> Hello, > > I am new in modelller. I have a problem. > > 1) I made an alignmnet file in PIR format - below > > >P1;1AX8 > structureX:1AX8:3 : :146 : :LEPTIN:HUMAN: 2.4: 0.215 > IQKVQDDTKT LIKTIVTRIN DI-------- ------LDFI PGLHPILTLS > KMDQTLAVYQ QILTSMPSRN VIQISNDLEN LRDLLHVLAF SKSCHLPEAS > GLETLDSLGG VLEASGYSTE VVALSRLQGS LQDMLWQLDL SPGC* > > >P1;spP41160 > sequence:spP41160:::::::: > VPIQKVQDDT KTLIKTIVTR INDISHTQSV SAKQRVTGLD FIPGLHPILS > LSKMDQTLAV YQQVLTSLPS QNVLQIANDL ENLRDLLHLL AFSKSCSLPQ > TSGLQKPESL DGVLEASLYS TEVVALSRLQ GSLQDILQQL DVSPEC* > > > 2) PDB FILE - 1AX8 > > 3) I used automodel class - default script > > # 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 = 'alignment2.ali', # alignment filename > knowns = '1AX8', # codes of the templates > sequence = 'spP41160') # code of the target > 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.make() # do the actual homology modelling > > > > 4) I am always having this same error > > Read the alignment from file : alignment2.ali > Total number of alignment positions: 146 > > # Code #_Res #_Segm PDB_code Name > ------------------------------------------------------------------------------- > 1 1AX8 145 1 1AX8 LEPTIN > 2 spP41160 161 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]: 2437705 2380.571 2.325 > openf5__224_> Open 11 OLD SEQUENTIAL ../atom_files\1AX8.pdb > rdabrk__291E> Sequence difference between alignment and pdb : > x (mismatch at alignment position 1) > Alignment IQKVQDDTKT LIKTIVTRIN DI LDFI PGLHPILTLS KMDQTLAVYQ QIL > PDB IQKVQDDTKTLIKTIVTRINDILDFIPGLHPILTLSKMDQTLAVYQQILTSMPSRN > Match * * * > Alignment residue (UNK) does not match pdb residue I (ILE), > for align code 1AX8 (atom file 1AX8), pdb residue number "3", chain " " > > Please check your alignment file header to be sure you correctly specified > the starting and ending residue numbers and chains. The alignment sequence > must match that from the atom file exactly. > > Another possibility is that some residues in the atom file are missing, > perhaps because they could not be resolved experimentally. (Note that Modeller > reads only the ATOM and HETATM records in PDB, NOT the SEQRES records.) > In this case, simply replace the section of your alignment corresponding > to these missing residues with gaps. > rdabrk__288W> Protein not accepted: 1 1AX8 > check_a_337E> Structure not read in (please consult the log file > for more details): 1 1AX8 > > > 5) I don't know what I did wrong. I don't understand this explanation that I have a sequence difference between alignmnet and PDB - I checked - starting residues are these same ILE - ILE. > > > - alignment file and script are in the automodel folder > - PDB is in the atom_files folder > > > I will be very grateful for any help. > > Yours sincerely, > > Karol Kaszuba
bestkarollo wrote: >> rdabrk__291E> Sequence difference between alignment and pdb : >> x (mismatch at alignment position 1) >> Alignment IQKVQDDTKT LIKTIVTRIN DI LDFI PGLHPILTLS KMDQTLAVYQ QIL >> PDB IQKVQDDTKTLIKTIVTRINDILDFIPGLHPILTLSKMDQTLAVYQQILTSMPSRN >> Match * * * >> Alignment residue (UNK) does not match pdb residue I (ILE), >> for align code 1AX8 (atom file 1AX8), pdb residue number "3", chain " "
You need to remove the spaces from your alignment file, since Modeller considers ' ' to be a valid residue type. As you can see above, the alignment sequence has spaces in, but the PDB sequence does not.
Ben Webb, Modeller Caretaker
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
bestkarollo wrote: > 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
Try a search for 'chain ID' in the archives; this question has been answered dozens of times. Two useful results of the search are: http://salilab.org/archives/modeller_usage/2005/msg00355.html http://salilab.org/modeller/manual/node176.html
The quotes are unnecessary.
> B)In one of my PDB files I have a chain ID which exists as number - 2 > this same question as above
The chain ID can be a number; you don't have to do anything special.
Ben Webb, Modeller Caretaker
What does this error mean?
rsplin_223E> Internal error: array too small: MAXSPL current maximum, current need: 400 866 recover____E> ERROR_STATUS >= STOP_ON_ERROR: 1 1
Thanks
Giacomo Bastianelli
Giacomo Bastianelli wrote: > What does this error mean? > > rsplin_223E> Internal error: array too small: MAXSPL > current maximum, current need: 400 866 > recover____E> ERROR_STATUS >= STOP_ON_ERROR: 1 1
It means Modeller has tried to replace a restraint with a cubic spline, but it requires too many points. You can work around this by setting spline_on_site to False, or by increasing spline_dx, but the underlying problem is usually that you have tried to build a model using multiple templates, which have dramatically different interatomic distances. This will usually result in very bad models, so you should look carefully at your choice of templates.
Ben Webb, Modeller Caretaker
-
bestkarollo -
Giacomo Bastianelli -
Modeller Caretaker