Re: Using a model file as one of the templates (fwd)

[sasson iris <>]

Hi Margot,
Thank you for your reply.

I know i may use multiple alignment. My problem concerns using models 
that were not inferred from alignments. That is, in addition to a multiple 
alignment i may have, i want modeller to use models of the query 
sequence.

for example:

if the sequence to model is : ATCE
i have a 3d file of it (pdb format):

ATOM .... CA ... ALA ... x_cord y_cord z_zord
ATOM .... CA ... THR ... x_cord y_cord z_zord
ATOM .... CA ... CYS ... x_cord y_cord z_zord
ATOM .... CA ... GLU ... x_cord y_cord z_zord

(of course, my sequence is longer).

I have no alignment of this, since the model contains the same sequence as 
the query (because it is a model of the query).
I have read the manual, modeller gets alignments as input, not models.

I want modeller to use the models i have and the multiple alignment i 
have, in order to generate a new model.
I do not know how to do this. I will be happy to check any suggestion you 
may have.

Thanks,
Iris.






On Fri, 11 Jul 2003, Margot Ernst wrote:

> Hi Iris,
> in principle you can use any model as template by adding it to the list of 
> "KNOWNS" in your topscript. 
> Modeller can use several templates at once. I recommend you look through the 
> appropriate examples in the documentation. In the tutorial chapter is a 
> topscript showing you how to model on 4 templates. They need to be present in 
> the alignment, of course and their pdb files have to be in the appropriate 
> atoms file directory. 
> good luck
> margot
> 
> On Thursday 10 July 2003 16:03, sasson iris wrote:
> > Hi,
> >
> > I send this question again because i got no reply.
> >
> > I want to create a model using modeller from a group of alignmnets and
> > models. Since modeller (if i understand correctly) uses only alignments
> > and no models (pdb format), i would like to create alignmnets from the
> > models i have, and give the alignment as one of the alignmnets in the
> > multiple alignmnet given as input to modeller. However, i have no idea how
> > to do this since i do not know what modeller actually does.
> > An alignment that may be created from a model i already have
> >
> >  is of identical sequences of query and template like this:
> > >P1;str
> >
> > structure :  str  :  : :  : : : : :
> > EFSVCGGRLIKLSHNSNSTKTSMNVNIYLPKHYYAQDFPRNKRIPTVFYLSGLTCTPDNASEKAFWQFQADKYGF
> >AIVFP EHLKPELLLEAVKATSWQDYVEIKKVHGFDHSYYFVSTFVPEHAEFHARNLGLI*
> >
> > >P1;query
> >
> > sequence :  query  :  : :  : : : : :
> > EFSVCGGRLIKLSHNSNSTKTSMNVNIYLPKHYYAQDFPRNKRIPTVFYLSGLTCTPDNASEKAFWQFQADKYGF
> >AIVFP EHLKPELLLEAVKATSWQDYVEIKKVHGFDHSYYFVSTFVPEHAEFHARNLGLI*
> >
> > and i have the model which is the str.pdb file.
> > I do not want modeller to put higher weight to this alignment than to the
> > others (which are to real templates). The sequence identity may yield this
> > result. How can i solve this?
> > Or if i ask it differently, what weight does modeller give to such
> > alignmnets? How can i change the sequence similarity to yield the required
> > result?
> > I will be happy to check any suggestion you may have.
> >
> > Thanks,
> > Iris.
> >
> >
> >
> > ---------- Forwarded message ----------
> > Date: Sun, 6 Jul 2003 15:37:31 +0300 (IDT)
> > From: sasson iris <>
> > To: Modeller Care <>
> > Cc: 
> > Subject: Using a model file as one of the templates
> >
> >
> > Hi,
> >
> > I want to use models as well as templates to build a new model using
> > modeller. That is, I have a few models that were not created by using an
> > alignment and some alignments.
> > How can i make modeller use all of which to build a new model?
> >
> > Thanks,
> > Iris.
> 
>