September 2008 - modeller_usage

how to fix some residues not lying in allowed regions of Ramachandran plot
by rsachdeva＠imtech.res.in 03 Sep '08

03 Sep '08

Dear All, I built 200 tetrameric models of my protein using 2 templates. I selected best model as the one having the least DOPE score. On ssessing the stereochemical quality of the model, I found that it had 28 outliers residues (phi, psi), that were lying in disallowed regions of Ramachandran plot. Most of these residues are functionally important and hence can not be ignored. Will it be fine to select each of these residues and model them using loop modelling? Or can anyone please suggest me some other (better) way of fixing such bad residues? With Regards Ruchi

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objective function
by Amanda Moraes 03 Sep '08

03 Sep '08

Hello! I heard that the lowest the objective function, better the model. But I haven´t found anywhere what is exactly objetive function and how it works. For example: I did with modeller 500 models from 3 templates, 500 models from 2 templates and 500 from 1 template. Can I compare the values of objective function from the 3 works? Or is it proportional for the number of templates used? Thank you in advance, Amanda Maia Novos endereços, o Yahoo! que você conhece. Crie um email novo com a sua cara @ymail.com ou @rocketmail.com. http://br.new.mail.yahoo.com/addresses

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'import site' failed; use -v for traceback
by DimitryASuplatov 02 Sep '08

02 Sep '08

Hello, when I execute Modeller 9v4 script I get python warning 'import site' failed; use -v for traceback Everything seems to work just fine though this message is a kind of annoying. I`ve searched the list and tried to tweak PYTHONHOME/PATH vars but that did not help. Furthermore I have python 2.5 installed and modeller uses built-in 2.3. Considering that I have no intentions of using external python modules could this message cause me a problem with my work? Thank you for your help. SDA

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