Multiple sequence alignment + modeling in one script
Dear modeler users,
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,
Best,
James S.
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
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 modeller-care@salilab.org:
> 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 > -- > modeller-care@salilab.org http://www.salilab.org/modeller/ > Modeller mail list: http://salilab.org/mailman/listinfo/modeller_usage >
On 4/15/14, 12:11 AM, James Starlight wrote: > 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?
See the documentation, like it suggests? ;) You need the .tar.gz installer, as detailed at http://salilab.org/modpipe/doc/install-ext.html#install-ext
> 2) Are there any usefull tutotials for the ModPipe besides presented in > readme ?
See above...
Ben Webb, Modeller Caretaker
Dear Ben,
I've done all this steps in accordance to manual with the exception that I have deb instead of tar.gz modeller file because I've not found the last one. Firstly I've extracted all data from the deb to the /modpipe-2.2.0/ext/mod/ using dpkg-deb -x modeller_9.13-1_amd64.deb ./
and than made all changes in the files in accordance to manual but while lunching setup I've obtained the same result:
You need to have a copy of MODELLER in the ext/mod/ directory. Please install it (see the documentation) then rerun this script.
Should I add some additional paths (both from modeller and for the modpipe) to the bash.bashrc ?
James
2014-04-15 22:55 GMT+04:00 Modeller Caretaker modeller-care@salilab.org:
> On 4/15/14, 12:11 AM, James Starlight wrote: > >> 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? >> > > See the documentation, like it suggests? ;) You need the .tar.gz > installer, as detailed at http://salilab.org/modpipe/ > doc/install-ext.html#install-ext > > > 2) Are there any usefull tutotials for the ModPipe besides presented in >> readme ? >> > > See above... > > > Ben Webb, Modeller Caretaker > -- > modeller-care@salilab.org http://www.salilab.org/modeller/ > Modeller mail list: http://salilab.org/mailman/listinfo/modeller_usage >
solved. :)
2014-04-16 12:57 GMT+04:00 James Starlight jmsstarlight@gmail.com:
> Dear Ben, > > I've done all this steps in accordance to manual with the exception that I > have deb instead of tar.gz modeller file because I've not found the last > one. > Firstly I've extracted all data from the deb to the /modpipe-2.2.0/ext/mod/ > using > dpkg-deb -x modeller_9.13-1_amd64.deb ./ > > and than made all changes in the files in accordance to manual > but while lunching setup I've obtained the same result: > > > You need to have a copy of MODELLER in the ext/mod/ directory. > Please install it (see the documentation) then rerun this script. > > > Should I add some additional paths (both from modeller and for the > modpipe) to the bash.bashrc ? > > James > > > > 2014-04-15 22:55 GMT+04:00 Modeller Caretaker modeller-care@salilab.org: > > On 4/15/14, 12:11 AM, James Starlight wrote: >> >>> 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? >>> >> >> See the documentation, like it suggests? ;) You need the .tar.gz >> installer, as detailed at http://salilab.org/modpipe/ >> doc/install-ext.html#install-ext >> >> >> 2) Are there any usefull tutotials for the ModPipe besides presented in >>> readme ? >>> >> >> See above... >> >> >> Ben Webb, Modeller Caretaker >> -- >> modeller-care@salilab.org http://www.salilab.org/modeller/ >> Modeller mail list: http://salilab.org/mailman/listinfo/modeller_usage >> > >
participants (2)
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James Starlight -
Modeller Caretaker