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µÚ¶þ²½ ½¨Á¢Ò»¸öget_ali.py ½Å±¾Îļþ
# get sequece of the 2FMX PDB file, and write to an alignment file.
log.verbose()
env = environ()
env.io.atom_files_directories = ['.', '../atom_file']
code = '2FMX'
m = model(env, file=code)
aln = alignment(env)
aln.append_model(m, align_codes=code)
aln.write(code+'.seq')
µÚÈý²½ £ºÔËÐÐ modpv7 get_ali.py ²úÉúÒ»¸ösequence Îļþ£º2FMX.seq
>P1;2FMX
structureX:2FMX: 13 :A:+556 :B:MOL_ID 1; MOLECULE GTP-BINDING PROTEIN SAR1B; CHAIN A, B; FRAGMENT RESIDUES 10-198; SYNONYM SAR1, GTBPB; ENGINEERED YES:MOL_ID 1; ORGANISM_SCIENTIFIC CRICETULUS GRISEUS; ORGANISM_COMMON CHINESE HAMSTER; ORGANISM_TAXID 10029; EXPRESSION_SYSTEM ESCHERICHIA COLI; EXPRESSION_SYSTEM_TAXID 562; EXPRESSION_SYSTEM_VECTOR_TYPE PLASMID; EXPRESSION_SYSTEM_PLASMID PET11D: 1.82:-1.00
SSVLQFLGLYKKTGKLVFLGLDNAGKTTLLHMLKDDRLGQHVPTLHPTSEELTIAGMTFTTFDLGRVWKNYLPAI
NGIVFLVDCADHERLLESKEELDSLMTDETIANVPILILGNKIDRPEAISEERLREMFGLYGQTTGKGSVSLKEL
NARPLEVFMCSVLKRQGYGEGFRWMAQYID
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>P1;2FMX
structureX:2FMX.pdb: 13 :A:4872 :A:undefined:undefined:-1.00:-1.00
SSVL---QFLGLYKKTGKLVFLGLDNAGKTTLLHMLKDDRLGQHVPTLHPTSEELTIAGMTFTTFDLGRVWKNYLPAI
NGIVFLVDCADHERLLESKEELDSLMTDETIANVPILILGNKIDRPEAISEERLREMFGLYGQTTGKGSVSLKEL
NARPLEVFMCSVLKRQGYGEGFRWMAQYID---
>P1;2FMX_fill
sequence:2FMX_fill: :A : :A ::: 0.00: 0.00
SSVLHJKQFLGLYKKTGKLVFLGLDNAGKTTLLHMLKDDRLGQHVPTLHPTSEELTIAGMTFTTFDLGRVWKNYLPAI
NGIVFLVDCADHERLLESKEELDSLMTDETIANVPILILGNKIDRPEAISEERLREMFGLYGQTTGKGSVSLKEL
NARPLEVFMCSVLKRQGYGEGFRWMAQYIDLPO
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from modeller import *
from modeller.automodel import * # Load the automodel class
log.verbose()
env = environ()
# directories for input atom files
env.io.atom_files_directories = ['.', '../atom_file']
class MyModel(loopmodel):
def select_atoms(self):
return selection(self.residue_range('1:A', '9:A'),
self.residue_range('68:A', '73:A'),
a = MyModel(env,
alnfile = 'alignment.ali',
knowns = '2FMX',
sequence = '2FMX_fill')
a.starting_model = 1
a.ending_model = 2
a.make()
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µÚ¶þ²½ ½¨Á¢Ò»¸öget_ali.py ½Å±¾Îļþ
# get sequece of the 2FMX PDB file, and write to an alignment file.
log.verbose()
env = environ()
env.io.atom_files_directories = ['.', '../atom_file']
code = '2FMX'
m = model(env, file=code)
aln = alignment(env)
aln.append_model(m, align_codes=code)
aln.write(code+'.seq')
µÚÈý²½ £ºÔËÐÐ modpv7 get_ali.py ²úÉúÒ»¸ösequence Îļþ£º2FMX.seq
>P1;2FMX
structureX:2FMX: 13 :A:+556 :B:MOL_ID 1; MOLECULE GTP-BINDING PROTEIN SAR1B; CHAIN A, B; FRAGMENT RESIDUES 10-198; SYNONYM SAR1, GTBPB; ENGINEERED YES:MOL_ID 1; ORGANISM_SCIENTIFIC CRICETULUS GRISEUS; ORGANISM_COMMON CHINESE HAMSTER; ORGANISM_TAXID 10029; EXPRESSION_SYSTEM ESCHERICHIA COLI; EXPRESSION_SYSTEM_TAXID 562; EXPRESSION_SYSTEM_VECTOR_TYPE PLASMID; EXPRESSION_SYSTEM_PLASMID PET11D: 1.82:-1.00
SSVLQFLGLYKKTGKLVFLGLDNAGKTTLLHMLKDDRLGQHVPTLHPTSEELTIAGMTFTTFDLGRVWKNYLPAI
NGIVFLVDCADHERLLESKEELDSLMTDETIANVPILILGNKIDRPEAISEERLREMFGLYGQTTGKGSVSLKEL
NARPLEVFMCSVLKRQGYGEGFRWMAQYID
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>P1;2FMX
structureX:2FMX.pdb: 13 :A:4890 :A:undefined:undefined:-1.00:-1.00
SSVL---QFLGLYKKTGKLVFLGLDNAGKTTLLHMLKDDRLGQHVPTLHPTSEELTIAGMTFTTFDLGRVWKNYLPAI
NGIVFLVDCADHERLLESKEELDSLMTDETIANVPILILGNKIDRPEAISEERLREMFGLYGQTTGKGSVSLKEL
NARPLEVFMCSVLKRQGYGEGFRWMAQYID---.wwwwwwwwwwww
>P1;2FMX_fill
sequence:2FMX_fill: :A : :A ::: 0.00: 0.00
SSVLHJKQFLGLYKKTGKLVFLGLDNAGKTTLLHMLKDDRLGQHVPTLHPTSEELTIAGMTFTTFDLGRVWKNYLPAI
NGIVFLVDCADHERLLESKEELDSLMTDETIANVPILILGNKIDRPEAISEERLREMFGLYGQTTGKGSVSLKEL
NARPLEVFMCSVLKRQGYGEGFRWMAQYIDLPO. wwwwwwwwwwww
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from modeller import *
from modeller.automodel import * # Load the automodel class
log.verbose()
env = environ()
env.io.water = True
env.io.hetatm = True
# directories for input atom files
env.io.atom_files_directories = ['.', '../atom_file']
class MyModel(loopmodel):
def select_atoms(self):
return selection(self.residue_range('1:A', '9:A'),
self.residue_range('68:A', '73:A'),
a = MyModel(env,
alnfile = 'alignment.ali',
knowns = '2FMX',
sequence = '2FMX_fill')
a.starting_model = 1
a.ending_model = 2
a.make()
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µÚ¶þ²½ ½¨Á¢Ò»¸öget_ali.py ½Å±¾Îļþ
# get sequece of the 2FMX PDB file, and write to an alignment file.
log.verbose()
env = environ()
env.io.water = True
env.io.hetatm = True
env.io.atom_files_directories = ['.', '../atom_file']
code = '2FMX'
m = model(env, file=code)
aln = alignment(env)
aln.append_model(m, align_codes=code)
aln.write(code+'.seq')
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µÚÈý²½ £ºÔËÐÐ modpv7 get_ali.py ²úÉúÒ»¸ösequence Îļþ£º2FMX.seq
>P1;2FMX
structureX:2FMX: 13 :A:+556 :B:MOL_ID 1; MOLECULE GTP-BINDING PROTEIN SAR1B; CHAIN A, B; FRAGMENT RESIDUES 10-198; SYNONYM SAR1, GTBPB; ENGINEERED YES:MOL_ID 1; ORGANISM_SCIENTIFIC CRICETULUS GRISEUS; ORGANISM_COMMON CHINESE HAMSTER; ORGANISM_TAXID 10029; EXPRESSION_SYSTEM ESCHERICHIA COLI; EXPRESSION_SYSTEM_TAXID 562; EXPRESSION_SYSTEM_VECTOR_TYPE PLASMID; EXPRESSION_SYSTEM_PLASMID PET11D: 1.82:-1.00
SSVLQFLGLYKKTGKLVFLGLDNAGKTTLLHMLKDDRLGQHVPTLHPTSEELTIAGMTFTTFDLGRVWKNYLPAI
NGIVFLVDCADHERLLESKEELDSLMTDETIANVPILILGNKIDRPEAISEERLREMFGLYGQTTGKGSVSLKEL
NARPLEVFMCSVLKRQGYGEGFRWMAQYID/SSVLQFLGLYKKTGKLVFLGLDNAGKTTLLHMLKDPTLHPTSEE
LTIAGMTFTTFDLGVWKNYLPAINGIVFLVDCADHERLLESKEELDSLMTDETIANVPILILGNKIDRPEAISEE
RLREMFGLYGQTTGKGSVSLKELNARPLEVFMCSVLKRQGYGEGFRWMAQYID/.x/.$x/wwwwwwwwwwwwww
wwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwww
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>P1;2FMX
structureX:2FMX.pdb: 13 :A:4872 :B:undefined:undefined:-1.00:-1.00
---------SSVLQFLGLYKKTGKLVFLGLDNAGKTTLLHMLKDDRLGQHVPTLHPTSEELTIAGMTFTTFDLG------RVWKNYLPAI
NGIVFLVDCADHERLLESKEELDSLMTDETIANVPILILGNKIDRPEAISEERLREMFGLYGQTTGKGSVSLKEL
NARPLEVFMCSVLKRQGYGEGFRWMAQYID/---------SSVLQFLGLYKKTGKLVFLGLDNAGKTTLLHMLKD-------PTLHPTSEE
LTIAGMTFTTFDLG-------VWKNYLPAINGIVFLVDCADHERLLESKEELDSLMTDETIANVPILILGNKIDRPEAISEE
RLREMFGLYGQTTGKGSVSLKELNARPLEVFMCSVLKRQGYGEGFRWMAQYID/.x/.$x/wwwwwwwwwwwwww
wwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwww
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>P1;2FMX_fill
sequence:2FMX_fill: :A : :B ::: 0.00: 0.00
HHHHHHSGFSSVLQFLGLYKKTGKLVFLGLDNAGKTTLLHMLKDDRLGQHVPTLHPTSEELTIAGMTFTTFDLGGHIQARRVWKNYLPAI
NGIVFLVDCADHERLLESKEELDSLMTDETIANVPILILGNKIDRPEAISEERLREMFGLYGQTTGKGSVSLKEL
NARPLEVFMCSVLKRQGYGEGFRWMAQYID/HHHHHHSGFSSVLQFLGLYKKTGKLVFLGLDNAGKTTLLHMLKDDRLGQHVPTLHPTSEE
LTIAGMTFTTFDLGGHIQARRVWKNYLPAINGIVFLVDCADHERLLESKEELDSLMTDETIANVPILILGNKIDRPEAISEE
RLREMFGLYGQTTGKGSVSLKELNARPLEVFMCSVLKRQGYGEGFRWMAQYID/.x/.$x/wwwwwwwwwwwwww
wwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwww
wwwwwwwww/wwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwww
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µÚÎå²½ ½¨Á¢Ò»¸öselect.pyÎļþ £¬ÔÚÕâ¸öÎļþÖÐÎÒÃÇÖ»ÓÅ»¯²¹È«µÄÄDz¿·Ö²Ð»ù¡£
from modeller import *
from modeller.automodel import * # Load the automodel class
log.verbose()
env = environ()
# directories for input atom files
env.io.atom_files_directories = ['.', '../atom_file']
env.io.water = True
env.io.hetatm = True
class MyModel(loopmodel):
def select_atoms(self):
return selection(self.residue_range('1:A', '9:A'),
self.residue_range('68:A', '73:A'),
self.residue_range('196:B', '204:B'),
self.residue_range('240:B', '246:B'),
self.residue_range('270:B', '276:B'))
a = MyModel(env,
alnfile = 'ali-ligand.ali',
knowns = '2FMX',
sequence = '2FMX_fill')
a.starting_model = 1
a.ending_model = 2
a.make()
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µÚÁù²½ ÔËÐÐ mod9v7 select.py ½á¹ûÌáÈ¡pdbÎļþ¼´¿ÉÉÏÃæ˵µÄÖ»ÊÇһЩ»ù±¾µÄ¶«Î÷£¬ÒªÏëÉîÈëµÄѧºÃModeller »¹Òª»¨µãʱ¼ä¿´¿´ÔÚÏßµÄtutorial
http://salilab.org/modeller/tutorial/
[ Last edited by lei0736 on 2009-11-24 at 22:03 ] |
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