homology modeling with Modeller

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amirhossein
amirhossein's picture
homology modeling with Modeller

Hi everyone,
my sequense has 5 domains and I successfully modeled each domain seperately but when I want model the whole sequence with multi template mode,the Modeller stopped the work ang giving the following error message:
"No atoms were read from the specified input PDB file, since the starting residue number or chain id in MODEL_SEGMENT(or the alignment file header) was not found"
your help is appreciated

Biju
Biju's picture
Amirhossein

Amirhossein
I have not used multitemplate model. But one of the reason could be that when many domains are present and the individual domains derived has not been fully chracterised from a crystallied full length protein by crystallography,NMR etc, no model will be generated to lack of sufficient homology.
Biju

Amit Singh
Amit Singh's picture
Hey,

Hey,
Modeller have several disadvantages, one of that is generation of proper alignment file. Try M4T Server it uses multiple template approach with some modifications & end modeling is done by Modeller only. It also provides DOPE Score as in Modeller. You can also try on I-Tasser, though it is for threading approach but generates good model if proper  templates are available. It can go upto 10 templates so normally you will get good protein structure. I have worked on both & am satisfied with both the results. Try tehm & feel free to contact for further details.
aks