[Chimera-users] Placing Autodock Vina Pocket around AA residues from RaptorX

[leifepeterson at sbcglobal.net]

Couple newbie questions:

 

1.	I don't know if any users have run RaptorX (U-Chicago) for
ligand-residue pocket prediction, but the results simply tell you the
specific AA residues are which are close to the pocket  For example the
locations could simply be e.g. the residues K252, Q256, and K260 in the
input PDB file.   So my question in terms of AA annotation in Chimera is,
how could I center Autodock Vina's pocket box around residues something like
K252, Q256, and K260? I looked through the select options and didn't see
where numbered residues could be selected.
2.	For 3D modeling when x-ray crystallography results are not available
in PDB, I commonly will submit a protein's FASTA sequence to SWISS-MODEL,
and then download the PDB and go through dock prep for the receptor and
minimization of the ligand(and adding e.e. hydrogens, etc.)   Isn't the
SWISS-MODEL approach an alternative for using the MODELLER add-on for
homology modeling.    The MODELLER run I just went through was really using
a lot of core resources, and the BLAST template results were complexes
between receptors and ligands, and sometimes DNA.  So isn't there an
advantage to  inputting a FASTA from Uniprot into SWISS-MODEL to obtain the
predicted 3D structure, when compared with the BLAST results required during
MODELLER runs? 

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