Dear Modeller users, if I want to model a protein consisting of two subunits, how can I include the already modelled subunit into the calculation when modelling the second subunit such that new loops "see" the other subunit? I am currently using the simple scripts from the tutorial of the manual. Best regards Norbert -------------------------------------------------------------- Dr. Norbert Straeter Tel. +49 (0)30 838-53456 Free University of Berlin Fax -56702 Institute of Chemistry -Crystallography- Takustrasse 6 14195 Berlin, Germany strater@chemie.fu-berlin.de http://userpage.chemie.fu-berlin.de/~strater/ --------------------------------------------------------------
Hello Norbert, Try to model the two units simultaneously, altogether. Simply use the whole continuous sequence/structure information. In this case the intersubunit distance restraints will be derived automatically i.e. the units will be oriented similarly as in the template complex and "see" each other. If the two units come from different templates (monomers) there is no trivial solution to guess the proper orientation of them. Andras Norbert Straeter wrote: > > Dear Modeller users, > > if I want to model a protein consisting of two subunits, how can I include > the already modelled subunit into the calculation when modelling the > second subunit such that new loops "see" the other subunit? I am currently > using the simple scripts from the tutorial of the manual. > > Best regards > > Norbert > > -------------------------------------------------------------- > Dr. Norbert Straeter > > Tel. +49 (0)30 838-53456 > Free University of Berlin Fax -56702 > Institute of Chemistry > -Crystallography- > Takustrasse 6 > 14195 Berlin, Germany strater@chemie.fu-berlin.de > > http://userpage.chemie.fu-berlin.de/~strater/ > -------------------------------------------------------------- -- , Andras Fiser, PhD # phone: (212) 327 7216 The Rockefeller University # fax: (212) 327 7540 Box 270, 1230 York Avenue # e-mail:fisera@rockefeller.edu New York, NY 10021-6399, USA # http://salilab.org/~andras
Hello Norbert, Try to model the two units simultaneously, altogether. Simply use the whole continuous sequence/structure information. In this case the intersubunit distance restraints will be derived automatically i.e. the units will be oriented similarly as in the template complex and "see" each other. If the two units come from different templates (monomers) there is no trivial solution to guess the proper orientation of them. Andras Norbert Straeter wrote: > > Dear Modeller users, > > if I want to model a protein consisting of two subunits, how can I include > the already modelled subunit into the calculation when modelling the > second subunit such that new loops "see" the other subunit? I am currently > using the simple scripts from the tutorial of the manual. > > Best regards > > Norbert > > -------------------------------------------------------------- > Dr. Norbert Straeter > > Tel. +49 (0)30 838-53456 > Free University of Berlin Fax -56702 > Institute of Chemistry > -Crystallography- > Takustrasse 6 > 14195 Berlin, Germany strater@chemie.fu-berlin.de > > http://userpage.chemie.fu-berlin.de/~strater/ > -------------------------------------------------------------- -- , Andras Fiser, PhD # phone: (212) 327 7216 The Rockefeller University # fax: (212) 327 7540 Box 270, 1230 York Avenue # e-mail:fisera@rockefeller.edu New York, NY 10021-6399, USA # http://salilab.org/~andras
participants (2)
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Andras Fiser -
Norbert Straeter