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
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