Problem with PDB file
Dear colleagues,
I�m facing a problem with Modeller6, and although it seems to be a common one (I�ve seen similar requests in the list archives), I just couldn�t fix it reading the previous posts nor the FAQ.
The PDB file I�m using as a template starts at residue 8 and ends at residue 315. So, my alignement is as follows: =======================================================
C; A sample alignment in the PIR format; used in tutorial >P1;1DKU structureX:1DKU:8 : :315 : :PRPP:bacilo: 1.90: 0.19 NLKIFSLNSNPELAKEIADIVGVQLGKCSVTRFSDGEVQINIEESIRGCDCYIIQSTSDPVNEHIMELLIMVDALKRASAKTINIVIPYYGY ARQDRKARSREPITAKLFANLLETAGATRVIALDLHAPQIQGFFDIPIDHLMGVPILGEYFEGKNLE--DIVIVSPDHGGVTRARKLADRLKAPIAIIDK RRPRPNVAEVMNIVGNIEGKTAILIDDIIDTAGTITLAANALVENGAKEVYACCTHPVLSGPAVERINNSTIKELVVTNSIKLPEEKK-IERFKQLSVGP LLAEAIIRVHEQQSVSYLFS----* >P1;HUMA sequence:HUMA:8 : :315 : :PRPP:Homo sapiens: 2.00:-1.00 NIKIFSGSSHQDLSQKIADRLGLELGKVVTKKFSNQETCVEIGESVRGEDVYIVQSGCGEINDNLMELLIMINACKIASASRVTAVIPCFPY ARQDKKDKSRAPISAKLVANMLSVAGADHIITMDLHASQIQGFFDIPVDNLYAEPAVLKWIRENISEWRNCTIVSPDAGGAKRVTSIADRLNVDFALIHK ERKKANEVDRMVLVGDVKDRVAILVDDMADTCGTICHAADKLLSAGATRVYAILTHGIFSGPAISRINNACFEAVVVTNTIPQEDKMKHCSKIQVIDISM ILAEAIRRTHNGESVSYLFSHVPL*
=======================================================
The .top file was directly edited from the example model-default.top, and is as follows:
====================================================== # Homology modelling by the MODELLER TOP routine 'model'.
INCLUDE # Include the predefined TOP routines
SET OUTPUT_CONTROL = 1 1 1 1 2 # uncomment to produce a large log file SET ALNFILE = 'ALIN.pir' # alignment filename SET KNOWNS = '1DKU' # codes of the templates SET SEQUENCE = 'HUMA' # code of the target SET ATOM_FILES_DIRECTORY = '/mod6v2/examples/tutorial-model/' # directories for input atom files SET STARTING_MODEL= 1 # index of the first model SET ENDING_MODEL = 1 # index of the last model # (determines how many models to calculate)
CALL ROUTINE = 'model' # do homology modelling
=====================================================
Both the alignement file "ALIN.pir" and PDB file "1DKU.pdb" are on the /mod6v2/examples/tutorial-model/ directory. But although the program actually opens this pdb file, it shows this message:
rdabrk__288W> Protein not accepted: 1 rdabrk__290E> Number of residues in the alignment and pdb files are different: 309 0 For alignment entry: 1 recover____E> ERROR_STATUS >= STOP_ON_ERROR: 1 1
Does anybody has any hint on how to fix this problem?
Thanks in advance, Lucas Bleicher
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> The PDB file I_m using as a template starts at residue > 8 and ends at residue 315. So, my alignement is as > follows:
You should check in the PDB file whether there are any additional (or missing) residues, so while the numbering may go from 8 to 315 for the ATOM entries, the sequence is shorter or longer (longer due to alternate residue positions, perhaps, but this is unlikely). You should also check the chain code for the PDB - if it is not blank (ie a letter between the residue name code and residue number) then you need to put the correct chain code in the structureX entry. From the numbers after the error message (309 0), it looks like *no* PDB file residues were read in, which suggests a problem with the chain code (or no residue number 8 at the beginning).
there are more things to check, but these are the basics! j.
participants (2)
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J B Procter -
Lucas Bleicher