[Chimera-users] Modelling of missing regions ussing Chimera

[Gleb Novicov]

Dear Elaine!

Thank you for your advises. Your new Modeller's module in new Chimera
release works perfect.

Could you tell me how I could define path to the modeller local
installation ? I have installed  Modeller on my Linux debian OS in the
default locations. As I understood in that case Modeller is the part of the
python modules. It's been installed both in the usr/lib/ and usr/include/
dirrs. Where the executable file is?

Thanks again,

Gleb

2012/8/7 Elaine Meng <meng at cgl.ucsf.edu>

> Hi Gleb,
> First you need to get a newer Chimera (version 1.7 daily build).   You
> cannot build missing segments with the production release (1.6) and older
> versions of Chimera -- the "Model Loops" tool in those older versions only
> allows re-modeling segments that are already in the protein, not building
> missing segments.  Daily build download:
> <http://www.cgl.ucsf.edu/chimera/download.html#daily>
>
> In Chimera 1.7 there have been many improvements in the Chimera-Modeller
> interface.   You can build missing segments using the "Model/Refine Loops"
> tool (in menu under Tools... Structure Editing).   For instructions, click
> the Help button on that tool or view its documentation here:
> <
> http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/multalignviewer/modeller.html#building
> >
>
> Another improvement is that you don't have do anything with a runmod.bat
> file on Windows, you only have to enter the location of the Modeller
> executable in the dialog (assuming you have installed Modeller  correctly).
>  Or, instead of your own installation you could just use our web service,
> which does not require you to install Modeller.
>
> I hope this helps
> Elaine
> ----------
> Elaine C. Meng, Ph.D.
> UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
>
> On Aug 4, 2012, at 4:44 AM, Gleb Novicov wrote:
>
> > Dear Chimera's users!
> > I need to model some missing segments ( In particular case I need to
> build missing N and C termi ) of my protein ussing Modeller's options.
>  Could you tell me about possible solution of that issue ?
> >
> > On my win7 I have installed Chimera as well as Modeller v 9.10 suite.
> >
> > I've defined Modeller pathways in the Chimera's Model pool options but
> when I've selected option Prune seection to define region of interest I
> didnt obtain anythinf from both of Chimera or Modeller. On other hand the
> option Structure -> Modeller tools also not available for me. Does it means
> that I've installed modeller incorrectly ?
> >
> > Also I've used  runmod.dat script with defined variables from which I
> obtained the below
> >
> > C:\Users\own\Desktop\worktemp>runmod.bat
> > usage: mod9.10 script [...]
> >
> > Doest this means that all work fine ?
> >
> > By the way after executing of that script I could not launch modeller by
> means of mod9.10.exe from modeller folder. The error from modeller was
> >
> > C:\Program Files\Modeller\bin>mod9.10.exe
> > FATAL ERROR: MODINSTALL9v10 environment variable not set: incomplete
> MODELLER in
> > stallation
> >
> >
> > Could you explain me whats I've done wrong and how I could fix this
> problem?
> >
> > Thanks for help
> >
> > Gleb
> > _______________________________________________
> > Chimera-users mailing list
> > Chimera-users at cgl.ucsf.edu
> > http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
>
>
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