ADL: help needed for evaluating the results

Husniye Irmak Cataloglu irmakc at
Fri Apr 10 05:12:44 PDT 2009

  We applied till 4th exercise but we sticked at it's 2nd step.

2. Visualize binding in a pocket by displaying molecular surfaces:
In the Dashboard, click on the circle under MS in the ind row
and in the hsg1_rigid row. Click on the diamond under Atom
to color the ligand surface by the element of the underlying
atom. Click on the diamond under DS to color hsg1_rigid by
David Goodsell colors.
This view of the docking allows you to see how the docked ligand
'fits' into the macromolecule. Clicking on the circles under MS allows
you to show and hide the various msms surfaces.

We can't see the macremolecule whatever we do. We just can see the  
ligand. Why can it be?

On Sat 04 Apr 2009 12:41:07 EEST, Liu Ji wrote:

> Hi Cataloglu,
> You can always use ADT to do analysis. Seriously did you read through the
> tutorial? The answers you need are well described in the first four
> exercises.
> Liu Ji
> 2009/4/4 Husniye Irmak Cataloglu <irmakc at>
>>   Hello all. We made a docking using Autodock 4.0 and applied all the steps
>> in the Autodock tutorial. However, we have some problems in the evaluation
>> part.
>> Where can we see the free energy and how can we see the ligand and protein
>> in the active binding site? Thanks everyone for your help.
>> Irmak Çataloğlu
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