def nat(pdbid,chainid):
cmd.view('v', 'store');
object = cmd.get_names()[0]
cmd.fetch(pdbid)
cmd.select("design_nat","%s and chain %s and not hydro"%(object,"B"))
cmd.select("native_nat","%s and chain %s and not hydro"%(pdbid,chainid))
cmd.select("other_nat","%s and not chain %s"%(pdbid,chainid))
cmd.hide("everything","other")
cmd.hide('(resn HOH)')
cmd.super("design_nat","native_nat")
cmd.select("none")
cmd.orient(object)
cmd.hide("lines","all");
cmd.show("sticks","native_nat");
cmd.show("cartoon","native_nat");
cmd.system("rm %s.pdb"%(pdbid));
cmd.view('v', 'recall')
def na():
cmd.view('v', 'store')
object = cmd.get_names()[0]
pdbid = object[0:4]
chainid = object[4:5]
cmd.fetch(pdbid)
cmd.select("design_na", "%s and chain %s" % (object, "B"))
cmd.select("native_na", "%s and chain %s" % (pdbid, chainid))
cmd.select("other_na", "%s and not chain %s" % (pdbid, chainid))
cmd.hide("everything", "other")
cmd.hide('(resn HOH)')
cmd.super("design_na", "native_na")
cmd.select("none")
cmd.orient(object)
cmd.system("rm %s.pdb" % (pdbid))
cmd.view('v', 'recall')
def example():
cmd.fetch('1d7q', async=0)
cmd.show_as('sticks')
with timing():
rmsf('all')
with timing():
spectrumproperty('rmsf', 'blue white red')
def uniprot_auto(pdb_id, selection='', withss=0, quiet=1):
'''
DESCRIPTION
Like "uniprot_features" but with automatic fetching of UniProtKB accession
and sequence mapping for given pdb_id from http://www.bioinf.org.uk/pdbsws/
ARGUMENTS
pdb_id = string: PDB accession ID
selection = string: atom selection {default: <pdb_id>, will be fetched if
no such object is loaded}
withss = 0/1: update secondary structure {default: 0}
'''
from urllib import urlopen
if len(pdb_id) != 4 or not pdb_id[0].isdigit():
print ' Error: invalid pdb_id:', pdb_id
raise CmdException
if not selection:
selection = pdb_id
if pdb_id not in cmd.get_names('all'):
cmd.fetch(pdb_id, async=0)
sele_chains = cmd.get_chains(selection)
mappings = {}
pdb_id = pdb_id.lower()
url = 'http://www.bioinf.org.uk/cgi-bin/pdbsws/query.pl?plain=1&qtype=pdb&all=yes&id=' + pdb_id
try:
for line in urlopen(url):
if not line.startswith(pdb_id):
continue
chain = line[5]
resno = line[20:25].strip()
acc = line[27:36].strip()
number = line[40:50].strip()
if not acc or not number:
continue
if chain not in mappings:
mappings[chain] = acc, resid_mapper()
if mappings[chain][0] != acc and chain in sele_chains:
raise ValueError('multiple accessions per chain not supported')
mappings[chain][1][int(number)] = resno
except Exception as e:
print ' Error:', e
raise CmdException
for chain, (acc, sm) in mappings.iteritems():
uniprot_features(acc, '(%s) and chain %s' % (selection, chain),
withss, 'feature_' + chain + '_', sm, quiet)
def na():
cmd.view('v', 'store')
object = cmd.get_names()[0]
if object[0] == 'd':
pdbid = object[1:5]
chainid = object[5:6]
else:
pdbid = object[0:4]
chainid = object[4:5]
cmd.fetch(pdbid)
cmd.select("design_na", "%s and chain %s and not hydro" % (object, "B"))
cmd.select("native_na", "%s and chain %s and not hydro" % (pdbid, chainid))
cmd.select("other_na", "%s and not chain %s" % (pdbid, chainid))
cmd.hide("everything", "other")
cmd.hide('(resn HOH)')
cmd.super("native_na", "design_na")
cmd.hide("lines", "all")
cmd.show("sticks", "native_na")
cmd.show("cartoon", "native_na")
cmd.select("none")
cmd.orient(object)
pdbid = pdbid.lower()
cmd.system("rm %s.pdb" % (pdbid))
cmd.view('v', 'recall')
def load(self):
self.manager.d = self
self.manager.m = None
self.manager.m = None # to also set prevm = None
# cmd.delete(self.manager.prevd.obj)
# cmd.delete(self.manager.prevd.pid)
# print self.manager.d.obj
# print self.manager.prevd.obj
# sys.exit()
cmd.delete("all")
cmd.load(self.getloadname(),self.obj,1)
cmd.remove(self.obj+" and not chain A")
cmd.fetch(self.pid)
cmd.remove("het or hydro")
cmd.color('gray',self.pid+' and elem C')
self.scores['rms'] = cmd.align(self.pid,self.obj+" and chain A")[0]
cmd.hide('ev')
cmd.show('lines')
cmd.show("car")
#cmd.disable(self.pid)
redopent(self.obj)
self.recalc_design_pos()
self.read_data_dir('avg_deg')
self.read_data_dir('ddG')
self.read_data_dir('rot_boltz')
self.read_bup()
self.read_tot_scores()
self.read_res_scores()
cmd.orient(self.obj+" or pnt*")
self.manager.m = self.remembermm
if self.manager.m: self.manager.m.focus()
if self.remembermv: cmd.set_view(self.remembermv)
def na():
cmd.view('v', 'store');
object = cmd.get_names()[0]
pdbid = object[0:4]
chainid = object[4:5]
cmd.fetch(pdbid)
cmd.select("design_na","%s and chain %s"%(object,"B"))
cmd.select("native_na","%s and chain %s"%(pdbid,chainid))
cmd.select("other_na","%s and not chain %s"%(pdbid,chainid))
cmd.hide("everything","other")
cmd.hide('(resn HOH)')
cmd.super("design_na","native_na")
cmd.select("none")
cmd.orient(object)
cmd.system("rm %s.pdb"%(pdbid));
cmd.view('v', 'recall')
def map_interaction_freq_to_structure(pdb,
chain,
interaction_freq_file,
exp_rep_id,
threshold=0.0):
### Background coloring settings
cmd.bg_color("white")
cmd.fetch(pdb)
cmd.hide()
cmd.show("cartoon")
cmd.cartoon("loop")
cmd.color("white", pdb)
cmd.set("dash_gap", 0)
cmd.set("dash_width", 5)
### Extract interaction frequency information
interaction_freq_info_list = getInteractionFreqList(
pdb, interaction_freq_file, exp_rep_id, threshold)
### Color interactions by frequency
print("color interactions by frequency")
for gpcrdb_pair, resid1, resid2, freq in interaction_freq_info_list:
cmd.distance(
"%s" % (gpcrdb_pair),
"%s and resi %d and name CA and chain %s" % (pdb, resid1, chain),
"%s and resi %d and name CA and chain %s" % (pdb, resid2, chain))
mapped_col = freq_to_grayscale(freq)
cmd.set("dash_color", mapped_col, gpcrdb_pair)
cmd.hide("labels")
def plot(self, outfile):
ctrl_id, case_id, snp_df_sub = self.score_on_var()
df = pd.merge(snp_df_sub, self.snps2aa, on='id')
#pymol.finish_launching()
cmd.reinitialize()
cmd.fetch(self.pdb)
cmd.alter(self.pdb, 'b = 0.5')
cmd.show_as('cartoon', self.pdb)
cmd.color('white', self.pdb)
for i, row in df.iterrows():
resi = row['structure_position']
chain = row['chain']
pheno = row['es']
selec = 'snp%s' % i
selec_atom = 'snp_atom%s' % i
cmd.select(selec,
'name ca and resi %s and chain %s' % (resi, chain))
cmd.create(selec_atom, selec)
cmd.set("sphere_scale", 0.8)
cmd.show('sphere', selec_atom)
cmd.alter(selec_atom, 'b=%s' % pheno)
cmd.spectrum("b",
"blue_white_red",
selec_atom,
maximum=1.0,
minimum=0.0)
cmd.bg_color("white")
cmd.zoom()
cmd.orient()
cmd.save('%s.pse' % outfile)
cmd.png('%s.png' % outfile, width=2400, height=2400, dpi=300, ray=1)
def na():
cmd.view('v', 'store');
object = cmd.get_names()[0]
if object[0] == 'd':
pdbid = object[1:5]
chainid = object[5:6]
else:
pdbid = object[0:4]
chainid = object[4:5]
cmd.fetch(pdbid)
cmd.select("design_na","%s and chain %s and not hydro"%(object,"B"))
cmd.select("native_na","%s and chain %s and not hydro"%(pdbid,chainid))
cmd.select("other_na","%s and not chain %s"%(pdbid,chainid))
cmd.hide("everything","other")
cmd.hide('(resn HOH)')
cmd.super("native_na","design_na")
cmd.hide("lines","all");
cmd.show("sticks","native_na");
cmd.show("cartoon","native_na");
cmd.select("none")
cmd.orient(object)
pdbid = pdbid.lower()
cmd.system("rm %s.pdb"%(pdbid));
cmd.view('v', 'recall')
def nat(pdbid, chainid):
cmd.view('v', 'store')
object = cmd.get_names()[0]
cmd.fetch(pdbid)
cmd.select("design_nat", "%s and chain %s and not hydro" % (object, "B"))
cmd.select("native_nat",
"%s and chain %s and not hydro" % (pdbid, chainid))
cmd.select("other_nat", "%s and not chain %s" % (pdbid, chainid))
cmd.hide("everything", "other")
cmd.hide('(resn HOH)')
cmd.super("design_nat", "native_nat")
cmd.select("none")
cmd.orient(object)
cmd.hide("lines", "all")
cmd.show("sticks", "native_nat")
cmd.show("cartoon", "native_nat")
cmd.system("rm %s.pdb" % (pdbid))
cmd.view('v', 'recall')
def q5():
'''
DESCRIPTION
Question 5: How many axial stacks of helices does
the ribozyme have?
The following commands created the scene for "q5":
delete all;fetch 3zp8, hammer, async=0;show cartoon, hammer;set_view (-0.5,0.18,-0.85,-0.17,-0.98,-0.11,-0.85,0.09,0.52,0.0,0.0,-167.2,-18.45,10.92,-12.11,126.37,208.02,-20.0);rock;
To reuse of parts or all of the above commands, copy and paste the commands
onto the command line or into a plain text file.
These commands are sufficient for most editing tasks:
To edit code, positon cursor on command line with left mouse button.
Control-e moves the cursor to the end of the line, even when it is out of view.
Control-a moves the cursor to the beginning of the line, even when it is out of view.
Up arrow key recalls last line of commands for editing.
These commands may not be available on all systems:
Shift-control-a selects everything from the right of the cursor to the end of the line.
Shift-control-e selects everything to the left of the cursor to the end of the line.
Command-f moves the cursor to the end of the current word.
Command-b moves the cursor to the begining of the current word.
Control-f moves the cursor to the right by one character.
Control-b moves the cursor to the left by one character.
'''
cmd.reinitialize()
cmd.fetch('3zp8', type='pdb', name= 'hammer', async='0')
cmd.show_as('cartoon','hammer')
cmd.rock()
cmd.set_view('(-0.5,0.18,-0.85,-0.17,-0.98,-0.11,-0.85,0.09,0.52,0.0,0.0,-167.2,-18.45,10.92,-12.11,126.37,208.02,-20.0);')
print('Enter "q5" to make the scene for question 5.')
print('Enter "help q5" to see question 5 and the commands to make the scene.')
def testFun(filePath):
import networkx as nx
cmd.delete("all")
cmd.fetch("1C3W")
cmd.hide("lines", "all")
cmd.show("cartoon", "1C3W")
cmd.color("green", "all")
#------------------------------ cmd.color("yellow", "resi 194 and resn GLU")
#------------------------------- cmd.show("sticks", "resi 194 and resn GLU")
highlightRes("GLUA0194", color="yellow")
highlightRes("GLUA0204", color="yellow")
g = loadHbTxt(filePath)
allNodes = nx.node_connected_component(g, "GLUA0194")
#===========================================================================
# print allNodes
#===========================================================================
accRes = {}
for line in open("/Users/xzhu/sibyl/BR/1C3W/hydro/def/raw/acc.res"):
fields = line.split()
resString = fields[1] + fields[2]
acc = float(fields[4])
accRes[resString] = acc
colorThreshold = 0.02
for eachResidue in accRes.keys():
if accRes[eachResidue] > colorThreshold:
if eachResidue in allNodes:
print eachResidue
highlightRes(eachResidue)
def main(sys_argv=sys.argv):
#pdbCode = '1XFH'.lower()
pdbCode = '2NWL'.lower()
pymol.finish_launching()
cmd.fetch(pdbCode)
xml = get_pdbtm_xml(pdbCode)
chains_dict = get_pdbtm_annotation(pdbCode, xml)
highlight_molecule(chains_dict, pdbCode.lower())
def Mutagenesis(kinase1, model, template,peptide_instance):
"""superposition the model and template, remove template and leave peptide behind """
"""replace peptide with instance peptide"""
list_name = peptide_instance
with open(input_data_folder+list_name,'r') as f:
instances = f.readlines()
instance = [x.strip() for x in instances]
print "your peptide: ", instance
for pep in instance:
cmd.delete('all')
cmd.fetch(model) # model_candidate, ex.chk1,chk2...
cmd.remove("hetatm") #remove the nonstandard residues
cmd.fetch(template) #mutagenesis template, ex.2phk
peptide_template = cmd.get_fastastr( "/"+template+'//B') #get the peptide from the template and generate another one for mutagenesis
peptide_template = peptide_template + 'G' #peptide of 2phk is 7 amino acid long, when our input peptide is 8 aa, we need to plus one character
for aa in peptide_template[6:].lower(): #creat template_peptide for mutagenesis
cmd._alt(aa)
firstaa = AAcode_1_to_3(peptide_template[6]) #translate template_peptide to 3 letter
low_firstaa = firstaa[0].lower()
cmd.alter(low_firstaa, 'chain = "B"') #select this template_peptide
cmd.show_as("cartoon")
cmd.align(model, template) #superpostion of model and template
cmd.align(low_firstaa,template) #superpostion of template_peptide and template
remove_part = "("+template+" and not resn ATP"+")"
cmd.select("remove_part",remove_part)
cmd.remove("remove_part") #remove the template except for ATP, there are only model and template_peptide
cmd.remove("resn hoh") #remove water
cmd.wizard("mutagenesis")
peptide_position = 0
for i in pep:
#the peptide_position starting point depends the first position of mutagenesis peptide
#pymol's peptide start from 1, not 0
mutagenesis_template = '/'+low_firstaa+ '///' + str(peptide_position + 2) # because of 2phk start at 2nd of peptide
#mutagenesis_template = '/' + template + '//B/' + str(peptide_position + 2)
cmd.get_wizard().do_select(mutagenesis_template) # select peptide position of mutation
replace_aminoacid = AAcode_1_to_3(pep)[peptide_position]
cmd.get_wizard().set_mode(replace_aminoacid) # select which residue want to mutate to
cmd.get_wizard().apply()
peptide_position += 1
filename = kinase1 + '_' + model + 'model_' + template + 'muta_' + pep + '.pdb' #build the canonical name
cmd.save(filename)
ATPchange(filename) #change ATP naming to the format of ATP.params
cmd.wizard(None)
return
def load(type, id):
# we clear pymol, make filename and path
quantum_target = []
target_features = []
cmd.delete('all')
file_name = f'{id}.{type}' if type is 'cif' else id
dataset_path = os.path.join('.', 'datasets', type)
path = os.path.join(dataset_path, file_name)
# we load the target
print(f'load {id} {path}')
if type is "cif":
if not os.path.exists(path):
cmd.fetch(id, path=dataset_path)
elif os.path.exists(path):
cmd.load(path)
elif type is "xyz":
cmd.load(path)
elif type is "rxn":
reactants, products = get_reactants_products(path)
print(f"{str(reactants)} ---> {str(products)}")
for product in products:
product_path = os.path.join('.', 'datasets', 'mol', product)
cmd.load(product_path)
# make target
clean_pymol()
model = cmd.get_model('all', 1)
target_positions = get_positions(model)
quantum_target = get_quantum_target(path) if type is "xyz" else None
target_features = get_features(model) if type is "rxn" else None
target_masses = get_masses(model) if type is "rxn" else None
target_numbers = get_numbers(model) if type is "rxn" else None
if type is 'rxn':
cmd.delete('all')
for reactant in reactants:
reactant_path = os.path.join('.', 'datasets', 'mol', reactant)
cmd.load(reactant_path)
clean_pymol()
model = cmd.get_model('all', 1)
# make the model inputs
if type is 'cif':
chains = cmd.get_chains('all')
if random.random() < P_UNDOCK:
undock(chains, type)
if random.random() < P_UNFOLD:
unfold(chains)
if type is 'rxn':
names = cmd.get_names('all')
undock(names, type)
positions = get_positions(model)
features = get_features(model)
masses = get_masses(model)
numbers = get_numbers(model)
return make_example(type, id, target_positions, positions, features,
masses, numbers, quantum_target, target_features,
target_masses, target_numbers)
def screenshotProteins():
# proteinsPath = ".\pdbs"
# set style parameters
# cmd.set("ray_opaque_background", 0)
# cmd.remove("solvent")
cmd.set("ambient", 0.3)
cmd.set("antialias", 1)
cmd.bg_color("white")
# cmd.set("direct", 1.0)
# cmd.set("ribbon_radius", 0.2)
# cmd.set("cartoon_highlight_color", "grey50")
# cmd.set("ray_trace_mode", 1)
# cmd.set("stick_radius", 0.2)
# cmd.set("mesh_radius", 0.02)
# loop thru folders
# for dir in os.walk(proteinsPath):
# proteinPath = dir[0]
# loop thru pdbs
# for file in os.listdir(proteinPath):
# if file.endswith('.pdb'):
csvFileName = "docked-protein-homomers.csv"
# to loop through csv
file = open(csvFileName, "r")
reader = csv.reader(file, delimiter=",")
k = 1
for row in reader:
for item in row:
print(k, item)
cmd.reinitialize()
# load the pdb file
cmd.fetch(item, path="./pdbs", type='pdb')
#pdbPath= "./pdbs/" + item + ".cif"
#cmd.load(pdbPath)
color = pickAColor()
cmd.color(color)
cmd.show("cartoon")
cmd.remove("solvent")
# take a screenshot
screenshotFileName = item + ".png"
screenshotPath = os.path.join('screenshots', screenshotFileName)
cmd.png(screenshotPath, 128, 128, ray=1)
# clear
cmd.delete("all")
k = k + 1
def Btn_DownloadPDB_Clicked(self):
PdbCode = self.FetchPDB.get()
try:
if self.PyMOL:
cmd.fetch(PdbCode, **{'async': 0})
cmd.refresh()
except:
self.DisplayMessage(' You entered an invalid PDB code.', 1)
self.FetchPDB.set('')
def analyze_surface_residues(pdb_id):
print('Analyzing surface residues for', pdb_id)
cmd.fetch(pdb_id)
findSurfaceResidues(
pdb_id, pdb_id=pdb_id, oxygen=True
) # Calls on findSurfaceResidues from FindSurfaceResidues.py
cmd.delete('all')
# Deletes the .cif file created by PyMol
path = pdb_id.lower() + '.cif'
if os.path.exists(path):
os.remove(path)
def Btn_DownloadPDB_Clicked(self):
PdbCode = self.FetchPDB.get()
try:
if self.PyMOL:
cmd.fetch(PdbCode, **{'async': 0})
cmd.refresh()
except:
self.DisplayMessage(' You entered an invalid PDB code.', 1)
self.FetchPDB.set('')
def chain_align_save(*args, **kwargs):
args = [ast.literal_eval(kvpair) for kvpair in args]
for pair in args:
cmd.fetch(str.lower(pair[0]))
create_subchain_object(pair[0], pair[1])
cmd.delete(str.lower(pair[0]))
for mobile in [ '{}.{}'.format(model, chain) for (model, chain) in args ][1:]:
cmd.super(mobile, "{}.{}".format(args[0][0], args[0][1]),reset=1,transform=1,quiet=0)
cmd.reset()
cmd.save('alignment.cif')
def load(pdb):
'''
This funciton loads a pdb into the PYMOL environment.
'''
cmd.fetch(str(pdb))
cmd.remove('solvent')
cmd.color('green')
file_name = str(pdb) + '.pdb'
cmd.save(file_name)
def feature3D(args):
import pymol
from pymol import cmd, util
# get parameters
pdb_id = args.pdb_id
short_win = args.short_win
large_win = args.large_win
contact_threshold = args.contact_threshold
feature_name = args.feature_name
# compute features for each residue in a labelled chain
residues, features, lip_indexes = prot_dataset.generate_test(
pdb_id,
short_win=short_win,
large_win=large_win,
contact_threshold=contact_threshold)
# make a dataframe
df = prot_dataset.as_dataframe(features, lip_indexes)
# get the array with desired feature
feature = df[feature_name]
# Open Pymol (not necessary from pyMOL 2.1)
pymol.finish_launching()
# Download the PDB
cmd.fetch(pdb_id, pdb_id)
# Hide lines
cmd.hide("lines", pdb_id)
# Show ribbon
cmd.show("cartoon", pdb_id)
# Set all B-factor to 0.0
cmd.alter("(all)", "b=0.0")
# for each residue
for i in range(0, len(residues)):
# Residue selection in Pymol syntax
residue_string = '{}/{}{}/'.format(residues[i].get_full_id()[2],
residues[i].id[1], '')
# Substitute the B-score with the feature score
cmd.alter(residue_string, "b={:2f}".format(feature[i]))
# If the residue is labelled as LIP show it as sphere
if lip_indexes[i] == 1:
cmd.show_as(
"spheres",
"chain {} and resi {}".format(residues[i].get_full_id()[2],
residues[i].id[1]))
# color by B-factor values
cmd.spectrum("b", palette="rainbow", selection="(all)")
def init():
cmd.reinitialize()
#LOAD FILES AND MAKE THE NECESSARY SELECTIONS FOR ALIGNMENT
cmd.load("pses/session_chlorine_minus1_merged.pse")
cmd.do("run axes.py")
cmd.do("run center_of_mass.py")
#cmd.load("geometry_complex_Cl.mol")
cmd.select("circ_complex", "organic")
cmd.fetch("pdbs/" + pdb)
cmd.select("water", "resn hoh")
#select ligand and bindingsite
cmd.select("ligand", "organic and not circ_complex")
cmd.select("chain_a", "chain a")
cmd.select("ligand_a", "ligand and chain_a")
def get_rec_plus_lig(pdb_id, lig, rec_file, lig_file, new_chain):
pymol.finish_launching()
cmd.delete('all')
cmd.fetch(pdb_id)
center_coords_rec(pdb_id)
cmd.select('lig', 'resn lig')
stored.list=[]
cmd.iterate('org', "stored.list.append((chain))")
chain = list(set(stored.list))[0][0]
cmd.select('lig', 'resn ' + lig + ' and chain ' + chain)
cmd.select('rec', 'poly and chain ' + chain)
cmd.alter('rec', 'chain=\'' + new_chain + '\'')
cmd.save(lig_file, 'lig')
cmd.save(rec_file, 'rec')
os.system('rm *.cif')
def testFetch(self):
with testing.mkdtemp() as fetch_path:
names = []
cmd.set('fetch_path', fetch_path)
cmd.set('fetch_host', 'pdb pdbe')
cmd.fetch('1avy', '1avy1', type='pdb1')
names += ['1avy1']
self.assertItemsEqual(cmd.get_names(), names)
self.assertEqual(cmd.count_states('1avy1'), 3)
cmd.fetch('1avy', type='2fofc')
names += ['1avy_2fofc']
self.assertItemsEqual(cmd.get_names(), names)
self.assertEqual(cmd.get_type('1avy_2fofc'), 'object:map')
def testFetch(self):
with testing.mkdtemp() as fetch_path:
names = []
cmd.set('fetch_path', fetch_path)
cmd.set('fetch_host', 'pdb pdbe')
cmd.fetch('1avy', '1avy1', type='pdb1')
names += ['1avy1']
self.assertItemsEqual(cmd.get_names(), names)
self.assertEqual(cmd.count_states('1avy1'), 3)
cmd.fetch('1avy', type='2fofc')
names += ['1avy_2fofc']
self.assertItemsEqual(cmd.get_names(), names)
self.assertEqual(cmd.get_type('1avy_2fofc'), 'object:map')
def q6():
'''
DESCRIPTION
Question 6: What is the average distance of the Na1044
ligand bonds? Give the residue numbers of the RNA
nucleotides and the sodium to identify them. How many
ligands are from RNA?
The following commands created the scene for "q6":
delete all;fetch 3zp8, hammer, async=0; rock;preset.ball_and_stick("all");distance ligand1, i. 1044, c. A and i. 22 and n. N7;distance ligand2, i. 1044, c. A and i. 21 and n. OP2;distance ligand3, i. 1044, i. 2121;distance ligand4, i. 1044, i. 2120;distance ligand5, i. 1044, i. 2122;distance ligand6, i. 1044, i. 2130;set_view (-0.87,0.18,-0.46,-0.39,-0.81,0.44,-0.29,0.56,0.78,-0.0,0.0,-20.47,-18.05,14.02,-18.89,17.47,23.47,-20.0);
To reuse of parts or all of the above commands, copy and paste the commands
onto the command line or into a plain text file.
These commands are sufficient for most editing tasks:
To edit code, positon cursor on command line with left mouse button.
Control-e moves the cursor to the end of the line, even when it is out of view.
Control-a moves the cursor to the beginning of the line, even when it is out of view.
Up arrow key recalls last line of commands for editing.
These commands may not be available on all systems:
Shift-control-a selects everything from the right of the cursor to the end of the line.
Shift-control-e selects everything to the left of the cursor to the end of the line.
Command-f moves the cursor to the end of the current word.
Command-b moves the cursor to the begining of the current word.
Control-f moves the cursor to the right by one character.
Control-b moves the cursor to the left by one character.
'''
cmd.reinitialize()
cmd.fetch('3zp8', type='pdb', name='hammer', async='0')
cmd.rock()
cmd.do('preset.ball_and_stick("all")')
cmd.distance('Sodiumligand1', ' resi 1044', 'chain A and i. 22 and n. N7')
cmd.distance('Sodiumligand2', 'resi 1044', 'chain A and i. 21 and n. OP2')
cmd.distance('Sodiumligand3', 'resi 1044', 'resi 2121')
cmd.distance('Sodiumligand4', 'resi 1044', 'resi 2120')
cmd.distance('Sodiumligand5', 'resi 1044', 'resi 2122')
cmd.distance('Sodiumligand6', 'resi 1044', 'resi 2130')
cmd.do('set label_size, -0.4')
cmd.set_view(
'(-0.87,0.18,-0.46,-0.39,-0.81,0.44,-0.29,0.56,0.78,-0.0,0.0,-20.47,-18.05,14.02,-18.89,17.47,23.47,-20.0);'
)
print('Enter "q6" to make the scene for question 6.')
print(
'Enter "help q6" to see question 6 and the commands to make the scene.'
)
def getnative():
v = cmd.get_view()
nats = []
for obj in cmd.get_object_list():
if len(obj) == 4:
nats.append(obj)
continue
pid = obj[:4]
if pid in nats:
continue
print "fetching native", pid
cmd.fetch(pid)
cmd.remove(pid + " and not chain A")
cmd.remove(pid + " and resn HOH")
cmd.align(pid, obj)
cmd.set_view(v)
def load_spike_structure():
cmd.delete('all')
cmd.set('fetch_path', 'pdbs')
cmd.fetch(pdb_name, name=pdb_name)
# Get rid of water/hydrogens in the structure
cmd.remove('solvent')
cmd.remove('hydrogens')
# Clean up the rest... remove all non-protein atoms (PyMOL 2.1+ only)
cmd.remove('(not polymer.protein)')
# Hide cartoon and show surface
cmd.hide('cartoon')
cmd.show('surface')
def q8():
'''
DESCRIPTION
Question 8: Find the unusual base pair between A21 and
G36. What is the length of the H-bonds between the bases
(ignore the H atoms in the distance measurement)? List
the distance with the residue name, residue number, and
atom name. What additional H-bond occurs between a base
in this base pair and a ribose ring of one of the two
nucleotides in this base pair?
The following commands created the scene for "q8":
fetch 3zp8, hammer, async=0;hide everything;show ribbon;show sticks, resi 21 or resi 36;set_view (-0.9,-0.19,0.39,0.39,-0.74,0.55,0.19,0.65,0.74,0.0,0.0,-37.58,-21.66,15.71,-23.32,35.42,39.74,-20.0);rock;
To reuse of parts or all of the above commands, copy and paste the commands
onto the command line or into a plain text file.
These commands are sufficient for most editing tasks:
To edit code, positon cursor on command line with left mouse button.
Control-e moves the cursor to the end of the line, even when it is out of view.
Control-a moves the cursor to the beginning of the line, even when it is out of view.
Up arrow key recalls last line of commands for editing.
These commands may not be available on all systems:
Shift-control-a selects everything from the right of the cursor to the end of the line.
Shift-control-e selects everything to the left of the cursor to the end of the line.
Command-f moves the cursor to the end of the current word.
Command-b moves the cursor to the begining of the current word.
Control-f moves the cursor to the right by one character.
Control-b moves the cursor to the left by one character.
'''
cmd.reinitialize()
cmd.fetch('3zp8', type='pdb', name='hammer', async='0')
cmd.show_as('ribbon', 'hammer')
cmd.rock()
cmd.hide('everything')
cmd.show_as('ribbon', 'all')
cmd.show_as('sticks', 'resi 21 or resi 36')
cmd.set_view(
'(-0.9,-0.19,0.39,0.39,-0.74,0.55,0.19,0.65,0.74,0.0,0.0,-37.58,-21.66,15.71,-23.32,35.42,39.74,-20.0);'
)
print('Enter "q8" to make the scene for question 8.')
print(
'Enter "help q8" to see question 8 and the commands to make the scene.'
)
def highlight_membrane(pdbCode, loaded=0, db=DB_ID_PDBTM, color=1):
loaded = int(loaded)
color = int(color)
if not loaded:
cmd.fetch(pdbCode[0:4])
if db==DB_ID_PDBTM:
xml = get_pdbtm_xml(pdbCode[0:4])
chains_dict = get_pdbtm_annotation(pdbCode[0:4], xml)
else:
if db==DB_ID_OPM:
opm_file = get_opm_file(pdbCode[0:4])
chains_dict = get_opm_annotation(opm_file)
else:
print 'Unkown database supplied: %s. Exiting' % (db)
exit(1)
highlight_molecule(chains_dict, pdbCode[0:4].lower(), loaded, pdbCode[4:5], color)
def align(self, target, pse=None):
if pse is not None:
cmd.load(pse)
self.load
cmd.align('{}'.format(self.pdb), '{}'.format(target))
elif os.path.exists(target):
cmd.load('{}'.format(target))
self.load
target_pdb = os.path.basename(target).split(".")[0]
cmd.align('{}'.format(self.pdb), '{}'.format(target_pdb))
else:
cmd.fetch('{}'.format(target))
self.load
cmd.align('{}'.format(self.pdb), '{}'.format(target))
def q4():
'''
DESCRIPTION
Question 4: What the dihedral angle about the disulfide
bond between MRG81 of chain F and Cys258 of chain C?
This is a cross link between the protein and the DNA. Is
this a cis or trans conformation of the bonds about the
S--S bond? Is this conformation energetically favorable
or unfavorable?
The following commands created the scene for "q4":
delete all; fetch 3v6d, HIVrt, async=0;preset.ball_and_stick("(c. C and i. 258) or (c. F and i. 817 )");set_view (0.21,-0.91,0.34,-0.84,0.01,0.54,-0.5,-0.4,-0.77,0.0,-0.0,-38.82,-39.67,-55.1,10.96,36.31,41.34,-20.0);
To reuse of parts or all of the above commands, copy and paste the commands
onto the command line or into a plain text file.
These commands are sufficient for most editing tasks:
To edit code, positon cursor on command line with left mouse button.
Control-e moves the cursor to the end of the line, even when it is out of view.
Control-a moves the cursor to the beginning of the line, even when it is out of view.
Up arrow key recalls last line of commands for editing.
These commands may not be available on all systems:
Shift-control-a selects everything from the right of the cursor to the end of the line.
Shift-control-e selects everything to the left of the cursor to the end of the line.
Command-f moves the cursor to the end of the current word.
Command-b moves the cursor to the begining of the current word.
Control-f moves the cursor to the right by one character.
Control-b moves the cursor to the left by one character.
'''
cmd.reinitialize()
cmd.fetch('3v6d', type='pdb', name='HIVrt', async='0')
cmd.do(
"preset.ball_and_stick(selection='(chain C and resi 258) or (chain F and resi 817 )')"
)
cmd.set_view(
'(0.21,-0.91,0.34,-0.84,0.01,0.54,-0.5,-0.4,-0.77,0.0,-0.0,-38.82,-39.67,-55.1,10.96,36.31,41.34,-20.0);'
)
cmd.rock()
print('Enter "q4" to make the scene for question 4.')
print(
'Enter "help q4" to see question 4 and the commands to make the scene.'
)
def results3D(args):
import pymol
from pymol import cmd, util
# get path adn pdb id
path = main_folder_path + args.path
# check if result file exists else print error
if not isfile(path):
print "File \"{}\" has not been found.".format(path)
return
# open file
file = open(path, 'r')
# get the header
header = file.next()
#extract pdb id from header
pdb_id = header.replace('>', '').replace('\n', '')
# Open Pymol (not necessary from pyMOL 2.1)
pymol.finish_launching()
# fetch pdb id
cmd.fetch(pdb_id, pdb_id)
# Hide lines
cmd.hide("lines", pdb_id)
# Show ribbon
cmd.show("cartoon", pdb_id)
# Set all B-factor to 0.0
cmd.alter("(all)", "b=0.0")
# for each line in the file
for line in file:
# split the line
identifier, prob, binary_prob = line.split()
model, chain, index, insertion_code, name = identifier.split('/')
# Residue selection in Pymol syntax
residue_string = '{}/{}{}/'.format(chain, index, '')
# Substitute the B-score with the LIP score
cmd.alter(residue_string, "b={:2f}".format(float(prob)))
# color all residues by their B-factor
cmd.spectrum("b", palette="rainbow", selection="(all)")
# close file
file.close()
return
def fetch_and_name_chains(cif_id):
'''
DESCRIPTION
1. Fecth a cif structure from the pdb
2. Rename the cif file accoring to its 4-letter PDB-code followed by its Genus species name
3. Create a PyMOL object for each of its chains and name them according to whats on the PDB
'''
polymers = pypdb.get_all_info(cif_id)['polymer']
taxonomy = set()
chain_to_name = {}
for poly in range(len(polymers)):
taxonomy.add(polymers[poly]['Taxonomy']['@name'])
polymer_description = polymers[poly]['polymerDescription'][
'@description'].split(',')[0]
entry_name = re.sub('\(|\)', '', polymer_description)
chain = polymers[poly]['chain']['@id']
name = re.sub('ribosomal\s|protein\s|60S\s|40S\s|subunit\s|\sprotein',
'',
entry_name,
flags=re.IGNORECASE)
chain_to_name[name] = chain
if len(taxonomy) > 1:
print('multiple species in structure')
exit
for organism in taxonomy:
Genus_species = organism.replace(' ', '_')
ge_sp = organism.split()
GeSp = ge_sp[0][:2] + ge_sp[1][0].capitalize() + ge_sp[1][1]
cmd.fetch(cif_id, cif_id + '_' + GeSp)
os.rename(cif_id + '.cif', cif_id + '_' + Genus_species + '.cif')
# os.remove(cif_id+'.cif') # Not sure why this isn't working
for obj_name in chain_to_name:
cmd.create(
GeSp + '_' + cif_id + '_' + obj_name,
cif_id + '_' + GeSp + ' and chain ' + chain_to_name[obj_name])
cmd.show_as('cartoon')
def q6():
'''
DESCRIPTION
Question 6: What is the average distance of the Na1044
ligand bonds? Give the residue numbers of the RNA
nucleotides and the sodium to identify them. How many
ligands are from RNA?
The following commands created the scene for "q6":
delete all;fetch 3zp8, hammer, async=0; rock;preset.ball_and_stick("all");distance ligand1, i. 1044, c. A and i. 22 and n. N7;distance ligand2, i. 1044, c. A and i. 21 and n. OP2;distance ligand3, i. 1044, i. 2121;distance ligand4, i. 1044, i. 2120;distance ligand5, i. 1044, i. 2122;distance ligand6, i. 1044, i. 2130;set_view (-0.87,0.18,-0.46,-0.39,-0.81,0.44,-0.29,0.56,0.78,-0.0,0.0,-20.47,-18.05,14.02,-18.89,17.47,23.47,-20.0);
To reuse of parts or all of the above commands, copy and paste the commands
onto the command line or into a plain text file.
These commands are sufficient for most editing tasks:
To edit code, positon cursor on command line with left mouse button.
Control-e moves the cursor to the end of the line, even when it is out of view.
Control-a moves the cursor to the beginning of the line, even when it is out of view.
Up arrow key recalls last line of commands for editing.
These commands may not be available on all systems:
Shift-control-a selects everything from the right of the cursor to the end of the line.
Shift-control-e selects everything to the left of the cursor to the end of the line.
Command-f moves the cursor to the end of the current word.
Command-b moves the cursor to the begining of the current word.
Control-f moves the cursor to the right by one character.
Control-b moves the cursor to the left by one character.
'''
cmd.reinitialize()
cmd.fetch('3zp8', type='pdb', name= 'hammer', async='0')
cmd.rock()
cmd.do('preset.ball_and_stick("all")')
cmd.distance('Sodiumligand1',' resi 1044', 'chain A and i. 22 and n. N7')
cmd.distance('Sodiumligand2', 'resi 1044', 'chain A and i. 21 and n. OP2')
cmd.distance('Sodiumligand3', 'resi 1044', 'resi 2121')
cmd.distance('Sodiumligand4', 'resi 1044', 'resi 2120')
cmd.distance('Sodiumligand5', 'resi 1044', 'resi 2122')
cmd.distance('Sodiumligand6', 'resi 1044', 'resi 2130')
cmd.do('set label_size, -0.4')
cmd.set_view('(-0.87,0.18,-0.46,-0.39,-0.81,0.44,-0.29,0.56,0.78,-0.0,0.0,-20.47,-18.05,14.02,-18.89,17.47,23.47,-20.0);')
print('Enter "q6" to make the scene for question 6.')
print('Enter "help q6" to see question 6 and the commands to make the scene.')
def q8():
'''
DESCRIPTION
Question 8: Find the unusual base pair between A21 and
G36. What is the length of the H-bonds between the bases
(ignore the H atoms in the distance measurement)? List
the distance with the residue name, residue number, and
atom name. What additional H-bond occurs between a base
in this base pair and a ribose ring of one of the two
nucleotides in this base pair?
The following commands created the scene for "q8":
fetch 3zp8, hammer, async=0;hide everything;show ribbon;show sticks, resi 21 or resi 36;set_view (-0.9,-0.19,0.39,0.39,-0.74,0.55,0.19,0.65,0.74,0.0,0.0,-37.58,-21.66,15.71,-23.32,35.42,39.74,-20.0);rock;
To reuse of parts or all of the above commands, copy and paste the commands
onto the command line or into a plain text file.
These commands are sufficient for most editing tasks:
To edit code, positon cursor on command line with left mouse button.
Control-e moves the cursor to the end of the line, even when it is out of view.
Control-a moves the cursor to the beginning of the line, even when it is out of view.
Up arrow key recalls last line of commands for editing.
These commands may not be available on all systems:
Shift-control-a selects everything from the right of the cursor to the end of the line.
Shift-control-e selects everything to the left of the cursor to the end of the line.
Command-f moves the cursor to the end of the current word.
Command-b moves the cursor to the begining of the current word.
Control-f moves the cursor to the right by one character.
Control-b moves the cursor to the left by one character.
'''
cmd.reinitialize()
cmd.fetch('3zp8', type='pdb', name= 'hammer', async='0')
cmd.show_as('ribbon', 'hammer')
cmd.rock()
cmd.hide('everything')
cmd.show_as( 'ribbon','all')
cmd.show_as('sticks', 'resi 21 or resi 36')
cmd.set_view('(-0.9,-0.19,0.39,0.39,-0.74,0.55,0.19,0.65,0.74,0.0,0.0,-37.58,-21.66,15.71,-23.32,35.42,39.74,-20.0);')
print('Enter "q8" to make the scene for question 8.')
print('Enter "help q8" to see question 8 and the commands to make the scene.')
def load_pdb(self, num_proteins_seen, screenshotting, pdb_file_name=""): # use pymol wiki
cmd.delete("all") # prevent memory issues
# choose a pdb id
if num_proteins_seen > len(self.pedagogy):
self.pdb_file_name = random.sample(self.pedagogy, 1)[0]
elif (num_proteins_seen < len(self.pedagogy) and pdb_file_name == ""):
self.pdb_file_name = self.pedagogy[num_proteins_seen]
# fetch or load pdb
self.pdb_file_path = "./pdbs/"+self.pdb_file_name+".pdb"
if not os.path.exists(self.pdb_file_path):
cmd.fetch(self.pdb_file_name, path="./inputs/pdbs", type="pdb")
elif os.path.exists(self.pdb_file_path):
cmd.load(self.pdb_file_path)
cmd.remove("solvent")
# summarize
print(self.params.run_time_stamp, " is loading ", num_proteins_seen, self.pdb_file_path)
print("")
num_atoms = cmd.count_atoms("all")
print("noise mean", self.params.noise_mean, "noise scale", self.params.noise_scale)
# convert pdb2tensor
original_model = cmd.get_model('all', 1)
original_coords_list = cmd.get_model('all', 1).get_coord_list()
original = tf.convert_to_tensor(np.array(original_coords_list), dtype=tf.float32)
chains = cmd.get_chains()
if (screenshotting):
self.current_pdb_screenshot_path = self.params.screenshot_folder_path + "/" + self.pdb_file_name + "-" + str(num_proteins_seen) + "/"
os.makedirs(self.current_pdb_screenshot_path)
prepare_pymol()
take_screenshot(self.params, self.pdb_file_name, num_proteins_seen, "0")
num_steps = random.randint(self.params.min_steps_in_undock, self.params.max_steps_in_undock)
self.undock(num_proteins_seen, screenshotting, num_steps, chains)
undocked_coords_list = cmd.get_model('all', 1).get_coord_list()
undocked = tf.convert_to_tensor(np.array(undocked_coords_list), dtype=tf.float32)
# calculate center of mass dict
self.center_of_mass_dict = AttrDict()
self.center_of_mass_dict["all"] = cmd.centerofmass("all")
for chain in chains:
self.center_of_mass_dict[chain] = cmd.centerofmass("chain {}".format(chain))
features = np.array([self.extract(atom) for atom in original_model.atom])
features = tf.convert_to_tensor(features, dtype=tf.float32)
#outputs
output_tuple = (self.center_of_mass_dict, num_steps, undocked, features, original, chains)
return output_tuple
def main():
parser=argparse.ArgumentParser()
parser.add_argument('-p', action='store', required=True, dest='pdbfile',
help='pathfile is a textfile of name of pdb')
parser.add_argument('-l', action='store', required=True, dest='loop',
help='loop is an int number')
parser.add_argument('-c', action='store', required=True, dest='chain',
help='the chain number is needed')
parser.add_argument('-c1', action='store', required=True, dest='chain1',
help='the chain number is needed')
inputs=parser.parse_args()
pdbfile=inputs.pdbfile
removechains='not chain '+inputs.chain+'+'+inputs.chain1
removechain='chain '+inputs.chain
loop=int(inputs.loop)
print "loop is %s "% loop
dirname=os.getcwd()+'/interface_analyzer/pdbdata/'+pdbfile
pdbfileselect=pdbfile.split('.')
savefile=os.getcwd()+'/interface_analyzer/pdbdata/'+pdbfileselect[0]+'_antigen.pdb'
print "remove antibody of complex,so can caculate the value of antigen sasa "
pymol.finish_launching()
if loop!=0:
pymol.cmd.reinitialize()
cmd.fetch(pdbfileselect[0],async=0)
#cmd.select('targetfile',pdbfileselect[0])
#cmd.save(dirname,(('targetfile')))
#cmd.delete(all)
#cmd.load(dirname)
cmd.remove(removechains)
#cmd.remove('solvent')
#cmd.remove('hydrogens')
#cmd.remove('hetatm')
cmd.select('target1',pdbfileselect[0])
cmd.save(dirname,(('target1')))
cmd.remove('solvent')
cmd.remove('hydrogens')
cmd.remove('not '+removechain)
cmd.select('target',pdbfileselect[0])
cmd.save(savefile,(('target')))
cmd.delete(all)
cmd.sync()
cmd.quit()
print "remove the antibody of complex have done"
def q7():
'''
DESCRIPTION
Question 7: Measure the longest dimension and the
shortest dimension of the ribozyme. Enter "rock" to
stop the rocking motion. What is the ratio of
the longest dimension to the shortest dimension? Is it
globular like a protein?
The following commands created the scene for "q7":
delete all;fetch 3zp8, hammer, async=0;show ribbon, hammer;set_view (0.62,0.14,0.78,0.13,-0.99,0.07,0.78,0.05,-0.63,-0.0,-0.0,-169.8,-16.43,9.44,-9.63,143.54,196.05,-20.0); rock;
To reuse of parts or all of the above commands, copy and paste the commands
onto the command line or into a plain text file.
These commands are sufficient for most editing tasks:
To edit code, positon cursor on command line with left mouse button.
Control-e moves the cursor to the end of the line, even when it is out of view.
Control-a moves the cursor to the beginning of the line, even when it is out of view.
Up arrow key recalls last line of commands for editing.
These commands may not be available on all systems:
Shift-control-a selects everything from the right of the cursor to the end of the line.
Shift-control-e selects everything to the left of the cursor to the end of the line.
Command-f moves the cursor to the end of the current word.
Command-b moves the cursor to the begining of the current word.
Control-f moves the cursor to the right by one character.
Control-b moves the cursor to the left by one character.
'''
cmd.reinitialize()
cmd.fetch('3zp8', type='pdb', name='hammer', async='0')
cmd.show_as('ribbon', 'hammer')
cmd.rock()
cmd.set_view(
'(0.62,0.14,0.78,0.13,-0.99,0.07,0.78,0.05,-0.63,-0.0,-0.0,-169.8,-16.43,9.44,-9.63,143.54,196.05,-20.0);'
)
print('Enter "q7" to make the scene for question 7.')
print(
'Enter "help q7" to see question 7 and the commands to make the scene.'
)
def load(type, id, screenshot=False):
# we clear pymol, make filename and path
cmd.delete('all')
file_name = f'{id}.{type}' if type is 'cif' else id
dataset_path = os.path.join(DATASETS_ROOT, type)
path = os.path.join(dataset_path, file_name)
# we load the target
print(f'load {id} {path}')
if type is "cif":
if not os.path.exists(path):
cmd.fetch(id, path=dataset_path)
elif os.path.exists(path):
cmd.load(path)
# make target
clean_pymol()
model = cmd.get_model('all', 1)
target = get_positions(model)
# make the model inputs
if screenshot:
prepare_pymol()
take_screenshot("0")
chains = cmd.get_chains('all')
if len(chains) == 0:
return False
if random.random() < P_UNDOCK:
print('undocking')
undock(chains, type)
if random.random() < P_UNFOLD:
print('unfolding')
unfold(chains)
model = cmd.get_model('all', 1)
positions = get_positions(model)
if positions.shape[0] > MAX_ATOMS:
print(f"{positions.shape[0]} IS TOO MANY ATOMS")
return False
features = get_features(model)
masses = get_masses(model)
numbers = get_numbers(model)
features = tf.concat([features, masses, numbers], -1)
target = tf.concat([target, features], -1)
return make_example(id, target, positions, features, masses)
def q3():
'''
DESCRIPTION
Question 3: In which groove of the DNA
is the protein making the most contacts?
Is this unusual?
The following commands created the scene for "q3":
delete all; fetch 3v6d, HIVrt, async=0; show cartoon, c. A or c. B;hide lines, c. A or c. B;set_view (0.53,-0.06,-0.84,0.82,-0.21,0.53,-0.21,-0.98,-0.07,-0.0,-0.0,-192.99,-29.84,8.42,47.76,178.27,207.7,-20.0);rock;
To reuse of parts or all of the above commands, copy and paste the commands
onto the command line or into a plain text file.
These commands are sufficient for most editing tasks:
To edit code, positon cursor on command line with left mouse button.
Control-e moves the cursor to the end of the line, even when it is out of view.
Control-a moves the cursor to the beginning of the line, even when it is out of view.
Up arrow key recalls last line of commands for editing.
These commands may not be available on all systems:
Shift-control-a selects everything from the right of the cursor to the end of the line.
Shift-control-e selects everything to the left of the cursor to the end of the line.
Command-f moves the cursor to the end of the current word.
Command-b moves the cursor to the begining of the current word.
Control-f moves the cursor to the right by one character.
Control-b moves the cursor to the left by one character.
'''
cmd.reinitialize()
cmd.fetch('3v6d', type='pdb', name='HIVrt', async='0')
cmd.show_as("cartoon", "c. A or c. B")
cmd.hide("lines", "c. A or c. B")
cmd.rock()
cmd.set_view(
'(0.53,-0.06,-0.84,0.82,-0.21,0.53,-0.21,-0.98,-0.07,-0.0,-0.0,-192.99,-29.84,8.42,47.76,178.27,207.7,-20.0);'
)
print('Enter "q3" to make the scene for question 3.')
print(
'Enter "help q3" to see question 3 and the commands to make the scene.'
)
def beautify_images(protein_name, residue_sets):
cmd.delete("all")
cmd.fetch(protein_name, async_=0)
cmd.color(
"0xFFFFFF"
) # colors the entire protein white (so that the predictions can be colored)
cmd.hide("lines")
cmd.hide("spheres")
cmd.show("cartoon")
sphere_size = f"vdw={SPHERE_SIZE}" # the size of the rendered sphere
for res_set in residue_sets:
cmd.color(res_set.color,
res_set.selection_string) # colors annotated blue
cmd.show("spheres", res_set.selection_string)
cmd.alter(res_set.selection_string,
sphere_size) # changes the sphere size
cmd.rebuild() # rerenders the spheres to the new size
# cmd.color(annotated.color, annotated.selection_string) # colors annotated blue
# cmd.color(wrong.color, wrong.selection_string) # colors wrongly predicted red
# cmd.color(correct.color, correct.selection_string) # colors correctly predicted green
# cmd.show("spheres", annotated.selection_string)
# cmd.show("spheres", correct.selection_string)
# cmd.show("spheres", wrong.selection_string)
# cmd.alter(wrong.selection_string, sphere_size) # changes the sphere size
# cmd.alter(correct.selection_string, sphere_size)
# cmd.alter(annotated.selection_string, sphere_size)
# cmd.rebuild() # rerenders the spheres to the new size
cmd.remove("resn hoh") # removes the HOH's from image
cmd.orient(residue_sets[0].selection_string)
cmd.zoom(complete=1)
cmd.set("depth_cue", "0") # removes shadows of depth
cmd.center(protein_name)
def testFetchLocal(self):
try:
import urllib.parse as urlparse
except ImportError:
import urlparse
# PyMOL 1.8.6 adds full URLs, remove them
import pymol
pdbpaths = pymol.importing.hostPaths['pdb']
pdbpaths[:] = [p for p in pdbpaths if '://' not in p]
with testing.mkdtemp() as fetch_path:
names = []
cmd.set('fetch_path', fetch_path)
cmd.set(
'fetch_host',
urlparse.urlunsplit(
['file', '',
self.datafile('pdb.mirror'), '', '']))
cmd.fetch('1avy', type='pdb')
names += ['1avy']
self.assertItemsEqual(cmd.get_names(), names)
cmd.fetch('1avyB', type='pdb')
names += ['1avyB']
self.assertItemsEqual(cmd.get_names(), names)
self.assertEqual(cmd.get_chains('1avyB'), ['B'])
cmd.fetch('1aq5', type='pdb', multiplex=1)
names += ['1aq5_%04d' % (i + 1) for i in range(20)]
self.assertItemsEqual(cmd.get_names(), names)
def testFetchLocal(self):
try:
import urllib.parse as urlparse
except ImportError:
import urlparse
# PyMOL 1.8.6 adds full URLs, remove them
import pymol
pdbpaths = pymol.importing.hostPaths['pdb']
pdbpaths[:] = [p for p in pdbpaths if '://' not in p]
with testing.mkdtemp() as fetch_path:
names = []
cmd.set('fetch_path', fetch_path)
cmd.set('fetch_host', urlparse.urlunsplit(['file', '',
self.datafile('pdb.mirror'), '', '']))
cmd.fetch('1avy', type='pdb')
names += ['1avy']
self.assertItemsEqual(cmd.get_names(), names)
cmd.fetch('1avyB', type='pdb')
names += ['1avyB']
self.assertItemsEqual(cmd.get_names(), names)
self.assertEqual(cmd.get_chains('1avyB'), ['B'])
cmd.fetch('1aq5', type='pdb', multiplex=1)
names += ['1aq5_%04d' % (i+1) for i in range(20)]
self.assertItemsEqual(cmd.get_names(), names)
def testFetchLocal(self):
try:
import urllib.parse as urlparse
except ImportError:
import urlparse
with testing.mkdtemp() as fetch_path:
names = []
cmd.set('fetch_path', fetch_path)
cmd.set(
'fetch_host',
urlparse.urlunsplit(
['file', '',
self.datafile('pdb.mirror'), '', '']))
cmd.fetch('1avy', type='pdb')
names += ['1avy']
self.assertItemsEqual(cmd.get_names(), names)
cmd.fetch('1avyB', type='pdb')
names += ['1avyB']
self.assertItemsEqual(cmd.get_names(), names)
self.assertEqual(cmd.get_chains('1avyB'), ['B'])
cmd.fetch('1aq5', type='pdb', multiplex=1)
names += ['1aq5_%04d' % (i + 1) for i in range(20)]
self.assertItemsEqual(cmd.get_names(), names)
def q4():
'''
DESCRIPTION
Question 4: What the dihedral angle about the disulfide
bond between MRG81 of chain F and Cys258 of chain C?
This is a cross link between the protein and the DNA. Is
this a cis or trans conformation of the bonds about the
S--S bond? Is this conformation energetically favorable
or unfavorable?
The following commands created the scene for "q4":
delete all; fetch 3v6d, HIVrt, async=0;preset.ball_and_stick("(c. C and i. 258) or (c. F and i. 817 )");set_view (0.21,-0.91,0.34,-0.84,0.01,0.54,-0.5,-0.4,-0.77,0.0,-0.0,-38.82,-39.67,-55.1,10.96,36.31,41.34,-20.0);
To reuse of parts or all of the above commands, copy and paste the commands
onto the command line or into a plain text file.
These commands are sufficient for most editing tasks:
To edit code, positon cursor on command line with left mouse button.
Control-e moves the cursor to the end of the line, even when it is out of view.
Control-a moves the cursor to the beginning of the line, even when it is out of view.
Up arrow key recalls last line of commands for editing.
These commands may not be available on all systems:
Shift-control-a selects everything from the right of the cursor to the end of the line.
Shift-control-e selects everything to the left of the cursor to the end of the line.
Command-f moves the cursor to the end of the current word.
Command-b moves the cursor to the begining of the current word.
Control-f moves the cursor to the right by one character.
Control-b moves the cursor to the left by one character.
'''
cmd.reinitialize()
cmd.fetch('3v6d',type='pdb',name='HIVrt',async='0')
cmd.do("preset.ball_and_stick(selection='(chain C and resi 258) or (chain F and resi 817 )')")
cmd.set_view('(0.21,-0.91,0.34,-0.84,0.01,0.54,-0.5,-0.4,-0.77,0.0,-0.0,-38.82,-39.67,-55.1,10.96,36.31,41.34,-20.0);')
cmd.rock()
print('Enter "q4" to make the scene for question 4.')
print('Enter "help q4" to see question 4 and the commands to make the scene.')
def q7():
'''
DESCRIPTION
Question 7: Measure the longest dimension and the
shortest dimension of the ribozyme. Enter "rock" to
stop the rocking motion. What is the ratio of
the longest dimension to the shortest dimension? Is it
globular like a protein?
The following commands created the scene for "q7":
delete all;fetch 3zp8, hammer, async=0;show ribbon, hammer;set_view (0.62,0.14,0.78,0.13,-0.99,0.07,0.78,0.05,-0.63,-0.0,-0.0,-169.8,-16.43,9.44,-9.63,143.54,196.05,-20.0); rock;
To reuse of parts or all of the above commands, copy and paste the commands
onto the command line or into a plain text file.
These commands are sufficient for most editing tasks:
To edit code, positon cursor on command line with left mouse button.
Control-e moves the cursor to the end of the line, even when it is out of view.
Control-a moves the cursor to the beginning of the line, even when it is out of view.
Up arrow key recalls last line of commands for editing.
These commands may not be available on all systems:
Shift-control-a selects everything from the right of the cursor to the end of the line.
Shift-control-e selects everything to the left of the cursor to the end of the line.
Command-f moves the cursor to the end of the current word.
Command-b moves the cursor to the begining of the current word.
Control-f moves the cursor to the right by one character.
Control-b moves the cursor to the left by one character.
'''
cmd.reinitialize()
cmd.fetch('3zp8', type='pdb', name= 'hammer', async='0')
cmd.show_as('ribbon', 'hammer')
cmd.rock()
cmd.set_view('(0.62,0.14,0.78,0.13,-0.99,0.07,0.78,0.05,-0.63,-0.0,-0.0,-169.8,-16.43,9.44,-9.63,143.54,196.05,-20.0);')
print('Enter "q7" to make the scene for question 7.')
print('Enter "help q7" to see question 7 and the commands to make the scene.')
def q3():
'''
DESCRIPTION
Question 3: In which groove of the DNA
is the protein making the most contacts?
Is this unusual?
The following commands created the scene for "q3":
delete all; fetch 3v6d, HIVrt, async=0; show cartoon, c. A or c. B;hide lines, c. A or c. B;set_view (0.53,-0.06,-0.84,0.82,-0.21,0.53,-0.21,-0.98,-0.07,-0.0,-0.0,-192.99,-29.84,8.42,47.76,178.27,207.7,-20.0);rock;
To reuse of parts or all of the above commands, copy and paste the commands
onto the command line or into a plain text file.
These commands are sufficient for most editing tasks:
To edit code, positon cursor on command line with left mouse button.
Control-e moves the cursor to the end of the line, even when it is out of view.
Control-a moves the cursor to the beginning of the line, even when it is out of view.
Up arrow key recalls last line of commands for editing.
These commands may not be available on all systems:
Shift-control-a selects everything from the right of the cursor to the end of the line.
Shift-control-e selects everything to the left of the cursor to the end of the line.
Command-f moves the cursor to the end of the current word.
Command-b moves the cursor to the begining of the current word.
Control-f moves the cursor to the right by one character.
Control-b moves the cursor to the left by one character.
'''
cmd.reinitialize()
cmd.fetch('3v6d', type='pdb', name= 'HIVrt', async='0')
cmd.show_as("cartoon","c. A or c. B")
cmd.hide("lines","c. A or c. B")
cmd.rock()
cmd.set_view('(0.53,-0.06,-0.84,0.82,-0.21,0.53,-0.21,-0.98,-0.07,-0.0,-0.0,-192.99,-29.84,8.42,47.76,178.27,207.7,-20.0);')
print('Enter "q3" to make the scene for question 3.')
print('Enter "help q3" to see question 3 and the commands to make the scene.')
def q2():
'''
DESCRIPTION
Question 2: Look along the helical axis of the DNA.
Is the DNA helix bent?
The following commands created the scene for "q2":
delete all; fetch 3v6d, HIVrt, async=0; rock;show cartoon, c. P or c. T;set_view (0.61,0.29,-0.73,0.78,-0.37,0.51,-0.12,-0.88,-0.45,-0.0,-0.0,-192.99,-29.84,8.42,47.76,178.27,207.7,-20.0);
To reuse of parts or all of the above commands, copy and paste the commands
onto the command line or into a plain text file.
These commands are sufficient for most editing tasks:
To edit code, positon cursor on command line with left mouse button.
Control-e moves the cursor to the end of the line, even when it is out of view.
Control-a moves the cursor to the beginning of the line, even when it is out of view.
Up arrow key recalls last line of commands for editing.
These commands may not be available on all systems:
Shift-control-a selects everything from the right of the cursor to the end of the line.
Shift-control-e selects everything to the left of the cursor to the end of the line.
Command-f moves the cursor to the end of the current word.
Command-b moves the cursor to the begining of the current word.
Control-f moves the cursor to the right by one character.
Control-b moves the cursor to the left by one character.
'''
cmd.reinitialize()
cmd.fetch('3v6d',type='pdb',name='HIVrt',async='0')
cmd.rock()
cmd.show_as("cartoon","chain P or chain T")
cmd.set_view('(0.61,0.29,-0.73,0.78,-0.37,0.51,-0.12,-0.88,-0.45,-0.0, 0.0,-192.99,-29.84,8.42,47.76,178.27,207.7,-20.0);')
print('Enter "q2" to make the scene for question 2.')
print('Enter "help q2" to see question 2 and the commands to make the scene.')
def q1():
'''
DESCRIPTION
Question 1: Explain how AZT terminates extension of the DNA chain.
The following commands created the scene for "q1":
delete all; fetch 3v6d, HIVrt, async=0; rock;preset.ball_and_stick("c. P and i. 822");set_view (-0.99,-0.1,0.06,0.09,-0.39,0.92,-0.07,0.92,0.39,0.0,0.0,-29.2,-10.56,24.72,39.27,23.02,35.38,-20.0);
To reuse of parts or all of the above commands, copy and paste the commands
onto the command line or into a plain text file.
These commands are sufficient for most editing tasks:
To edit code, positon cursor on command line with left mouse button.
Control-e moves the cursor to the end of the line, even when it is out of view.
Control-a moves the cursor to the beginning of the line, even when it is out of view.
Up arrow key recalls last line of commands for editing.
These commands may not be available on all systems:
Shift-control-a selects everything from the right of the cursor to the end of the line.
Shift-control-e selects everything to the left of the cursor to the end of the line.
Command-f moves the cursor to the end of the current word.
Command-b moves the cursor to the begining of the current word.
Control-f moves the cursor to the right by one character.
Control-b moves the cursor to the left by one character.
'''
cmd.reinitialize()
cmd.fetch('3v6d', type='pdb', name='HIVrt',async='0')
cmd.rock()
preset.ball_and_stick('c. P and i. 822')
cmd.set_view('(-0.99,-0.1,0.06,0.09,-0.39,0.92,-0.07,\
0.92,0.39,0.0,0.0,-29.2,-10.56,24.72,39.27,\
23.02,35.38,-20.0)')
print('Enter "q1" to set scene for question 1.')
print('Enter "help q1" for more information.')
def callback(*args):
code = var_code.get()
type = get_trunc(var_type)
if type == 'pdb':
code += var_chain.get()
try:
result = cmd.fetch(code, type=type)
if result == -1:
raise CmdException('You entered an invalid pdb code: ' + code)
except CmdException as e:
import tkMessageBox
tkMessageBox.showerror('Error', str(e), parent=self)
return
cmd.log('fetch %s, type=%s, async=0\n' % (code, type))
if not var_keep.get():
self.destroy()
def __init__(self, app):
import tkSimpleDialog
import tkMessageBox
import urllib
import gzip
import os
import string
pdbCode = tkSimpleDialog.askstring('PDB Loader Service',
'Please enter a 4-digit pdb code:',
parent=app.root)
if pdbCode: # None is returned for user cancel
result = cmd.fetch(pdbCode)
if result==-1:
tkMessageBox.showerror('Invalid Code',
'You entered an invalid pdb code: ' + pdbCode,
parent=app.root)
def testFetchLocal(self):
import urlparse
with testing.mkdtemp() as fetch_path:
names = []
cmd.set('fetch_path', fetch_path)
cmd.set('fetch_host', urlparse.urlunsplit(['file', '',
self.datafile('pdb.mirror'), '', '']))
cmd.fetch('1avy')
names += ['1avy']
self.assertItemsEqual(cmd.get_names(), names)
cmd.fetch('1avyB')
names += ['1avyB']
self.assertItemsEqual(cmd.get_names(), names)
self.assertEqual(cmd.get_chains('1avyB'), ['B'])
cmd.fetch('1aq5', multiplex=1)
names += ['1aq5_%04d' % (i+1) for i in range(20)]
self.assertItemsEqual(cmd.get_names(), names)
obj.extend( [ NORMAL] + n0 )
if not hand:
obj.extend( [ VERTEX ] + v0 + [ VERTEX ] + v1 )
else:
obj.extend( [ VERTEX ] + v1 + [ VERTEX ] + v0 )
obj.extend( [END] )
# then we load it into PyMOL
cmd.load_cgo(obj,'cgo06')
# position haemolysin through pore
if 1:
cmd.fetch("7ahl",async=0)
cmd.transform_selection("7ahl",
(0.70349078502033213, 0.19033556773811347, -0.68474258132841503, -11.993190038310882,
-0.15869362855324043, 0.98121371667870472, 0.10970571819737528, -29.939406659327624,
0.69276001846262825, 0.03148755047390385, 0.72048024614206196, -26.250180846754432,
0.0, 0.0, 0.0, 1.0))
cmd.show_as("cartoon","7ahl")
cmd.do("util.cbc")
cmd.set_view((\
-0.589197695, -0.440498680, 0.677344978,\
0.574851871, -0.817646086, -0.031699535,\
0.567794442, 0.370693058, 0.734975874,\
0.000004128, -0.000099868, -651.343872070,\
-4.874452114, 8.360315323, 11.387301445,\
target.send(hand)
else:
target.send(None)
@coroutine
def select_all():
previous_hand = None
while True:
hand = (yield)
if hand and not previous_hand:
cmd.select('all')
elif previous_hand and not hand:
cmd.select('none')
previous_hand = hand
cmd.fetch('1rx1')
cmd.orient()
listener = PymolListener(
broadcaster([
hands_splitter(
pinch_filter(
broadcaster([
hand_rotator(),
select_all()]
))
),
multi_hands_filter(
frame_scaler()
)
]))
import pymol
from pymol import cmd
#pymol.pymol_argv = [ 'pymol', '-qc'] # Quiet / no GUI
pymol.finish_launching()
cmd.fetch('1TUP', async=False)
cmd.disable('all')
cmd.enable('1TUP')
cmd.hide('all')
cmd.show('sphere', 'name zn')
cmd.show('surface', 'chain A+B+C')
cmd.show('cartoon', 'chain E+F')
cmd.scene('S0', action='store', view=0, frame=0, animate=-1)
cmd.show('cartoon')
cmd.hide('surface')
cmd.scene('S1', action='store', view=0, frame=0, animate=-1)
cmd.hide('cartoon', 'chain A+B+C')
cmd.show('mesh', 'chain A')
cmd.show('sticks', 'chain A+B+C')
cmd.scene('S2', action='store', view=0, frame=0, animate=-1)
cmd.set('ray_trace_mode', 0)
cmd.mset(1, 500)
cmd.frame(0)
Then enter the name of an alias from the list above, for example:
site11
To reuse of parts or all of the above commands, copy and paste the commands
onto the command line or into a plain text file.
These commands are sufficient for most editing tasks:
To edit code, positon cursor on command line with left mouse button.
Control-e moves the cursor to the end of the line, even when it is out of view.
Control-a moves the cursor to the beginning of the line, even when it is out of view.
Up arrow key recalls last line of commands for editing.
These commands may not be available on all systems:
Shift-control-a selects everything from the right of the cursor to the end of the line.
Shift-control-e selects everything to the left of the cursor to the end of the line.
Command-f moves the cursor to the end of the current word.
Command-b moves the cursor to the begining of the current word.
Control-f moves the cursor to the right by one character.
Control-b moves the cursor to the left by one character.
"""
cmd.extend('wtT4L',wtT4L)
print(wtT4L.__doc__)
cmd.bg_color("white")
cmd.fetch(code="3fa0", name="wtT4L",state = 0,async='0')
cmd.alias('site11', 'zoom resi 11; preset.technical("wtT4L")')
cmd.alias('site31', 'preset.ball_and_stick("wtT4L");@S3_File.pml;set_view (0.31,-0.93,0.21,0.92,0.24,-0.29,0.22,0.28,0.93,-0.09,-0.05,-9.88,37.55,10.06,30.09,20.0,23.82,-20.0);')
cmd.alias('site96', 'preset.technical("wtT4L");set_view (-0.75,-0.65,0.11,0.62,-0.75,-0.22,0.22,-0.1,0.97,0.0,-0.0,-32.32,29.16,-1.45,6.77,27.32,37.32,-20.0);')
cmd.alias('site99', 'preset.ball_and_stick("wtT4L");color bluewhite, i. 99; set_view (-0.24,-0.95,-0.21,0.51,0.07,-0.85,0.83,-0.32,0.46,0.03,-0.5,-5.37,22.35,-18.6,18.83,29.89,37.68,-20.0);')
cmd.alias('site145', 'preset.technical("wtT4L");set_view (0.02,-0.63,-0.78,0.37,0.73,-0.56,0.93,-0.27,0.24,0.19,-0.3,-0.0,24.28,2 .24,13.53,15.23,21.26,-20.0);')
obj.extend( [ NORMAL] + n0 )
if not hand:
obj.extend( [ VERTEX ] + v0 + [ VERTEX ] + v1 )
else:
obj.extend( [ VERTEX ] + v1 + [ VERTEX ] + v0 )
obj.extend( [END] )
# then we load it into PyMOL
cmd.load_cgo(obj,'cgo06')
# position haemolysin through pore
if 1:
cmd.fetch("7ahl")
cmd.transform_selection("7ahl",
(0.70349078502033213, 0.19033556773811347, -0.68474258132841503, -11.993190038310882,
-0.15869362855324043, 0.98121371667870472, 0.10970571819737528, -29.939406659327624,
0.69276001846262825, 0.03148755047390385, 0.72048024614206196, -26.250180846754432,
0.0, 0.0, 0.0, 1.0))
cmd.show_as("cartoon","7ahl")
cmd.do("util.cbc")
cmd.set_view((\
-0.589197695, -0.440498680, 0.677344978,\
0.574851871, -0.817646086, -0.031699535,\
0.567794442, 0.370693058, 0.734975874,\
0.000004128, -0.000099868, -651.343872070,\
-4.874452114, 8.360315323, 11.387301445,\