Model with ligand from template
Hello all, I have some doubt on modelling with ligand and need your help. I have go over the tutorial on ligand but still I am not able to create my own. I would like to include the ligand from the template pdb for the the models. In my case, the substrate is cellotetraose (4 glucose units). Should one or four dots (....) to be added at the end of the alignment? My other question in how do you build the alignment file (ali)? Do you simply add the dots to the alignment file or is there any tricks? (I am wondering do we need to modify the PDB file to include the BLK or HETATOM, and then create the ali?) When I tried to simply add the dots to the ali file and ran the script to build the model, I got error with the structures not being recognized and it complained about the sequence length. Please kindly give us some advice or share with me your own precious experience if you've already done the same thing. Thank you so much!
Sincerely yours, Jas
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hori koshii wrote: > Hello all, I have some doubt on modelling with ligand and need your help. > I have go over the tutorial on ligand but still I am not able to create > my own.
See http://salilab.org/archives/modeller_usage/2007/msg00071.html and other posts in that thread.
> In my case, the substrate is cellotetraose (4 glucose units). Should one > or four dots (....) to be added at the end of the alignment?
Each one-letter code in your alignment corresponds to one residue, so if each glucose unit in your PDB has a different residue number, that's four dots. If they're all in one PDB residue, one dot.
> My other question in how do you build the alignment file (ali)? Do you > simply add the dots to the alignment file or is there any tricks?
Simply add the dots to your alignment. Residues in the alignment file are listed in the same order as in the PDB.
> wondering do we need to modify the PDB file to include the BLK or > HETATOM, and then create the ali?)
There should be no need to modify your PDB file.
> When I tried to simply add the dots to the ali file and ran the script > to build the model, I got error with the structures not being recognized > and it complained about the sequence length.
You have to turn on env.io.hetatm first, otherwise Modeller will only read the regular amino acids (ATOM records). See the examples in the manual and tutorials.
Ben Webb, Modeller Caretaker
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hori koshii -
Modeller Caretaker