I think that you can check the unfolded structures first. After all, the
modeller just did homology modelling. I guest your align file should like
this:
>P1;proteinA
structureX:proteinA
aaaaaaaaaaaaaaaaaaaaaaaaaaaa----------------------------------*
>P1;proteinB
structureX:proteinB
----------------------------bbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbb*
>P1;chimera
sequence:chimera
aaaaaaaaaaaaaaaaaaaaaaaaaaaabbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbb*
But on this topic, I have a question. If I want to get a model from
tweo different protein , how can I obtain satisfactory relative
orientation of modeled domains in such cases, orient the two template
structures appropriately before the modeling ?
Sincerely,
Shiyong
MDL in Peking University
Tel1:+86(0)62757520
e-mail:
http://mdl.ipc.pku.edu.cn/~syliu
On Thu, 17 Jun 2004, Benoit Charloteaux wrote:
> Dear Modeller users,
>
> I want to build a model of a chimeric protein based on two distinct
> structures. I have tried as explained in the FAQ section of the manual
> (question 4), but I only get completely unfolded structures.
>
> Is it possible to build a chimeric model with this procedure? Where does
> this problem come from?
> Any possible explanation or suggestion would be greatly appreciated!
>
> To check my procedure, I have tried the following :
>
> I used an older prediction that worked and which is based on a single
> template structure.
>
> Target xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
> proteinA aaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaa
>
>
> I made a copy of the template structure file and renamed it to do as if
> there was two distinct template structures. I tried to build a kind of
> chimeric model based on these template structures as follow :
>
> Target xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
> proteinA aaaaaaaaaaaaaaaaaaaaaaaaaaaa----------------------------------
> proteinA -------------------------aaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaa
>
> Since the two template structures used for the prediction correspond to
> the same file, the relative orientation of both structures is correct
> (the atom coordinates are the same).
>
> The predicted 3-D model is completely unfolded too.
>
> Sincerely,
>
> CHARLOTEAUX Benoit
> Centre de Biophysique Moleculaire Numerique
> Faculte Universitaire des Sciences Agronomiques de Gembloux
> Passage des deportes, 2
> B-5030 Gembloux
> Belgium
> Tel1:+32(0)81/62.25.32
> Tel2:+32(0)81/62.25.21
> Fax:+32(0)81/62.25.22
> e-mail:
> http://www.fsagx.ac.be/bp/
>
>
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