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Re: [modeller_usage] Multiple sequence alignment + modeling in one script



Thanks for the suggestion!

I've forced with small problem during installation of the ModPipe: while running setup file it ask me

You need to have a copy of MODELLER in the ext/mod/ directory.
Please install it (see the documentation) then rerun this script.

(here my modeller have been installed in the default dirs using
sudo env KEY_MODELLER=***** dpkg -i modeller_9.13-1_amd64.deb

how I could provide correct install path to dpkg?


2) Are there any usefull tutotials for the ModPipe besides presented in readme ?



2014-04-15 0:32 GMT+04:00 Modeller Caretaker <" target="_blank">>:
On 4/14/14, 4:43 AM, James Starlight wrote:
I'm looking for the posible modeling script which could do:

i - multiple sequence alignment of several sequences agains target
sequence (for which experimental structure is exist) to detect common
functional-relevant motifs in each sequence of ensemble

ii- select the aligned sequence from the ensemble

iii- make a homology model for this structure based on the provided
experimental (reference) structure including S-S bridges and ligand's
coppied from the reference.

Please provide me with simolple python example of such fussion of
sequence analysis and homology modeling,

What you're describing isn't particularly simple, so I doubt a "simple python example" will be forthcoming. ;) One solution would be to use ModPipe (http://salilab.org/modpipe/).

        Ben Webb, Modeller Caretaker
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