Fwd: Customised Modeling - Template is NMR Structure
Respected Sir
I am new user of Modeller. *I don't have any background in python.*
I have to use a template, whose PDB ID is 1APS. It is *NMR Model *with four models.
I have to use only *first model of this NMR* structure.
For this template, I have *50 Query sequences* in 50 separate ".fasta files" in PIR FORMAT.
*Description of PIR Format of Query sequences:*
*First line: *>1APS_1; Mutant_Y15M
*Second Line:* I think this line is optional - I HAVE OMITTED THIS LINE. My second line is PROTEIN SEQUENCE in Capital letters ending with " * ".
Can you guide me with* steps* of how to model 50 Query sequences with template 1APS (first model).
I am mailing *ATTACHMENT* (in both .zip and .tar.gz format) containing 50 Query sequences and 1APS PDB file downloaded from Protein Databank.
It would be of great help.
Thanks a ton.
Regards Priya
On 05/10/2013 03:13 AM, Priya Chaudhary wrote: > I have to use a template, whose PDB ID is 1APS. It is *NMR Model *with > four models. > > I have to use only *first model of this NMR* structure.
This is fine - Modeller will only read the first model from NMR structures.
> For this template, I have *50 Query sequences* in 50 separate ".fasta > files" in PIR FORMAT.
Are they FASTA files or PIR files? You need PIR files for modeling.
> *Description of PIR Format of Query sequences:* > > *First line: *>1APS_1; Mutant_Y15M > > *Second Line:* I think this line is optional - I HAVE OMITTED THIS LINE. > My second line is PROTEIN SEQUENCE in Capital letters ending with " * ".
What you describe is not a valid PIR file. You can find a description of the file format at http://salilab.org/modeller/9.11/manual/node476.html
Ben Webb, Modeller Caretaker
participants (2)
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Modeller Caretaker -
Priya Chaudhary