multiple-template no overlap
Hi: My target protein is a member of GPCR.I used multiple template to build the model, there was no overlap among the templates. The final model was not reasonable. The C-tail and N-tail were away from transmember region, simultaneity,located flank of transmember region.I want to know, was there any restraints on 'MODELLER'? the following is alignment: >P1;proteinA structureX:proteinA aaaaaaaaaaaaaaaaaaaaaaaaaaaa----------------------------------* >P1;proteinB structureX:proteinB ----------------------------bbbbbbbbbbbbbbbbbbbbbbbbb---------* >P1;proteinC structureX:proteinC -----------------------------------------------------ccccccccc* >P1;model sequence:model aaaaaaaaaaaaaaaaaaaaaaaaaaaabbbbbbbbbbbbbbbbbbbbbbbbbcccccccccc* The following was my script: from modeller import * from modeller.automodel import * env = environ() a = automodel(env, alnfile='model_mult.ali', knowns=('proteinA','proteinB', 'proteinC' ), sequence='model') a.starting_model = 1 a.ending_model = 1 a.make() was I missing something important? Or, did it in a wrong way? looking for your reply! thanks!
jinlian05@lzu.cn wrote: > Hi: > My target protein is a member of GPCR.I used multiple template to build the model, > there was no overlap among the templates. The final model was not reasonable. The > C-tail and N-tail were away from transmember region, simultaneity,located flank of > transmember region.I want to know, was there any restraints on 'MODELLER'?
See my earlier post on a very similar subject: http://salilab.org/archives/modeller_usage/2007/msg00307.html
Because you have no overlap in your alignment between your three templates, Modeller has no information about the relative orientations of the three domains. You will need to introduce templates for the overlap regions, or failing that, add manual restraints on the orientations.
Ben Webb, Modeller Caretaker
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jinlian05＠lzu.cn -
Modeller Caretaker