def open_file(self, requestevent, replyevent):
from chimera import openModels, UserError, replyobj
try:
listdesc = requestevent.AEGetParamDesc(AEc.keyDirectObject,
AEc.typeAEList)
for i in xrange(listdesc.AECountItems()):
aliasdesc = listdesc.AEGetNthDesc(i + 1, AEc.typeAlias)[1]
alias = File.Alias(rawdata=aliasdesc.data)
fsref = alias.FSResolveAlias(None)[0]
pathname = fsref.as_pathname()
#print "GOT OPEN FOR %s" % pathname
openModels.open(pathname)
except UserError, what:
replyobj.error("%s" % what)
def open_file(self, requestevent, replyevent):
from chimera import openModels, UserError, replyobj
try:
listdesc = requestevent.AEGetParamDesc(AEc.keyDirectObject,
AEc.typeAEList)
for i in xrange(listdesc.AECountItems()):
aliasdesc = listdesc.AEGetNthDesc(i + 1, AEc.typeAlias)[1]
alias = File.Alias(rawdata=aliasdesc.data)
fsref = alias.FSResolveAlias(None)[0]
pathname = fsref.as_pathname()
#print "GOT OPEN FOR %s" % pathname
openModels.open(pathname)
except UserError, what:
replyobj.error("%s" % what)
def make_2btv_multiscale_model():
# Open 2btv by fetching it from the RCSB
from chimera import openModels
m = openModels.open('2btv', 'PDBID')[0]
# Color atoms by element
from chimera import actions
map(actions.colorAtomByElement, m.atoms)
# 2btv does not have biological oligomer (BIOMT) matrices.
# So get 120 matrices for a crystal unit cell with 2 virus particles
# and use only first 60 to get just one particle.
import PDBmatrices
slist = PDBmatrices.pdb_smtry_matrices(m.pdbHeaders)
mlist = PDBmatrices.pdb_mtrix_matrices(m.pdbHeaders)
matrices = PDBmatrices.matrix_products(slist, mlist)
matrices = matrices[:60]
# Make copies of molecule.
from MultiScale import molecule_copies
mcopies = molecule_copies(m, matrices)
# Define groups and colors.
from MultiScale import make_chain_groups, make_group
p_trimers = make_chain_groups('P trimer', ('P', 'C', 'D'),
mcopies,
color=(.5, .6, .9, 1)) # RGBA, A=opacity
q_trimers = make_chain_groups('Q trimer', ('Q', 'E', 'F'),
mcopies,
color=(.7, .7, .8, 1))
r_trimers = make_chain_groups('R trimer', ('R', 'G', 'H'),
mcopies,
color=(.9, .8, .7, 1))
s_trimers = make_chain_groups('S trimer', ('S', 'I', 'J'),
mcopies,
color=(.7, .5, .6, 1))
# T trimers are made up of a monomer from each of 3 transformed molecules.
t_triples = ((1, 20, 23), (2, 22, 27), (3, 26, 60), (4, 44, 59),
(5, 16, 43), (6, 18, 40), (7, 17, 42), (8, 41, 55),
(9, 49, 54), (10, 36, 48), (11, 25, 38), (12, 37, 47),
(13, 35, 46), (14, 29, 34), (15, 21, 28), (19, 24, 39),
(30, 33, 56), (31, 50, 53), (32, 52, 57), (45, 51, 58))
t_mcopies = map(
lambda (i, j, k): (mcopies[i - 1], mcopies[j - 1], mcopies[k - 1]),
t_triples)
t_trimers = make_chain_groups('T trimer', ('T', ),
t_mcopies,
color=(.5, .9, .6, 1))
all_trimers = p_trimers + q_trimers + r_trimers + s_trimers + t_trimers
outer_layer = make_group('Outer layer', all_trimers)
dimers = make_chain_groups('VP3 dimer', ('A', 'B'),
mcopies,
chain_colors=((.7, .5, .9, 1), (.5, .8, .8, 1)))
inner_layer = make_group('Inner layer', dimers)
capsid = make_group('Bluetongue capsid', (outer_layer, inner_layer))
import MultiScale
d = MultiScale.show_multiscale_model_dialog()
d.add_models([capsid])
def main():
print sys.argv
if len(sys.argv) != 3: # if no input
print "ERROR: Wrong number of inputs"
print "syntax: chimera --nogui --script \"chimera_move_pdb.py pdbinput output_prefix\""
print len(sys.argv)
return
input_pdb = sys.argv[1]
output_prefix = sys.argv[2]
print "pdb input = " + input_pdb
print "output prefix = "+ output_prefix
model = openModels.open(input_pdb)
#prep(model)
start = 0.0
#list = [start]
for i in range(10):
start = start + 0.03
#list.append(start)
runCommand("move x 0.03 ")
print output_prefix+"."+str(start)+".pdb"
runCommand("write 0 "+output_prefix+"."+str(start)+".pdb")
def main():
print sys.argv
if len(sys.argv) != 3: # if no input
print "ERROR: Wrong number of inputs"
print "syntax: chimera --nogui --script \"chimera_dockprep.py pdbinput output_prefix\""
print len(sys.argv)
return
#models = openModels.list(modelTypes=[chimera.Molecule])
input_pdb = sys.argv[1]
output_prefix = sys.argv[2]
print "pdb input = " + input_pdb
print "output prefix = " + output_prefix
#runCommand("open " + input_pdb)
#models = chimera.openModels.list(modelTypes=[chimera.Molecule])
#model = models
model = openModels.open(input_pdb)
#runCommand("del @H,H?,H??,H???") # remove all hydrogens
writeMol2(model, output_prefix + "before_dockprep.mol2")
prep(model)
runCommand("write 0 " + output_prefix + ".pdb")
writeMol2(model, output_prefix + ".mol2")
runCommand("del HC") # remove all non-polar hydrogens
runCommand("write 0 " + output_prefix + "_polarH.pdb")
runCommand("del @H,H?,H??,H???") # remove all hydrogens
runCommand("write 0 " + output_prefix + "_noH.pdb")
def cal_SASA(input_pdb, output_prefix):
print "pdb inputs = " + input_pdb
print "output prefix = " + output_prefix
model = openModels.open(input_pdb)
runCommand("surf :all")
out = open(output_prefix + "sasa.txt", "w")
x = '---------------------------------------------------------------------------------\n'
print "list " + str(list(model))
for m in openModels.list(modelTypes=[Molecule]):
msas = 0
for r in m.residues:
try:
sas = r.areaSAS
except AttributeError:
continue
msas = msas + sas
out.write('%s,%f\n' % (r, sas))
out.write(x)
out.write('%s,%f\n' % (m, msas))
out.write('\n')
out.close()
runCommand("del")
print msas
return msas
def generate_images(cubs, pdbs):
if 'CHIMERA' not in os.environ:
sys.exit("To render movies, you must run the script with "
"pychimera: pychimera wfnmovie.py [...]")
from chimera import runCommand as rc, openModels
print('Generating .png images for {} cub/pdb files'.format(len(cubs)))
for i, (cub, pdb) in tqdm(enumerate(zip(cubs, pdbs))):
cubmodel = openModels.open(cub)[0]
pdbmodel = openModels.open(pdb)[0]
rc('vol #0 level 0.70')
rc('scolor #0 gradient #0 cmap rainbow')
rc('transp 50 #0')
rc('turn y 180')
rc('turn x -60')
rc('focus')
rc('copy file {}.png width 1280 height 720'.format(cub.split('.')[0]))
openModels.close([cubmodel, pdbmodel])
def make_2btv_multiscale_model():
# Open 2btv by fetching it from the RCSB
from chimera import openModels
m = openModels.open('2btv', 'PDBID')[0]
# Color atoms by element
from chimera import actions
map(actions.colorAtomByElement, m.atoms)
# 2btv does not have biological oligomer (BIOMT) matrices.
# So get 120 matrices for a crystal unit cell with 2 virus particles
# and use only first 60 to get just one particle.
import PDBmatrices
slist = PDBmatrices.pdb_smtry_matrices(m.pdbHeaders)
mlist = PDBmatrices.pdb_mtrix_matrices(m.pdbHeaders)
matrices = PDBmatrices.matrix_products(slist, mlist)
matrices = matrices[:60]
# Make copies of molecule.
from MultiScale import molecule_copies
mcopies = molecule_copies(m, matrices)
# Define groups and colors.
from MultiScale import make_chain_groups, make_group
p_trimers = make_chain_groups('P trimer', ('P','C','D'), mcopies,
color = (.5, .6, .9, 1)) # RGBA, A=opacity
q_trimers = make_chain_groups('Q trimer', ('Q','E','F'), mcopies,
color = (.7, .7, .8, 1))
r_trimers = make_chain_groups('R trimer', ('R','G','H'), mcopies,
color = (.9, .8, .7, 1))
s_trimers = make_chain_groups('S trimer', ('S','I','J'), mcopies,
color = (.7, .5, .6, 1))
# T trimers are made up of a monomer from each of 3 transformed molecules.
t_triples = ((1,20,23),(2,22,27),(3,26,60),(4,44,59),(5,16,43),
(6,18,40),(7,17,42),(8,41,55),(9,49,54),(10,36,48),
(11,25,38),(12,37,47),(13,35,46),(14,29,34),(15,21,28),
(19,24,39),(30,33,56),(31,50,53),(32,52,57),(45,51,58))
t_mcopies = map(lambda (i,j,k): (mcopies[i-1],mcopies[j-1],mcopies[k-1]),
t_triples)
t_trimers = make_chain_groups('T trimer', ('T',), t_mcopies,
color = (.5, .9, .6, 1))
all_trimers = p_trimers + q_trimers + r_trimers + s_trimers + t_trimers
outer_layer = make_group('Outer layer', all_trimers)
dimers = make_chain_groups('VP3 dimer', ('A','B'), mcopies,
chain_colors = ((.7, .5, .9, 1),
(.5, .8, .8, 1)))
inner_layer = make_group('Inner layer', dimers)
capsid = make_group('Bluetongue capsid', (outer_layer, inner_layer))
import MultiScale
d = MultiScale.show_multiscale_model_dialog()
d.add_models([capsid])
def main():
print sys.argv
if len(sys.argv) != 3: # if no input
print "ERROR: Wrong number of inputs"
print "syntax: chimera --nogui --script \"chimera_open_save.py pdbinput output_prefix\""
print len(sys.argv)
return
#models = openModels.list(modelTypes=[chimera.Molecule])
input_file = sys.argv[1]
output_prefix = sys.argv[2]
print "input = " + input_file
model = openModels.open(input_file)
writeMol2(model, output_prefix + "_chimera.mol2")
def open_map(parms, mapFileName, structure):
from chimera import openModels
mapCURR = openModels.open(mapFileName)[0]
if parms.mapType == 'sigma':
#normalize map to mean of 0 and stdev of 1
scaledDen = make_normalized_map(mapCURR)
elif parms.mapType == 'volume':
scaledDen = mapCURR
else:
print 'ERROR: Unrecognized map type!'
sys.exit()
#extend map to 5.0 A beyond pdb coordinates
return bounding_xray_map_symmetry(structure.atoms, 5.0, scaledDen)
def fetch_emdb_map(id, open_fit_pdbs = False, open_models = True):
site = 'ftp.ebi.ac.uk'
url_pattern = 'ftp://%s/pub/databases/emdb/structures/EMD-%s/map/%s'
xml_url_pattern = 'ftp://%s/pub/databases/emdb/structures/EMD-%s/header/%s'
from chimera.replyobj import status, info
status('Fetching %s from %s...\n' % (id,site), blankAfter = False)
# Fetch map.
map_name = 'emd_%s.map' % id
map_gz_name = map_name + '.gz'
map_url = url_pattern % (site, id, map_gz_name)
name = 'EMDB %s' % id
minimum_map_size = 8192 # bytes
from chimera import fetch
map_path, headers = fetch.fetch_file(map_url, name, minimum_map_size,
'EMDB', map_name, uncompress = True)
# Display map.
status('Opening map %s...\n' % map_name, blankAfter = False)
from VolumeViewer import open_volume_file
models = open_volume_file(map_path, 'ccp4', map_name, 'surface',
open_models = open_models)
if open_fit_pdbs:
# Find fit pdb ids.
status('EMDB %s: looking for fits PDBs\n' % id)
pdb_ids = fit_pdb_ids_from_web_service(id)
msg = ('EMDB %s has %d fit PDB models: %s\n'
% (id, len(pdb_ids), ','.join(pdb_ids)))
status(msg)
info(msg)
if pdb_ids:
mlist = []
from chimera import _openPDBIDModel, openModels
for pdb_id in pdb_ids:
status('Opening %s\n' % pdb_id)
if open_models:
m = openModels.open(pdb_id, 'PDBID')
else:
m = _openPDBIDModel(pdb_id)
mlist.extend(m)
models.extend(mlist)
return models
def main():
print sys.argv
if len(sys.argv) != 3 and len(sys.argv) != 4: # if no input
print "ERROR: Wrong number of inputs"
print "syntax: chimera --nogui --script \"chimera_dockprep.py pdbinput output_prefix keepH\""
print len(sys.argv)
return
#models = openModels.list(modelTypes=[chimera.Molecule])
input_pdb = sys.argv[1]
output_prefix = sys.argv[2]
if len(sys.argv) == 4:
if (sys.argv[3] == 'yes'):
keepH = True
elif (sys.argv[3] == 'no'):
keepH = False
else:
print("keepH must be yes or no, setting it to no.")
keepH = False
else:
keepH = False
print "pdb input = " + input_pdb
print "output prefix = " + output_prefix
#runCommand("open " + input_pdb)
#models = chimera.openModels.list(modelTypes=[chimera.Molecule])
#model = models
model = openModels.open(input_pdb)
if not (keepH):
runCommand("del @H,H?,H??,H???") # remove all hydrogens
writeMol2(model, output_prefix+"before_dockprep.mol2")
prep(model)
runCommand("write 0 "+output_prefix+".pdb")
writeMol2(model, output_prefix+".mol2")
runCommand("del HC") # remove all non-polar hydrogens
runCommand("write 0 "+output_prefix+"_polarH.pdb")
runCommand("del @H,H?,H??,H???") # remove all hydrogens
runCommand("write 0 "+output_prefix+"_noH.pdb")
def make_multiscale_models(pdbs):
if len(pdbs) == 0:
return
from chimera import openModels
from matrix import chimera_xform
import MultiScale
mm = MultiScale.multiscale_manager()
for pdb_path, tflist in pdbs:
pdb = openModels.open(pdb_path)[0]
# Multiscale keeps the original pdb unmoved.
# Make it align with surfaces.
pdb.openState.localXform(chimera_xform(tflist[0]))
mgroup = mm.molecule_multimer(pdb, tflist)
multiscale_single_color([mgroup], random_color(pdb.name))
MultiScale.show_multiscale_model_dialog()
def main():
print sys.argv
if not (len(sys.argv) == 4 or len(sys.argv) == 3): # if no input
print "ERROR: Wrong number of inputs"
print "syntax: chimera --nogui --script \"chimera_addh.py pdbinput output_prefix [keepH] \""
print len(sys.argv)
return
#models = openModels.list(modelTypes=[chimera.Molecule])
input_pdb = sys.argv[1]
output_prefix = sys.argv[2]
if (len(sys.argv) == 4):
hflag = sys.argv[3]
else:
hflag = "no"
print "pdb input = " + input_pdb
print "output prefix = " + output_prefix
print "hflag = " + hflag
#runCommand("open " + input_pdb)
#models = chimera.openModels.list(modelTypes=[chimera.Molecule])
#model = models
model = openModels.open(input_pdb)
if hflag != "keepH":
print(
"hydrogens will be removed. if you want to kept the hydrogens pass keepH as 3 argument."
)
runCommand("del @H,H?,H??,H???") # remove all hydrogens
writeMol2(model, output_prefix + "before_dockprep.mol2")
#prep(model)
runCommand("addh")
runCommand("write 0 " + output_prefix + ".pdb")
writeMol2(model, output_prefix + ".mol2")
runCommand("del HC") # remove all non-polar hydrogens
runCommand("write 0 " + output_prefix + "_polarH.pdb")
runCommand("del @H,H?,H??,H???") # remove all hydrogens
runCommand("write 0 " + output_prefix + "_noH.pdb")
from Bio.PDB.Polypeptide import PPBuilder
import L_fasta2pir
from L_aln_tools import muscle_aln
# from dna_tools_simple import change_dna_seq_in_pdb
os.environ['LD_LIBRARY_PATH']='/Library/modeller-9.14/lib/mac10v4'
from modeller import * # Load standard Modeller classes
from modeller.automodel import * # Load the automodel class
#####
#Extract chains with Chimera
nucl_xen=openModels.open('1kx5.pdb',type='PDB')
# nucl_yeast=openModels.open('1id3.pdb',type='PDB')
# h2a_xen=Seq(str(nucl[0].sequence('C')))
# h2a_yeast=Seq(str(nuclZ[0].sequence('C')))
rc('select :.A :.B :.C :.D :.E :.F :.G :.H')
rc('write selected format pdb #0 xen_nucl.pdb')
# rc('write selected format pdb #1 h2a_yeast_xray.pdb')
#generate alignments
#Biopython extracts seqs from pdb
p = PDBParser(PERMISSIVE=1)
s = p.get_structure('1kx5', '1kx5.pdb')
ppb=PPBuilder()
seqs_xen=dict()
for i in ['A','B','C','D','E','F','G','H']:
seqs_xen[i]=ppb.build_peptides(s[0][i])[0].get_sequence()
from StringIO import StringIO
from Bio.PDB.PDBParser import PDBParser
from Bio.PDB.Polypeptide import PPBuilder
import L_fasta2pir
from L_aln_tools import muscle_aln
# from dna_tools_simple import change_dna_seq_in_pdb
os.environ['LD_LIBRARY_PATH'] = '/Library/modeller-9.14/lib/mac10v4'
from modeller import * # Load standard Modeller classes
from modeller.automodel import * # Load the automodel class
#####
#Extract chains with Chimera
nucl_xen = openModels.open('1kx5.pdb', type='PDB')
# nucl_yeast=openModels.open('1id3.pdb',type='PDB')
# h2a_xen=Seq(str(nucl[0].sequence('C')))
# h2a_yeast=Seq(str(nuclZ[0].sequence('C')))
rc('select :.A :.B :.C :.D :.E :.F :.G :.H')
rc('write selected format pdb #0 xen_nucl.pdb')
# rc('write selected format pdb #1 h2a_yeast_xray.pdb')
#generate alignments
#Biopython extracts seqs from pdb
p = PDBParser(PERMISSIVE=1)
s = p.get_structure('1kx5', '1kx5.pdb')
ppb = PPBuilder()
seqs_xen = dict()
for i in ['A', 'B', 'C', 'D', 'E', 'F', 'G', 'H']:
seqs_xen[i] = ppb.build_peptides(s[0][i])[0].get_sequence()
def open_last_session():
'Open the top file in the session file history list'
paths = recent_opened_files(session_files=True)
if paths:
from chimera import openModels
openModels.open(paths[0], type="Python")
