Re: [PyMOL] visualize autodock vina results

Hi Leila, Both methods works for me. You are using a really old PyMOL version. I don't know if that is the problem but I think you should upgrade PyMOL. Osvaldo PS: Please use the reply button, to keep the whole conversation on the same thread. On Tue, Jul 14, 2015 at 10:49 AM, leila karami wr

[PyMOL] visualize autodock vina results

I am sure that I am in working directory. To prevent this mistake, I selected desktop as working directory. (I put out.pdbqt and pr.pdb files in desktop and then load them). I am using pymol-0_99rc6-bin-win32 on windows 7. My input files are as follows: https://www.dropbox.com/s/hx94orra4pumx82/

Re: [PyMOL] visualize autodock vina results

Both methods work for me. Are you sure you are opening the correct obj3.pdb file? Maybe you are saving the obj3.pdb file to a different directory and opening an old obj3 file. Wich PyMOL version are you using and on which operating system? On Tue, Jul 14, 2015 at 10:25 AM, leila karami wrote:

[PyMOL] visualize autodock vina results

Dear Osvaldo, I used 2 following ways: 1) load out.pdbqt,obj1 load pr.pdb, obj2 split_states obj1 create obj3, (obj1_0001, obj2) save obj3.pdb, obj3 2) load out.pdbqt,obj1 load pr.pdb, obj2 split_states obj1 save obj3.pdb, (obj1_0001, obj2) Unfortunately, in both cases, when I open obj3.pdb fil

Re: [PyMOL] visualize autodock vina results

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 wrote: > Dear pymol users, > > I am visualizing autodock vina results using PyMOL: > > I open out.pdbqt (c

[PyMOL] visualize autodock vina results

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) + pr

Re: [PyMOL] visualize autodock vina results

Dear Leila, What OS are jou using ? If it is windows you may try the for windows modified PyMol plugin de Daniel Seeliger from our web site (http://eipl.cnrs-mrs.fr/bioinformatic.php), which allows to create a poses.pdb file usable in PyMol and its measurements wizard. best regards Goetz L

Re: [PyMOL] visualize autodock vina results

Dear Leila, What you want is the create command, you should write something like: create new_object, (pose1, protein) Cheers, Osvaldo. On Mon, Jul 13, 2015 at 3:58 AM, leila karami wrote: Dear PyMOL users, > > I am visualizing autodock vina resul

[PyMOL] visualize autodock vina results

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) + pr