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[modeller_usage] (no subject)



>   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