Hi Michael,
In case of several templates Modeller at first strcuturally superposes them,
before deriving the strcutural restraints.
The error means, that the structures do not have any overlap i.e. not
superposable. In your alignment the aligned sequences have different length
which is incorrect, and the second sequence is kind of inserted in the first
one, where there are only gapped positions (no structural overlap at all).
these two problems should be corrected.
Andras
Michel Giorgi wrote:
>
> Dear Modellers,
>
> I try to model my target protein on several templates (a big one and 6
> very small ones), moreless as it is indicated in question 4 of the FACs.
>
> Unfortunately the program ends in error when checking the alignements,
> with the following error message:
>
> ###################
> fit2xyz_E> number of equivalent positions < 3: 0
> recover__> MODELLER_STATUS >= STOP_ON_ERROR: 1 1
> ###################
>
> My alignement file looks like this:
>
> >P1;temp1
> structure:temp1: 45:: 356::
> NECLGTIGPVTPLDASDFALDIRMPGVT-PKESDTYFCMSMRLPVD-EEAFVIDFKP--------RASMDTVHHMLL
>
> FGC----------------------------N--MPSSTGSYWFCDEGTCTDKAN----ILYAWARNAPPTRLPKGV
>
> GFRVGGETGSKYFVLQVHYGDI-----NHKDCSGVSVHLTRVPQPLIAGMYLMMSVDT---VIPPGEKVVNADISC-
>
> -----------QYKMYPMHVFAYRVHTHHLG-KVVSGYRVRNGQ-WTLIGRQN-------------------PQLP-
>
> -QAFYPVEHPVDVTFGDILAARCVFTGEGRTEATHIGGTSSDEMCNLYIMYYMEAKYALSFMTCTKNVAPDMFRTIP
>
> AEANIPIII*
>
> >P1;temp2
> structure:temp2: 74:: 81::
> ---------------------------------------------------------KVTEGSEQ*
>
> >P1;temp3
> structure:temp3: 85:: 97::
> -----------------------------------------------------------------------------
>
> ---AAKIITHPNFNGN*
>
> >P1;temp4
> structure:temp4: 17:: 30::
> -----------------------------------------------------------------------------
>
> ----------------CKHSMK-YRLSFCRK*
>
> >P1;temp5
> structure:temp5: 258:: 269::
> -----------------------------------------------------------------------------
>
> -----------------------------------------------------------------------------
>
> ----------------------------------------------------------------------------P
>
> DWCTASGTPAS*
>
> >P1;temp6
> structure:temp6: 75:: 93::
> -----------------------------------------------------------------------------
>
> -----------------------------------------------------------------------------
>
> -----------------------------------------------------------------------------
>
> -----------------------------------------------------KYVPHFKPGKELRDRANIY*
>
> >P1;temp7
> structure:temp7: 30:: 47::
> -----------------------------------------------------------------------------
>
> -----------------------------------------------------------------------------
>
> -----------------------------------------------------------------------------
>
> -----------------------------------------------------FHPPHI-EIQMLKNGKKIP*
>
> >P1;target
> sequence:target:
> LLKPSIPKPALPADTC--TMEIRAPDVLIPGQQTTYWCYVTELPDGFPRHHIVMYEPIVTEGNEA-----LV66MEV
>
> FQCAAEFRDHPHFSGPCDSKMKPQRLNFCRH----------------------------VLAAWALGAKAFYYPEEA
>
> GLAFGGPGSSRFLRLEV6YHNPLVIT-GRRDSSGIRLYYTAALRRFDAGIMELGLAYTPVMAIPPQETAFVLTGYCT
>
> DKCTQLALPAS-----GIHIFASQLHTHLTGRKVVTVL-ARDGRETEIVNRDNHYSPHFQEIRMLKKVVSVQ-----
>
> --------------PGDVLITSCTYNTEDRRLATVGGFGILEEMCVNYVHYYPQTQLEL----CKSAVDPGFLHKYF
>
> RLVNR--LL*
>
> Has anyone an idea about the problem? The error is the same if i only
> use the 2 first templates for instance.
> Thank you, regards.
>
> --
> Michel GIORGI
> Lab. de Cristallochimie
> Faculte de St. Jerome
> Marseille, cedex 20, FRANCE
--
,
Andras Fiser, PhD # phone: (212) 327 7206
The Rockefeller University # fax: (212) 327 7540
Box 270, 1230 York Avenue # e-mail:
New York, NY 10021-6399, USA # http://salilab.org/~andras