Hello - I am trying to run a query where the sequence and the template are partial sequences. I have adjusted the PDB file coordinates for the template structure by selecting only the residues I am interested in, and then renumbering.
Is this possible? I am getting an error as follows: "Either the format of the FASTA alignment is wrong or the PDB file for the template protein is missing in the uploaded file."
ex.
>sequence 1
[sequence entered below]
>template sequence
[sequence entered below]
ATOM 1 N LEU 1 10.85 30.821 2.186
ATOM 2 CA LEU 1 12.095 31.185 1.51
ATOM 3 C LEU 1 11.806 31.986 0.263
ATOM 4 O LEU 1 12.42 33.015 0.02
ATOM 5 CB LEU 1 12.888 29.939 1.111
ATOM 6 CG LEU 1 13.602 29.141 2.202
ATOM 7 CD1 LEU 1 14.323 27.944 1.581
ATOM 8 CD2 LEU 1 14.581 30.024 2.984
ATOM 9 N ALA 2 10.867 31.492 -0.53
ATOM 10 CA ALA 2 10.433 32.171 -1.741
ATOM 11 C ALA 2 9.89 33.578 -1.473
ATOM 12 O ALA 2 10.035 34.461 -2.314
ATOM 13 CB ALA 2 9.391 31.33 -2.45
run a query using partial sequences/partial alignments
Re: run a query using partial sequences/partial alignments
Hello,
Yes, this is possible. If you know the alignment between your protein sequence and the template structure, you may specify this under Option 1: Assign additional restraints and templates to guide I-TASSER modeling. When you click on this option, there will be an explanation link that you can follow to explain how to upload your template information.
Yes, this is possible. If you know the alignment between your protein sequence and the template structure, you may specify this under Option 1: Assign additional restraints and templates to guide I-TASSER modeling. When you click on this option, there will be an explanation link that you can follow to explain how to upload your template information.
Re: run a query using partial sequences/partial alignments
Hello robpearc,
Thank you for your reply - Can you be more specific about the template information?
I have copied over a template of the file that I am submitting in my original comment for reference. I have used the template explanation link (I think) you refer to (https://zhanglab.dcmb.med.umich.edu/I-T ... raint.html) and followed the instructions for the FASTA input. Even following these instructions, I am getting an error, so I am looking to see what I might be missing.
For example: I am submitting only a part of the alignment for both proteins. In the example, there are many gaps in the input sequence: Does this imply that I need to include the entire template sequence?
Thank you for your reply - Can you be more specific about the template information?
I have copied over a template of the file that I am submitting in my original comment for reference. I have used the template explanation link (I think) you refer to (https://zhanglab.dcmb.med.umich.edu/I-T ... raint.html) and followed the instructions for the FASTA input. Even following these instructions, I am getting an error, so I am looking to see what I might be missing.
For example: I am submitting only a part of the alignment for both proteins. In the example, there are many gaps in the input sequence: Does this imply that I need to include the entire template sequence?