[modeller_usage] CORRECT SECOND LINE with CHAIN ID

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