Dear Modeller users,
I try to model homedimer with few point mutations using hometrimer as a template. In the alignment file I specified to use only chain A and chain B from the template, but the out put dimer model has different monomer-monomer interface than template. I used standard script( http://salilab.org/modeller/9v4/manual/node28.html) and the alignment file:
>P1;inv3HD sequence:inv3HD:1:.: 331 ::MODELLING PROTEIN:undefined:: MKPVTLYDVAEYAGVSYQTVSRVVNQASHVSAKTREKVEAAMAELNYIPNRVAQQLAGKQSLLIGVATSSLA LHAPSQIVAAIKSRADQLGASVVVPMVERSGVEACKAAVHNLLAQRVSGLIINYPLDDQDAIAVEAACTNVP ALFLDVSDQTPINSIIFSHEDGTRLGVEHLVALGHQQIALLAGPLSSVSARLRLAGWHKYLTLNQIQPIAER EGDWSAMSGFQQTMQMLNEGIVPTAMLVANDQMALGAMRAIAESGLRVGADISVVGYDDTEDSSCYIPPLTT IKQDFRLLGQTSVDRLLQLSQGQAVKGNQLLPVSLVKRKTTLA\MKPVTLYDVAEYAGVSYQTVSRVVNQAS HVSAKTREKVEAAMAELNYIPNRVAQQLAGKQSLLIGVATSSLALHAPSQIVAAIKSRADQLGASVVVPMVE RSGVEACKAAVHNLLAQRVSGLIINYPLDDQDAIAVEAACTNVPALFLDVSDQTPINSIIFSHEDGTRLGVE HLVALGHQQIALLAGPLSSVSARLRLAGWHKYLTLNQIQPIAEREGDWSAMSGFQQTMQMLNEGIVPTAMLV ANDQMALGAMRAIAESGLRVGADISVVGYDDTEDSSCYIPPLTTIKQDFRLLGQTSVDRLLQLSQGQAVKGN QLLPVSLVKRKTTLA* >P1;1EFA structureX:1EFA:2:A: 329 :.:LAC REPRESSOR:undefined:: -KPVTLYDVAEYAGVSYQTVSRVVNQASHVSAKTREKVEAAMAELNYIPNRVAQQLAGKQSLLIGVATSSLA LHAPSQIVAAIKSRADQLGASVVVSMVERSGVEACKTAVHNLLAQRVSGLIINYPLDDQDAIAVEAACTNVP ALFLDVSDQTPINSIIFSHEDGTRLGVEHLVALGHQQIALLAGPLSSVSARLRLAGWHKYLTRNQIQPIAER EGDWSAMSGFQQTMQMLNEGIVPTAMLVANDQMALGAMRAITESGLRVGADISVVGYDDTEDSSCYIPPLTT IKQDFRLLGQTSVDRLLQLSQGQAVKGNQLLPVSLVKRKTTLA* >P1;1EFA structureX:1EFA:2:B: 329 :.:LAC REPRESSOR:undefined:: -KPVTLYDVAEYAGVSYQTVSRVVNQASHVSAKTREKVEAAMAELNYIPNRVAQQLAGKQSLLIGVATSSLA LHAPSQIVAAIKSRADQLGASVVVSMVERSGVEACKTAVHNLLAQRVSGLIINYPLDDQDAIAVEAACTNVP ALFLDVSDQTPINSIIFSHEDGTRLGVEHLVALGHQQIALLAGPLSSVSARLRLAGWHKYLTRNQIQPIAER EGDWSAMSGFQQTMQMLNEGIVPTAMLVANDQMALGAMRAITESGLRVGADISVVGYDDTEDSSCYIPPLTT IKQDFRLLGQTSVDRLLQLSQGQAVKGNQLLPVSLVKRKTTLA*
Thank you very much in advance for any tips
-Manjunatha Karpenahalli
--- On Tue, 29/7/08, Modeller Caretaker modeller-care@salilab.org wrote: From: Modeller Caretaker modeller-care@salilab.org Subject: Re: [modeller_usage] Oligomer Modelling To: manju_88@yahoo.com Cc: modeller_usage@salilab.org Date: Tuesday, 29 July, 2008, 8:28 PM
Manjunatha Karpenahalli wrote: > Is it possible to model home-tetramer using modeller?
Sure, see: http://salilab.org/modeller/9v4/manual/node28.html
That example is for a dimer, but it is straightforward to use a similar script to model a tetramer.
Ben Webb, Modeller Caretaker