
o_a1_atom = o_dict[scr_a1]
if (n_hb_dict.has_key(n_a1_atom) and
o_hb_dict.has_key(o_a1_atom)):
for n_hb_atom in n_hb_dict[n_a1_atom]:
for o_hb_atom in o_hb_dict[o_a1_atom]:
n_hb_scr = scr_dict[n_hb_atom]
o_hb_scr = scr_dict[o_hb_atom]
b0 = ca_dict[n_hb_scr]
if b0!=None:
b2 = gap[gap_idx[b0]+2]
if b2!=None:
b2_scr = scr_dict[b2]
if b2_scr == o_hb_scr:
b1 = gap[gap_idx[b0]+1]
ss[a1] = 'S'
ss[b0] = 'S'
if ss[b1]=='L': ss[b1]='s'
ss[b2] = 'S'
valid = 1
repeat = 1
if not valid:
ss[a1] = 'L'
c = c + 1
# automatically fill 1 residue gaps in helices and well-defined sheets
c = 4
cc = len(gap)-6
while c<cc:
a1 = gap[c]
a3 = gap[c+2]
ss_a1 = ss[a1]
ss_a3 = ss[a3]
if (ss_a1==ss_a3) and (ss_a1 in ['S','H']):
a2 = gap[c+1]
ss[a2] = ss_a1
c = c + 1
# remove singleton sheet residues
c = 4
cc = len(gap)-4
while c<cc:
a0 = gap[c-1]
a1 = gap[c]
a2 = gap[c+1]
if ss[a1] in ['s','S']:
if ((not ss[a0] in ['s','S']) and
(not ss[a2] in ['s','S'])):
ss[a1] = 'L'
c = c + 1
# remove sheet residues which aren't next to another sheet
c = 4
cc = len(gap)-4
while c<cc:
a1 = gap[c]
if ss[a1]=='S':
a1 = gap[c]
scr_a1 = scr_dict[a1]
# look for hydrogen bonds to another sheet
n_a1_atom = n_dict[scr_a1]
o_a1_atom = o_dict[scr_a1]
certain = 0
if n_hb_dict.has_key(n_a1_atom):
for n_hb_atom in n_hb_dict[n_a1_atom]:
n_hb_ca_atom=ca_dict[scr_dict[n_hb_atom]]
if ss[n_hb_ca_atom]=='S':
certain = 1
break
if o_hb_dict.has_key(o_a1_atom):
for o_hb_atom in o_hb_dict[o_a1_atom]:
o_hb_ca_atom=ca_dict[scr_dict[o_hb_atom]]
if ss[o_hb_ca_atom]=='S':
certain = 1
break
if not certain:
ss[a1] = 's'
c = c + 1
# remove questionable sheet residues
c = 4
cc = len(gap)-4
while c<cc:
a0 = gap[c-1]
a1 = gap[c]
a2 = gap[c+1]
if ss[a1]=='s':
if (not ((ss[a0]=='S') and (ss[a2]=='S'))):
ss[a1] = 'L'
c = c + 1
# extend helices if hydrogen bonding requirements are met
rep_dict = {}
repeat = 1
while repeat:
repeat = 0
c = 4
cc = len(gap)-4
while c<cc:
a = gap[c]
if not rep_dict.has_key(a):
if ss[gap[c+1]]=='H':
rep_dict[a] = 1
if ss[a]!='H': # N-terminal end
aO = o_dict[scr_dict[a]]
ap4N = n_dict[scr_dict[gap[c+4]]]
ap3N = n_dict[scr_dict[gap[c+3]]]
if hb_dict.has_key((ap4N,aO)) or hb_dict.has_key((ap3N,aO)):
ss[a]='H'
repeat = 1
c = c - 5
if c<4: c=4
if ss[gap[c-1]]=='H':
a = gap[c]
if ss[a]!='H': # C-terminal end
rep_dict[a] = 1
aN = n_dict[scr_dict[a]]
am4O = o_dict[scr_dict[gap[c-4]]]
am3O = o_dict[scr_dict[gap[c-3]]]
if hb_dict.has_key((aN,am4O)) or hb_dict.has_key((aN,am3O)):
ss[a]='H'
repeat = 1
c = c - 5
if c<4: c=4
c = c + 1
# remove doubleton helices
c = 4
cc = len(gap)-5
while c<cc:
a0 = gap[c-1]
a1 = gap[c]
a2 = gap[c+1]
a3 = gap[c+2]
ss_a0 = ss[gap[c-1]]
ss_a1 = ss[gap[c]]
ss_a2 = ss[gap[c+1]]
ss_a3 = ss[gap[c+2]]
if ss_a1=='H':
if (ss_a2==ss_a1) and (ss_a0!=ss_a2) and (ss_a2!=ss_a3):
ss[a1] = 'L'
ss[a2] = 'L'
c = c + 1
# remove totally unreasonable helix and sheet residues
c = 4
cc = len(gap)-5
while c<cc:
a1 = gap[c]
ss_a1 = ss[gap[c]]
if ss_a1=='H':
if phipsi.has_key(a1):
(phi,psi) = phipsi[a1]
if (phi>0) and (phi<150):
ss[a1] = 'L'
elif((psi<-120) or (psi>140)):
ss[a1] = 'L'
elif ss_a1 in ['S','s']:
if phipsi.has_key(a1):
(phi,psi) = phipsi[a1]
if (phi>45) and (phi<160):
ss[a1] = 'L'
# if (psi<-30) and (psi>-150):
if (psi<-65) and (psi>-150):
ss[a1] = 'L'
c = c + 1
for x in range(1,3):
# remove singleton sheet residues
c = 4
cc = len(gap)-4
while c<cc:
a0 = gap[c-1]
a1 = gap[c]
a2 = gap[c+1]
if ss[a1] in ['s','S']:
if ((not ss[a0] in ['s','S']) and
(not ss[a2] in ['s','S'])):
ss[a1] = 'L'
c = c + 1
# remove sheet residues which aren't next to another sheet
c = 4
cc = len(gap)-4
while c<cc:
a1 = gap[c]
if ss[a1]=='S':
a1 = gap[c]
scr_a1 = scr_dict[a1]
# look for hydrogen bonds to another sheet
n_a1_atom = n_dict[scr_a1]
o_a1_atom = o_dict[scr_a1]
certain = 0
if n_hb_dict.has_key(n_a1_atom):
for n_hb_atom in n_hb_dict[n_a1_atom]:
n_hb_ca_atom=ca_dict[scr_dict[n_hb_atom]]
if ss[n_hb_ca_atom]=='S':
certain = 1
break
if o_hb_dict.has_key(o_a1_atom):
for o_hb_atom in o_hb_dict[o_a1_atom]:
o_hb_ca_atom=ca_dict[scr_dict[o_hb_atom]]
if ss[o_hb_ca_atom]=='S':
certain = 1
break
if not certain:
ss[a1] = 's'
c = c + 1
# remove questionable sheet residues
c = 4
cc = len(gap)-4
while c<cc:
a0 = gap[c-1]
a1 = gap[c]
a2 = gap[c+1]
if ss[a1]=='s':
if (not ((ss[a0]=='S') and (ss[a2]=='S'))):
ss[a1] = 'L'
c = c + 1
# lst = ss.keys()
# lst.sort()
# for a in lst: print scr_dict[a],ss[a]
# assign protein
for a in cas:
if ss[a]=='s':
ss[a]='S'
cmd.alter(sss1,"ss ='L'")
for a in cas:
if ss[a]!='L':
cmd.alter("(%s`%d)"%a,"ss='%s'"%ss[a])
cmd.feedback("pop")
del pymol._ss # IMPORTANT
cmd.delete(sss1)
cmd.rebuild(selection,'cartoon')
#
# print conn_hash.keys()
print " util.ss: assignment complete."
def ColorByDisplacementCA(objSel1, objSel2, super1='all', super2='all', doColor="True", doAlign="True", AlignedWhite='yes'):
### First create backup copies; names starting with __ (underscores) are normally hidden by PyMOL
tObj1, tObj2, aln = "__tempObj1", "__tempObj2", "__aln"
if strTrue(doAlign):
### Create temp objects
cmd.create( tObj1, objSel1 )
cmd.create( tObj2, objSel2 )
### Align and make create an object aln which indicates which atoms were paired between the two structures
### Super is must faster than align http://www.pymolwiki.org/index.php/Super
cmd.super(tObj1 + ' and ' + str(super1), tObj2 + ' and ' + str(super2), object=aln)
### Modify the original matrix of object1 from the alignment
cmd.matrix_copy(tObj1, objSel1)
else:
### Create temp objects
cmd.create( tObj1, objSel1 )
cmd.create( tObj2, objSel2 )
### Align and make create an object aln which indicates which atoms were paired between the two structures
### Super is must faster than align http://www.pymolwiki.org/index.php/Super
cmd.super(tObj1 + ' and ' + str(super1), tObj2 + ' and ' + str(super2), object=aln)
### Modify the B-factor columns of the original objects,
### in order to identify the residues NOT used for alignment, later on
cmd.alter( objSel1 + " or " + objSel2, "b=-0.2")
cmd.alter( tObj1 + " or " + tObj2, "chain='A'")
cmd.alter( tObj1 + " or " + tObj2, "segi='A'")
### Update pymol internal representations; one of these should do the trick
cmd.refresh(); cmd.rebuild(); cmd.sort(tObj1); cmd.sort(tObj2)
### Create lists for storage
stored.alnAres, stored.alnBres = [], []
### Iterate over objects
if AlignedWhite=='yes':
cmd.iterate(tObj1 + " and n. CA and not " + aln, "stored.alnAres.append(resi)")
cmd.iterate(tObj2 + " and n. CA and not " + aln, "stored.alnBres.append(resi)")
else:
cmd.iterate(tObj1 + " and n. CA", "stored.alnAres.append(resi)")
cmd.iterate(tObj2 + " and n. CA", "stored.alnBres.append(resi)")
### Change the B-factors for EACH object
displacementUpdateB(tObj1,stored.alnAres,tObj2,stored.alnBres)
### Store the NEW B-factors
stored.alnAnb, stored.alnBnb = [], []
### Iterate over objects and get b
if AlignedWhite=='yes':
### Iterate over objects which is not aligned
cmd.iterate(tObj1 + " and n. CA and not " + aln, "stored.alnAnb.append(b)" )
cmd.iterate(tObj2 + " and n. CA and not " + aln, "stored.alnBnb.append(b)" )
else:
### Or Iterate over all objects with CA
cmd.iterate(tObj1 + " and n. CA", "stored.alnAnb.append(b)" )
cmd.iterate(tObj2 + " and n. CA", "stored.alnBnb.append(b)" )
### Get rid of all intermediate objects and clean up
cmd.delete(tObj1)
cmd.delete(tObj2)
cmd.delete(aln)
### Assign the just stored NEW B-factors to the original objects
for x in range(len(stored.alnAres)):
cmd.alter(objSel1 + " and n. CA and i. " + str(stored.alnAres[x]), "b = " + str(stored.alnAnb[x]))
for x in range(len(stored.alnBres)):
cmd.alter(objSel2 + " and n. CA and i. " + str(stored.alnBres[x]), "b = " + str(stored.alnBnb[x]))
cmd.rebuild(); cmd.refresh(); cmd.sort(objSel1); cmd.sort(objSel2)
### Provide some useful information
stored.allRMSDval = []
stored.allRMSDval = stored.alnAnb + stored.alnBnb
print "\nColorByDisplacementCA completed successfully."
print "The MAXIMUM Displacement is: "+str(max(stored.allRMSDval)) +" residue "+str(stored.alnAres[int(stored.allRMSDval.index(max(stored.allRMSDval)))])
if strTrue(doColor):
### Showcase what we did
#cmd.orient()
#cmd.hide("all")
cmd.show("cartoon", objSel1 + " or " + objSel2)
### Select the residues not used for alignment; they still have their B-factors as "-0.2"
cmd.select("notUsedForAln", "b = -0.2")
### White-wash the residues not used for alignment
cmd.color("white", "notUsedForAln")
### Select the residues not in both pdb files; they have their B-factors as "-0. 01"
cmd.select("ResNotInBothPDB", "b = -0.01")
### White-wash the residues not used for alignment
cmd.color("black", "ResNotInBothPDB")
### Color the residues used for alignment according to their B-factors (Displacment values)
# cmd.spectrum("b", 'rainbow', "((" + objSel1 + " and n. CA) or (n. CA and " + objSel2 +" )) and not notUsedForAln+ResNotInBothPDB")
cmd.spectrum("b", 'rainbow', "((" + objSel1 + " and n. CA) or (n. CA and " + objSel2 +" )) and not (notUsedForAln or ResNotInBothPDB)")
### Delete the selection of atoms not used for alignment
### If you would like to keep this selection intact,
### just comment "cmd.delete" line and
### uncomment the "cmd.disable" line abowe.
cmd.disable("notUsedForAln")
cmd.delete("notUsedForAln")
cmd.disable("ResNotInBothPDB")
cmd.delete("ResNotInBothPDB")
print "\nObjects are now colored by C-alpha displacement deviation."
print "Blue is minimum and red is maximum..."
print "White is those residues used in the alignment algorithm. Can be turned off in top of algorithm."
print "Black is residues that does not exist in both files..."
def colorByRMSD(objSel1, objSel2, doAlign="True", doPretty=None):
"""
colorByRMSD -- align two structures and show the structural deviations
in color to more easily see variable regions.
PARAMS
objSel1 (valid PyMOL object or selection)
The first object to align.
objSel2 (valid PyMOL object or selection)
The second object to align
doAlign (boolean, either True or False)
Should this script align your proteins or just leave them as is?
If doAlign=True then your original proteins are aligned.
If False, then they are not. Regardless, the B-factors are changed.
DEFAULT: True
doPretty (boolean, either True or False)
If doPretty=True then a simple representation is created to
highlight the differences. If False, then no changes are made.
DEFAULT: False
RETURNS
None.
SIDE-EFFECTS
Modifies the B-factor columns in your original structures.
"""
# First create backup copies; names starting with __ (underscores) are
# normally hidden by PyMOL
tObj1, tObj2, aln = "__tempObj1", "__tempObj2", "__aln"
if strTrue(doAlign):
# perform the alignment
cmd.create( tObj1, objSel1 )
cmd.create( tObj2, objSel2 )
cmd.super( tObj1, tObj2, object=aln )
cmd.matrix_copy(tObj1, objSel1)
else:
# perform the alignment
cmd.create( tObj1, objSel1 )
cmd.create( tObj2, objSel2 )
cmd.super( tObj1, tObj2, object=aln )
# Modify the B-factor columns of the original objects,
# in order to identify the residues NOT used for alignment, later on
cmd.alter( objSel1 + " or " + objSel2, "b=-10")
cmd.alter( tObj1 + " or " + tObj2, "chain='A'")
cmd.alter( tObj1 + " or " + tObj2, "segi='A'")
# Update pymol internal representations; one of these should do the trick
cmd.refresh(); cmd.rebuild(); cmd.sort(tObj1); cmd.sort(tObj2)
# Create lists for storage
stored.alnAres, stored.alnBres = [], []
# Get the residue identifiers from the alignment object "aln"
cmd.iterate(tObj1 + " and n. CA and " + aln, "stored.alnAres.append(resi)")
cmd.iterate(tObj2 + " and n. CA and " + aln, "stored.alnBres.append(resi)")
# Change the B-factors for EACH object
rmsUpdateB(tObj1,stored.alnAres,tObj2,stored.alnBres)
# Store the NEW B-factors
stored.alnAnb, stored.alnBnb = [], []
cmd.iterate(tObj1 + " and n. CA and " + aln, "stored.alnAnb.append(b)" )
cmd.iterate(tObj2 + " and n. CA and " + aln, "stored.alnBnb.append(b)" )
# Get rid of all intermediate objects and clean up
cmd.delete(tObj1)
cmd.delete(tObj2)
cmd.delete(aln)
# Assign the just stored NEW B-factors to the original objects
for x in range(len(stored.alnAres)):
cmd.alter(objSel1 + " and n. CA and i. " + str(stored.alnAres[x]), "b = " + str(stored.alnAnb[x]))
for x in range(len(stored.alnBres)):
cmd.alter(objSel2 + " and n. CA and i. " + str(stored.alnBres[x]), "b = " + str(stored.alnBnb[x]))
cmd.rebuild(); cmd.refresh(); cmd.sort(objSel1); cmd.sort(objSel2)
# Provide some useful information
stored.allRMSDval = []
stored.allRMSDval = stored.alnAnb + stored.alnBnb
print "\nColorByRMSD completed successfully."
print "The MINIMUM RMSD value is: "+str(min(stored.allRMSDval))
print "The MAXIMUM RMSD value is: "+str(max(stored.allRMSDval))
if doPretty!=None:
# Showcase what we did
cmd.orient()
cmd.hide("all")
cmd.show_as("cartoon", objSel1 + " or " + objSel2)
# Select the residues not used for alignment; they still have their B-factors as "-10"
cmd.select("notUsedForAln", "b < 0")
# White-wash the residues not used for alignment
cmd.color("white", "notUsedForAln")
# Color the residues used for alignment according to their B-factors (RMSD values)
cmd.spectrum("b", 'rainbow', "((" + objSel1 + " and n. CA) or (n. CA and " + objSel2 +" )) and not notUsedForAln")
# Delete the selection of atoms not used for alignment
# If you would like to keep this selection intact,
# just comment "cmd.delete" line and
# uncomment the "cmd.disable" line below.
cmd.delete("notUsedForAln")
# cmd.disable("notUsedForAln")
print "\nObjects are now colored by C-alpha RMS deviation."
print "All residues with RMSD values greater than the maximum are colored white..."
def colorByRMSD(objSel1, objSel2, doAlign="True", doPretty=None):
"""
colorByRMSD -- align two structures and show the structural deviations
in color to more easily see variable regions.
PARAMS
objSel1 (valid PyMOL object or selection)
The first object to align.
objSel2 (valid PyMOL object or selection)
The second object to align
doAlign (boolean, either True or False)
Should this script align your proteins or just leave them as is?
If doAlign=True then your original proteins are aligned.
If False, then they are not. Regardless, the B-factors are changed.
DEFAULT: True
doPretty (boolean, either True or False)
If doPretty=True then a simple representation is created to
highlight the differences. If False, then no changes are made.
DEFAULT: False
RETURNS
None.
SIDE-EFFECTS
Modifies the B-factor columns in your original structures.
"""
# First create backup copies; names starting with __ (underscores) are
# normally hidden by PyMOL
tObj1, tObj2, aln = "__tempObj1", "__tempObj2", "__aln"
if strTrue(doAlign):
# perform the alignment
cmd.create( tObj1, objSel1 )
cmd.create( tObj2, objSel2 )
cmd.super( tObj1, tObj2, object=aln )
cmd.matrix_copy(tObj1, objSel1)
else:
# perform the alignment
cmd.create( tObj1, objSel1 )
cmd.create( tObj2, objSel2 )
cmd.super( tObj1, tObj2, object=aln )
# Modify the B-factor columns of the original objects,
# in order to identify the residues NOT used for alignment, later on
cmd.alter( objSel1 + " or " + objSel2, "b=-10")
cmd.alter( tObj1 + " or " + tObj2, "chain='A'")
cmd.alter( tObj1 + " or " + tObj2, "segi='A'")
# Update pymol internal representations; one of these should do the trick
cmd.refresh(); cmd.rebuild(); cmd.sort(tObj1); cmd.sort(tObj2)
# Create lists for storage
stored.alnAres, stored.alnBres = [], []
# Get the residue identifiers from the alignment object "aln"
cmd.iterate(tObj1 + " and n. CA and " + aln, "stored.alnAres.append(resi)")
cmd.iterate(tObj2 + " and n. CA and " + aln, "stored.alnBres.append(resi)")
# Change the B-factors for EACH object
rmsUpdateB(tObj1,stored.alnAres,tObj2,stored.alnBres)
# Store the NEW B-factors
stored.alnAnb, stored.alnBnb = [], []
cmd.iterate(tObj1 + " and n. CA and " + aln, "stored.alnAnb.append(b)" )
cmd.iterate(tObj2 + " and n. CA and " + aln, "stored.alnBnb.append(b)" )
# Get rid of all intermediate objects and clean up
cmd.delete(tObj1)
cmd.delete(tObj2)
cmd.delete(aln)
# Assign the just stored NEW B-factors to the original objects
for x in range(len(stored.alnAres)):
cmd.alter(objSel1 + " and n. CA and i. " + str(stored.alnAres[x]), "b = " + str(stored.alnAnb[x]))
for x in range(len(stored.alnBres)):
cmd.alter(objSel2 + " and n. CA and i. " + str(stored.alnBres[x]), "b = " + str(stored.alnBnb[x]))
cmd.rebuild(); cmd.refresh(); cmd.sort(objSel1); cmd.sort(objSel2)
# Provide some useful information
stored.allRMSDval = []
stored.allRMSDval = stored.alnAnb + stored.alnBnb
print "\nColorByRMSD completed successfully."
print "The MINIMUM RMSD value is: "+str(min(stored.allRMSDval))
print "The MAXIMUM RMSD value is: "+str(max(stored.allRMSDval))
if doPretty!=None:
# Showcase what we did
cmd.orient()
cmd.hide("all")
cmd.show_as("cartoon", objSel1 + " or " + objSel2)
# Select the residues not used for alignment; they still have their B-factors as "-10"
cmd.select("notUsedForAln", "b < 0")
# White-wash the residues not used for alignment
cmd.color("white", "notUsedForAln")
# Color the residues used for alignment according to their B-factors (RMSD values)
cmd.spectrum("b", 'rainbow', "((" + objSel1 + " and n. CA) or (n. CA and " + objSel2 +" )) and not notUsedForAln")
# Delete the selection of atoms not used for alignment
# If you would like to keep this selection intact,
# just comment "cmd.delete" line and
# uncomment the "cmd.disable" line below.
cmd.delete("notUsedForAln")
# cmd.disable("notUsedForAln")
print "\nObjects are now colored by C-alpha RMS deviation."
print "All residues with RMSD values greater than the maximum are colored white..."
