> 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