[modeller_usage] CORRECT SECOND LINE with CHAIN ID
To:
Subject: [modeller_usage] CORRECT SECOND LINE with CHAIN ID
From: bestkarollo <>
Date: Mon, 09 Oct 2006 17:31:26 +0200
Hello,
Thank you for previous advice - it helped.
I have another problem
1) I aligned structures with one sequence - alignmnent below
>P1;1ALU
structureX:1ALU:19 : :184 : : : : :
-------------------LTSSERIDKQIRYILDGISALRKETCN---KSNMCE---------NLNLPKMAEK--DGC---F-------QSGFNEETCLVKIITGLLEFEVYL-EYLQNRFE------SSEEQA-------RAVQMSTKVLIQFLQKKAKNLDA-----ITTPDPTTNASLLT--KLQAQNQW-LQDMTTHLILRSFKEFLQSSLRALRQM--------------------------------------------------------------------------------------------------*
>P1;1CNT
structureX:1CNT:12 : :187 : : : : :
---------------------------------------HRRDLCS---RS------IWLARKIRSDLTALTESYVKHQ---G-------LL--TEAERLQENLQAYRTFHVLLARLLEGDFH------QAI----------HTLLLQVAAFAYQIEELMILL-------EYKIPRNFEKKLWGLKVLQELSQWTVRSIHDLRFISSHQT----------GI----------------------------------------------------------------------------------P---------------*
>P1;1I1R
structureX:1I1RB:'6:B 172:B' : : : :
-------------------EFEKDLLIQRLNWMLWVIDECFRDLCY---RTGICKGILEPAAIFHLKLPAINDT--DHC---G-------LIGFNETSCLKKLADGFFEFEVL-FKFLTTEFG------KSVINV-------DVMELLTKTLGWDIQEELNKLTK-----THYSPPKFDRGLLG--RLQGLKYW-VRHFASFYVLSAMEKFAGQAVRVLDSI----------------------------------------------------------------------------------P---------------*
>P1;1AX8
structureX:1AX8:3 : :146 : :LEPTIN:HUMAN: 2.4: 0.215
------------------IQKVQDDTKTLIKTIVTRINDI----------------------------------------LDF-------IPGLHPILTLSKMDQTLAVYQQIL-TSMPS---------RNVIQI---SNDLENLRDLLHVLAFSK--------------SCHLPEAS-----GLETLDSLGG-VLEASGYSTEVVALSRLQGSLQDMLWQLD------------------------------------------------------------------------LSPGC--------------------*
>P1;spP41160
sequence:spP41160:1 : :146 : : : : :
----------------VPIQKVQDDTKTLIKTIVTRINDI--------------------------SHTQSVSAKQRVTGLDF-------IPGLHPILSLSKMDQTLAVYQQVL-TSLPS---------QNVLQI---ANDLENLRDLLHLLAFSK--------------SCSLPQTS-----GLQKPESLDG-VLEASLYSTEVVALSRLQGSLQDILQQLD------------------------------------------------------------------------VSPEC--------------------*
>P1;1EVS
structureX:1EVS:4 : :187 : : : : :
------------GSCSKEYRVLLGQLQKQTDLMQD-TSRLLDPYIRI-------QGLDVPKLREH-CRERPGAFPSE-E---T-------LRGLGRRGFLQTLNATLGCVLHRL-ADLEQRLPKAQDLERSGLNIEDLEK-LQMARPNILGLRNNIYCMA-QLLD-----------------------NASDA-FQRKLEGCRFLHGYHRFMHSVGRVFSKW--------------------------------------------------------------------------------------------------*
>P1;1LKI
structureX:1LKI:9 : :180 : : : : :
NATCAIR-----HPCHGN---LMNQIKNQLAQLNGSANALFISYYTA-------QGEPFPNNVEKLCAPNMTDFPSF-------------HGNGTEKTKLVELYRMVAYLSASL-TNITRDQ---KVLNPTAV--SLQVK-LNATIDVMRGLLSNVLCRLCNKYRVGHVDVPPVPDH-----------SDKEA-FQRKKLGCQLLGTYKQVISVVVQAF-----------------------------------------------------------------------------------------------------*
>P1;1PVH
structureX:1PVH:12 : :180 : : : : :
---CAIR-----HPCHNN---LMNQIRSQLAQLNGSANALFILYYTA-------QGEPFPNNLDKLCGPNVTDFPPF-------------HANGTEKAKLVELYRIVVYLGTSL-GNITRDQ---KILNPSAL--SLHSK-LNATADILRGLLSNVLCRLCSKYHVGHVDVTYGPDT-----------SGKDV-FQKKKLGCQLLGKYKQIIAVLAQAF-----------------------------------------------------------------------------------------------------*
>P1;1F6F
structureX:1F6F:1 : :197 : : : : :
A-QHPPYCRNQPGKCQIPLQSLFDRATTVANYNSKLAGEMVNRFDEQYV--------------I-NCHTSSITTPNSKA---E-------AINTEDKILFKLVISLLHSWDEPL-HHAVTEL---A-----NP--ALLTK-AQEIKEKAKVLVDGVEVIQKRIH-PGEK-NEPYPVWS-----EQSSLTSQDE-NVRRVAFYRLFHCLHRDSSKIYTYLRIL----------------------------------------------------------------------------------KCRLT---SC------*
>P1;1N9D
structureM:1N9D:1 : :199 : : : : :
----LPICPGGAARCQVTLRDLFDRAVVLSHYIHNLSSEMFSEFDKRYT---HGRGF-ITKAIN-SCHTSSLATPEDKE---Q-------AQQMNQKDFLSLIVSILRSWNEPL-YHLVTEV---RGMQEAPE--AILSK-AVEIEEQTKRLLEGMELIVSQVH-PETKENEIYPVWS-----GLPSLQMADE-ESRLSAYYNLLHCLRRDSHKIDNYLKLL----------------------------------------------------------------------------------KCRIIHNNNC------*
>P1;1HWG
structureX:1HWG:1 : :190 : : : : :
-------------FPTIPLSRLFDNAMLRAHRLHQLAFDTYQEFEEAYIPKEQKYSF-LQNPQTSLCFSESIPTPSNRE---E-------TQQKSNLELLRISLLLIQSWLEPV-QFLRSVF---A-----NS--LVYGASDSNVYDLLKDLEEGIQTLMGRLE-DGS------PRTG-----QIFKQTYSKF-DDALLKNYGLLYCFRKDMDKVETFLRIV----------------------------------------------------------------------------------QCRSVEGSCG------*
>P1;1BGC
structureX:1BGC:9 : :173 : : : : :
----------------SLPQSFLLKCLEQVRKIQADGAELQERLCA---AH-------------KLCHPEELMLLRHSLGIPQAPLSSCSSQSLQLRGCLNQLHGGLFLYQGLL-QALAGISP---ELAPTL----------DTLQLDVTDFATNIWLQMEDLGA-----APAMPTF-------------TSA-FQRRAGGVLVASQLHRFLELAYRGLRYLA-------------------------------------------------------------------------------------------------*
>P1;1RHG
structureX:1RHG:9 : :172 : : : : :
-----------------LPQSFLLKCLEQVRKIQGDGAALQEKLCA---TY-------------KLCHPEELVLLGHSLGIPWAPL---------LAGCLSQLHSGLFLYQGLL-QALEGISP---ELGPTL----------DTLQLDVADFATTIWQQMEELGM--------MPAF-------------ASA-FQRRAGGVLVASHLQSFLEVSYRVLRHLA-------------------------------------------------------------------------------------------------*
2) I obtained an error
openf5__224_> Open 11 OLD SEQUENTIAL $(LIB)/restyp.lib
openf5__224_> Open 11 OLD SEQUENTIAL ${MODINSTALL8v2}/modlib/resdih.lib
rdrdih__263_> Number of dihedral angle types : 9
Maximal number of dihedral angle optima: 3
Dihedral angle names : Alph Phi Psi Omeg chi1 chi2 chi3 chi4 chi5
openf5__224_> Open 11 OLD SEQUENTIAL ${MODINSTALL8v2}/modlib/radii.lib
openf5__224_> Open 11 OLD SEQUENTIAL ${MODINSTALL8v2}/modlib/radii14.lib
openf5__224_> Open 11 OLD SEQUENTIAL ${MODINSTALL8v2}/modlib/af_mnchdef.lib
rdwilmo_274_> Mainchain residue conformation classes: APBLE
openf5__224_> Open 11 OLD SEQUENTIAL ${MODINSTALL8v2}/modlib/mnch.lib
rdclass_257_> Number of classes: 5
openf5__224_> Open 11 OLD SEQUENTIAL ${MODINSTALL8v2}/modlib/mnch1.lib
openf5__224_> Open 11 OLD SEQUENTIAL ${MODINSTALL8v2}/modlib/mnch2.lib
openf5__224_> Open 11 OLD SEQUENTIAL ${MODINSTALL8v2}/modlib/mnch3.lib
openf5__224_> Open 11 OLD SEQUENTIAL ${MODINSTALL8v2}/modlib/xs4.mat
rdrrwgh_268_> Number of residue types: 21
runcmd______> alignment.append(align_codes=['1AX8', '1ALU', '1CNT', '1I1R', '1EVS', '1LKI', '1PVH', '1F6F', '1N9D', '1HWG', '1BGC', '1RHG', 'spP41160'], atom_files=[], file='MSA-CYTOKIN-T-COFFEE.ali', (def)remove_gaps=True, (def)alignment_format='PIR', add_sequence=True, (def)rewind_file=False, (def)close_file=True)
openf___224_> Open MSA-CYTOKIN-T-COFFEE.ali
Dynamically allocated memory at amaxalignment [B,kB,MB]: 2270569 2217.353 2.165
Dynamically allocated memory at amaxalignment [B,kB,MB]: 2293501 2239.747 2.187
Dynamically allocated memory at amaxalignment [B,kB,MB]: 2316901 2262.599 2.210
Dynamically allocated memory at amaxalignment [B,kB,MB]: 2363701 2308.302 2.254
Dynamically allocated memory at amaxalignment [B,kB,MB]: 2457301 2399.708 2.343
Read the alignment from file : MSA-CYTOKIN-T-COFFEE.ali
Total number of alignment positions: 238
# Code #_Res #_Segm PDB_code Name
-------------------------------------------------------------------------------
1 1AX8 130 1 1AX8 LEPTIN
2 1ALU 157 1 1ALU
3 1CNT 130 1 1CNT
4 1I1R 167 1 1I1R
5 1EVS 163 1 1EVS
6 1LKI 172 1 1LKI
7 1PVH 169 1 1PVH
8 1F6F 183 1 1F6F
9 1N9D 199 1 1N9D
10 1HWG 184 1 1HWG
11 1BGC 158 1 1BGC
12 1RHG 145 1 1RHG
13 spP41160 146 1 spP41160
runcmd______> alignment.check()
check_a_343_> >> BEGINNING OF COMMAND
openf5__224_> Open 11 OLD SEQUENTIAL ../atom_files\1AX8.pdb
Dynamically allocated memory at amaxstructure [B,kB,MB]: 2531305 2471.978 2.414
openf5__224_> Open 11 OLD SEQUENTIAL ../atom_files\1AX8.pdb
openf5__224_> Open 11 OLD SEQUENTIAL ../atom_files\1ALU.pdb
Dynamically allocated memory at amaxstructure [B,kB,MB]: 2621619 2560.175 2.500
openf5__224_> Open 11 OLD SEQUENTIAL ../atom_files\1ALU.pdb
openf5__224_> Open 11 OLD SEQUENTIAL ../atom_files\1CNT.pdb
rdpdb___303E> No atoms were read from the specified input PDB file, since the
starting residue number and/or chain id in MODEL_SEGMENT (or
the alignment file header) was not found;
requested starting position: residue number " 12", chain " "
rdabrk__288W> Protein not accepted: 3 1CNT
openf5__224_> Open 11 OLD SEQUENTIAL ../atom_files\1I1R.pdb
rdpdb___303E> No atoms were read from the specified input PDB file, since the
starting residue number and/or chain id in MODEL_SEGMENT (or
the alignment file header) was not found;
requested starting position: residue number " 6", chain " "
rdabrk__288W> Protein not accepted: 4 1I1R
openf5__224_> Open 11 OLD SEQUENTIAL ../atom_files\1EVS.pdb
rdpdb___303E> No atoms were read from the specified input PDB file, since the
starting residue number and/or chain id in MODEL_SEGMENT (or
the alignment file header) was not found;
requested starting position: residue number " 4", chain " "
rdabrk__288W> Protein not accepted: 5 1EVS
openf5__224_> Open 11 OLD SEQUENTIAL ../atom_files\1LKI.pdb
Dynamically allocated memory at amaxstructure [B,kB,MB]: 2719647 2655.905 2.594
openf5__224_> Open 11 OLD SEQUENTIAL ../atom_files\1LKI.pdb
openf5__224_> Open 11 OLD SEQUENTIAL ../atom_files\1PVH.pdb
rdpdb___303E> No atoms were read from the specified input PDB file, since the
starting residue number and/or chain id in MODEL_SEGMENT (or
the alignment file header) was not found;
requested starting position: residue number " 12", chain " "
rdabrk__288W> Protein not accepted: 7 1PVH
openf5__224_> Open 11 OLD SEQUENTIAL ../atom_files\1F6F.pdb
rdpdb___303E> No atoms were read from the specified input PDB file, since the
starting residue number and/or chain id in MODEL_SEGMENT (or
the alignment file header) was not found;
requested starting position: residue number " 1", chain " "
rdabrk__288W> Protein not accepted: 8 1F6F
openf5__224_> Open 11 OLD SEQUENTIAL ../atom_files\1N9D.pdb
rdpdb___303E> No atoms were read from the specified input PDB file, since the
starting residue number and/or chain id in MODEL_SEGMENT (or
the alignment file header) was not found;
requested starting position: residue number " 1", chain " "
rdabrk__288W> Protein not accepted: 9 1N9D
openf5__224_> Open 11 OLD SEQUENTIAL ../atom_files\1HWG.pdb
rdpdb___303E> No atoms were read from the specified input PDB file, since the
starting residue number and/or chain id in MODEL_SEGMENT (or
the alignment file header) was not found;
requested starting position: residue number " 1", chain " "
rdabrk__288W> Protein not accepted: 10 1HWG
openf5__224_> Open 11 OLD SEQUENTIAL ../atom_files\1BGC.pdb
Dynamically allocated memory at amaxstructure [B,kB,MB]: 2808743 2742.913 2.679
openf5__224_> Open 11 OLD SEQUENTIAL ../atom_files\1BGC.pdb
openf5__224_> Open 11 OLD SEQUENTIAL ../atom_files\1RHG.pdb
rdpdb___303E> No atoms were read from the specified input PDB file, since the
starting residue number and/or chain id in MODEL_SEGMENT (or
the alignment file header) was not found;
requested starting position: residue number " 9", chain " "
rdabrk__288W> Protein not accepted: 12 1RHG
check_a_337E> Structure not read in (please consult the log file
for more details): 3 1CNT
3) Residue position is corect so I think that I have to specify
CHAIN ID and tried it - for example:
>P1;1I1RB
structureX:1I1RB:'6:B 172:B' : : : :
or
structureX:1I1RB:6 :A:172 :A: : : :
- it didn't help - so my question is
A)how looks a correct second line when I have to use chain ID
B)In one of my PDB files I have a chain ID which exists as number - 2
this same question as above
4) Script below
# Homology modelling by the automodel class
from modeller.automodel import * # Load the automodel class
log.verbose() # request verbose output
env = environ() # create a new MODELLER environment to build this model in
# directories for input atom files
env.io.atom_files_directory = './:../atom_files'
a = automodel(env,
alnfile = 'MSA-CYTOKIN-T-COFFEE.ali',
knowns = ('1AX8','1ALU','1CNT','1I1R','1EVS','1LKI','1PVH','1F6F','1N9D','1HWG','1BGC','1RHG'), # codes of the templates
sequence = 'spP41160',
assess_methods=assess.DOPE)
a.starting_model = 1 # index of the first model
a.ending_model = 1 # index of the last model
# (determines how many models to calculate)
a.md_level = refine.slow_large
a.make() # do the actual homology modelling
Yours sincerely,
Karol Kaszuba