ADL: regarding active site
rhuey at scripps.edu
Mon Jun 15 11:15:07 PDT 2009
> ....... Main problem I found is the grid is
> not generated at the point I am specifying.
> For example I am attaching a protein structure and a ligand.
> For this system, the active site includes residues 100, 103, 105, 179,181,
> 188,190, 227.
> I tried by different ways to assign the grid occupying all these residues,
I'm not sure what exactly is causing this problem for you...
However, one likely source of confusion is that in ADT numbers used as
'selection criteria' are interpreted as indicies not as names...
Here is an example:
1. Use File->Read Molecule to read 3DM2.pdb into ADT
2. Type 100 in the Residue entry in the "Select From String" widget
(opened by Select->SelectFromString), then "Add"
This results in selecting residue VAL106.
To select residue "LEU A 100", type LEU100 in the Residue entry and A
in the Chain entry followed by Add.
If on the other hand, you would like to select residues near residue GWE
A 999, do this:
1-clear the selection if any first
2-type GWE* in the Residue entry followed Add
3-use Select->Spherical Region.
In the widget which open,
-click on 'current selection'
-adjust the Selection Sphere Radius as you wish
-click on select which results in a selection containing atoms.
Set the selection to Residues with Select->Set Selection Level
Here are results from Select->Select SphericalRegion for 3DM2, using
selection comprised of residue GWE*
-radius 3 selected 2 atoms from residues:
TYR188 (index 180)
VAL106 (index 100)
-radius 3.1 selected 7 Atoms from residues:
ASN103 - 97
TYR188 - 180
GLY190 - 182
TYR181 - 173
LEU234 - 226
VAL106 - 100
PRO225 - 217
Select From String does support some regular expressions which are
matched to names. Here you could have used *100 or ...100
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