Hi Leila,
I can't reproduce your error. Your code works for me.
Did you try the following
save obj3.pdb, obj1_0001, obj2
Cheers,
Osvaldo
On Tue, Jul 14, 2015 at 5:02 AM, leila karami <karami.lei...@gmail.com>
wrote:
> Dear pymol users,
>
> I am visualizing autodock vina results using PyMOL:
>
> I open out.pdbqt (containing 9 docked conformations of ligand)
> I open pr.pdb (containing protein structure)
>
> I want to have 1 pdb file containing one of conformations of ligand
> (for example number 1 which is the best pose) + protein structure.
> To this, I used following:
>
> load out.pdbqt,obj1
> load pr.pdb, obj2
>
> split_states obj1
>
> create obj3, (obj1_0001, obj2)
>
> save obj3.pdb, obj3
>
> In pymol, I see the following:
>
> all
> obj1
> obj2
> obj1_0001
> obj1_0002
> obj1_0003
> obj1_0004
> obj1_0005
> obj1_0006
> obj1_0007
> obj1_0008
> obj1_0009
> obj3
>
> After deactivating all except obj3, in obj3, I see protein + first state
> of my ligand in pymol, but when I open obj3.pdb file using the text editor,
> there as only END word. I want to use this obj3.pdb file as an input for
> ligplot program.
>
> What is the reason of this state?
>
> Best,
> Leila
>
>
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