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
------------------------------------------------------------------------------
Don't Limit Your Business. Reach for the Cloud.
GigeNET's Cloud Solutions provide you with the tools and support that
you need to offload your IT needs and focus on growing your business.
Configured For All Businesses. Start Your Cloud Today.
https://www.gigenetcloud.com/
_______________________________________________
PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net)
Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
