Hi,
I got this error message while running modeller:
fit2xyz_E> number of equivalent positions < 3: 0 recover__> MODELLER_STATUS >= STOP_ON_ERROR: 1 1
THE .TOP FILE IS:
# Very fast homology modelling by the MODELLER TOP routine 'model'. INCLUDE # Include the predefined TOP routines SET ALNFILE = 'motilin_giulio4.align' # alignment filename SET KNOWNS = '1f88' '2EIA' # codes of the templates SET SEQUENCE = '1mot' # code of the target SET ATOM_FILES_DIRECTORY = '/lab/giulio/KOSAN/motilin/homology' SET STARTING_MODEL = 1 SET ENDING_MODEL = 1 CALL ROUTINE = 'model' # do homology modelling
THE ALIGNMENT IS:
>P1;1mot sequence:1mot: 1: : 412: :6a684b4cd3365f9a226ebadbae3b60b3MGSPKTMG 6-386::-1.00:-1.00 MGSPWNGSDGPEGAREPP---WPALPPCDERRCSPFPLGALVPVTAVCLCLFVVGVSGNVVTVMLIGRYRDMRTT TNLYLGSMAVSDLLILLGLPFDLYRLWRSRPWVFGPLLCRLSLYVGEGCTYATLLHMTALSVERYLAICRPLRAR VLVTRRRVRALIAVLWAVALLSAGPFLFL----------------------------VGVEQDPGISVVPGLNGT ARIASSPLASSPPLWLSRAPPP-----SPPSGPETAEAAALFSRECRPSPAQLGALRVMLWVTTAYFFLPFLCLS ILYGLIGRELWSSRRPLRGPAASGRERGHRQTVRVLLVVVLAFIICWLPFHVGRIIYINTEDSRMMYFSQYFNIV ALQLFYLSASINPILYNLISKKYRAAAFKLLLARKSRPRGFHRSRDTAGEVAGDTGGDTVGYTETSANVKTMG* >P1;1f88 structureX:1f88: 1:A: 328:A:1-332::-1.00:-1.00 ----MNGTEGPNFYVPFSNKTGVVRSPFEAPQYYLAEPWQFSMLAAYMFLLIMLGFPINFLTLYVTVQHKKLRTP LNYILLNLAVADLFMVFGGFTTTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSN- FRFGENHAIMGVAFTWVMALACAAPPLVGWSRYIPEGMQCSCGIDYYTPHEETNNES------------------ ---------------------------------------------------------FVIYMFVVHFIIPLIVIF FCYGQLVFTVKEAAA----SATT--QKAEKEVTRMVIIMVIAFLICWLPYAGVAFYIFTHQG---SDFGPIFMTI PAFFAKTSAVYNPVIYIMMNKQFRNCMVTTLCCGKNP-------------------STTVSKTETSQVAPA--* >P1;2EIA structureX:2EIA: 52:A: 99:A:unknown:unknown:-1:-1 --------------------------------------------------------------------------- --------------------------------------------------------------------------- ------------------------------------------------------------EMNAFLDVVPGQAGQ KQILLDAIDKIADDWDNRHPLPNAPLVAPPQGP------------------------------------------ --------------------------------------------------------------------------- -------------------------------------------------------------------------*
What does the error mean? The alignment seems to be ok...
Thank you very much for your help
Giulio Rastelli
Hi Giulio
The error means that there is no overlap in between the two template structures (which is the case indeed, if you look at the alignment, the second template inserted into a niche) so the program can not orient the two structures with respect to each other, therefore it is not possible to derive equivalent positions either etc. The process stops. In case of multiple templates you need at least a 3 atom overlap among them.
best wishes,
Andras
> > Hi, > > I got this error message while running modeller: > > fit2xyz_E> number of equivalent positions < 3: 0 recover__> > MODELLER_STATUS >= STOP_ON_ERROR: 1 1 > > THE .TOP FILE IS: > > # Very fast homology modelling by the MODELLER TOP routine 'model'. > INCLUDE # Include the predefined TOP routines > SET ALNFILE = 'motilin_giulio4.align' # alignment filename > SET KNOWNS = '1f88' '2EIA' # codes of the templates > SET SEQUENCE = '1mot' # code of the target > SET ATOM_FILES_DIRECTORY = '/lab/giulio/KOSAN/motilin/homology' > SET STARTING_MODEL = 1 > SET ENDING_MODEL = 1 > CALL ROUTINE = 'model' # do homology modelling > > THE ALIGNMENT IS: > > >P1;1mot sequence:1mot: 1: : 412: > :6a684b4cd3365f9a226ebadbae3b60b3MGSPKTMG 6-386::-1.00:-1.00 > MGSPWNGSDGPEGAREPP---WPALPPCDERRCSPFPLGALVPVTAVCLCLFVVGVSGNVVTVMLIGRYRDMRTT > TNLYLGSMAVSDLLILLGLPFDLYRLWRSRPWVFGPLLCRLSLYVGEGCTYATLLHMTALSVERYLAICRPLRAR > VLVTRRRVRALIAVLWAVALLSAGPFLFL----------------------------VGVEQDPGISVVPGLNGT > ARIASSPLASSPPLWLSRAPPP-----SPPSGPETAEAAALFSRECRPSPAQLGALRVMLWVTTAYFFLPFLCLS > ILYGLIGRELWSSRRPLRGPAASGRERGHRQTVRVLLVVVLAFIICWLPFHVGRIIYINTEDSRMMYFSQYFNIV > ALQLFYLSASINPILYNLISKKYRAAAFKLLLARKSRPRGFHRSRDTAGEVAGDTGGDTVGYTETSANVKTMG*
> >P1;1f88 structureX:1f88: 1:A: 328:A:1-332::-1.00:-1.00 > ----MNGTEGPNFYVPFSNKTGVVRSPFEAPQYYLAEPWQFSMLAAYMFLLIMLGFPINFLTLYVTVQHKKLRTP > LNYILLNLAVADLFMVFGGFTTTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSN- > FRFGENHAIMGVAFTWVMALACAAPPLVGWSRYIPEGMQCSCGIDYYTPHEETNNES------------------ > ---------------------------------------------------------FVIYMFVVHFIIPLIVIF > FCYGQLVFTVKEAAA----SATT--QKAEKEVTRMVIIMVIAFLICWLPYAGVAFYIFTHQG---SDFGPIFMTI > PAFFAKTSAVYNPVIYIMMNKQFRNCMVTTLCCGKNP-------------------STTVSKTETSQVAPA--*
> >P1;2EIA structureX:2EIA: 52:A: 99:A:unknown:unknown:-1:-1 > --------------------------------------------------------------------------- > --------------------------------------------------------------------------- > ------------------------------------------------------------EMNAFLDVVPGQAGQ > KQILLDAIDKIADDWDNRHPLPNAPLVAPPQGP------------------------------------------ > --------------------------------------------------------------------------- > -------------------------------------------------------------------------* > > What does the error mean? The alignment seems to be ok... > > Thank you very much for your help > > Giulio Rastelli
participants (2)
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Andras Fiser -
Giulio Rastelli