def render_callback(self, frame):
try:
self.molecule.deleteCoordSet(self.molecule.coordSets[frame])
except:
pass
self.molecule.LoadFrame(frame + 1)
Midas.match("#0:1-545", "#1:1-545")
Midas.undisplay("#0")
Midas.color("byatom", "#0")
Midas.undisplay("#0.=H=")
Midas.wait(1)
t = time.time()
pct_complete = self.frames_done / float(self.frames_total) * 100
if self.frames_done:
time_to_complete = (t - self.t0) / self.frames_done * (
self.frames_total - self.frames_done)
else:
time_to_complete = 0
self.f.write(
"Rendered frame %d (%d of %d, %d-%d), %5.2f%% complete, %5.2f seconds remaining)\n"
% (frame, self.frames_done, self.frames_total, start, stop,
pct_complete, time_to_complete))
self.f.flush()
self.frames_done += 1
return True
def update_model_color(self):
model_id = openModels.listIds()[-1][0]
if not self.keep_selection:
Midas.color('orange red', '#%d' % self.movie_id)
else:
Midas.color('forest green', '#%d' % model_id)
Midas.color('byhet', '#%d' % model_id)
Midas.color('forest green', '#%d' % self.movie_id)
Midas.color('byhet', '#%d' % self.movie_id)
def MethodOne():
Midas.close("all")
openMolecule(pdbid)
efhand = "#0:117-147"
calcium = "#0:151.het"
backboneAtoms = "@n,c,ca,o"
negRes = "::asp,glu"
# Display EF-Hand
Midas.represent("bs", efhand)
Midas.show(efhand + "&" + negRes)
Midas.color("green", efhand + "&" + negRes)
Midas.color("cyan", "#0:135")
Midas.color("byatom", efhand + backboneAtoms)
# Midas.resrepr("edged", efhand)
Midas.resrepr("smooth", "#0")
# Display Calcium
Midas.display(calcium)
Midas.color("cyan", calcium)
Midas.vdwdefine("ca", "ca", 0.5, calcium)
Midas.represent("sphere", calcium)
# Adjust View
Midas.center(calcium)
Midas.cofr(calcium)
chimera.viewer.scaleFactor = 7
# Add Feature Shells
s = FeatureShellNode(6, 1, sphereColor=(.2, 0, .4), sphereTransparency=.1)
t = apply(newTranslation, getLocation(calcium))
t.addChild(s.spheres)
useVRML(t, name="FEATURE Spheres")
t = apply(newTranslation, getLocation(calcium))
t.addChild(s.circles)
useVRML(t, name="FEATURE Rings")
# Add Markers
markerSize = 1
markerColor = "yellow"
alphaLoc = (26.768, 15.445, 3.308)
betaLoc = (24.006, 18.672, 1.650)
centroidLoc = (27.1862, 17.9809, 1.31815)
g = GroupNode()
g.addChild(newMarker(alphaLoc, markerSize, markerColor))
g.addChild(newMarker(betaLoc, markerSize, markerColor))
g.addChild(newMarker(centroidLoc, markerSize, markerColor))
#useVRML(g,name="FEATURE Markers")
# Show Water
water = "#0:231.water"
Midas.display(water)
Midas.vdwdefine("hoh", "o", 0.2, water)
Midas.represent("sphere", water)
def NDBColors(residues):
import Midas
color_names = set(std['NDB color'] for std in standard_bases.values())
colors = {}
for n in color_names:
colors[n] = []
for r in residues:
try:
info = standard_bases[nucleic3to1[r.type]]
except KeyError:
continue
color = info['NDB color']
colors[color].append(r)
for color, residues in colors.items():
if residues:
Midas.color(color, residues)
Midas.ribcolor(color, residues)
def _displayMotif(self, motif):
# obtain modelNo
modelNo = myvrml.getModelNo(motif.pdbid.lower())
if modelNo == None:
print "No Model"
return
group = myvrml.GroupNode()
# obtain chain residue numbers
chainRes = []
mol = chimera.openModels.list(id=modelNo)[0]
residues = mol.residues
residues.sort(lambda a, b: cmp(a.id.position, b.id.position))
for res in residues:
if res.id.chainId.strip() == motif.chainid:
chainRes.append(res)
# Hilight motif
motifSel = "#%d:%d-%d.%s" % (
modelNo, chainRes[motif.start].id.position,
chainRes[motif.end - 1].id.position, motif.chainid)
if gVerbose:
print "MOTIFSEL:", motifSel
print "START RES:", chainRes[motif.start].type,
print "STOP RES:", chainRes[motif.end - 1].type
Midas.color("red", motifSel)
Midas.rescolor("red", motifSel)
if gHaveCore:
# Hilight coreMotif
coreMotifSel = "#%d:%d-%d.%s" % (
modelNo, chainRes[motif.coreStart].id.position,
chainRes[motif.coreEnd - 1].id.position, motif.chainid)
print "CORESEL:", coreMotifSel
Midas.color("yellow", coreMotifSel)
print motif
return group
#path = "C:/Users/dhaslam/Downloads/274635.all_in_one/274635.all_in_one/274635.contactmap.txt"
path = sys.argv[1]
it = 0
i = 0
breakVar = 0
noRepeat = int(sys.argv[2])
with open(path) as inf:
for line in inf:
AA1, AA2, trash1, trash2, trash3 = line.strip().split(",")
next(inf)
if it == 38:
break
if float(trash3) < float(sys.argv[3]):
break
if noRepeat == 1:
for i in range(0, len(AAList)):
if AA1 == AAList[i] or AA2 == AAList[i]:
breakVar = 1
if breakVar == 1:
break
Midas.color(colors[it], sel=':' + str(AA1))
Midas.color(colors[it], sel=':' + str(AA2))
it = it + 1
AAList.append(AA1)
AAList.append(AA2)
