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 sassonir@cs.bgu.ac.il > > To: Modeller Care modeller-care@salilab.org > > Cc: modeller_usage@salilab.org > > 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. > >