> 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