RE: [PyMOL] Selecting objects to move
Leslie, Well it seems a mis-spoke. I tried to write a script which does what you layed out, but it turns out that the current the API functions for moving moleculs don't have quite enough power to do this efficiently (even in version 0.73). My time is probably better spent refining "rotate" and "translate" than describing some kind of elaborate work-around which would enable you to do this right now. Can we revisit this in a month or two? Electrostatic surfaces are also a few months away still, unless someone can provide me with source code for a drop-in PB solver. Cheers, Warren > From: Leslie Hall [mailto:hal...@uthscsa.edu] > I am trying to make these changes automatically. > Essentially, I would > like to have a script to make a movie where; > > First, I want to load pdb files that contain four molecules > (A, A, B, and > B). Initially, I what to hide all four molecules. Then > show the dimer AA > in the center of the screen. Have this dimer rotate around > X. Then show a > conformational change in this dimer where you hold one of the > molecules (A) > stationary, while you rotate the other molecule A in X by 100 degrees. > After this is done, I then want to show one molecules of B on > the left side > and the other molecule B on the right side of the dimer of > AA. Finally I > want to show the molecule B's moving and docking with the > dimer (AA) in its > new conformation. > > Also, is it posible to make this movie showing electrostatic surface? > > Les > > >
Re: [PyMOL] Selecting objects to move
"DeLano, Warren" wrote: > > From: Leslie Hall [mailto:hal...@uthscsa.edu] > > > I have just started using PyMol and had a question about > > moving selected > > objects in an animation. > > Here is basically what I want to do. > > > > 1.Load two separate pdb files. > > 2.Be able to move the two molecules independently of each other. > > 3.Show a conformational change in one of the molecules. > > 4.Move the two molecules independently and show them docking with > > each other. > > Leslie, > >Are you trying to perform these changes manually using the mouse, or > automatically using the Python API? The manual approach is documented > in the manual, but the Python API approach was neither documented nor > complete in 0.68. > >It is complete now in version (0.73) but still isn't well documented. > If you provide some more details about how you're planning on doing > this, I could probably post a couple examples for you. Warren, I am trying to make these changes automatically. Essentially, I would like to have a script to make a movie where; First, I want to load pdb files that contain four molecules (A, A, B, and B). Initially, I what to hide all four molecules. Then show the dimer AA in the center of the screen. Have this dimer rotate around X. Then show a conformational change in this dimer where you hold one of the molecules (A) stationary, while you rotate the other molecule A in X by 100 degrees. After this is done, I then want to show one molecules of B on the left side and the other molecule B on the right side of the dimer of AA. Finally I want to show the molecule B's moving and docking with the dimer (AA) in its new conformation. Also, is it posible to make this movie showing electrostatic surface? Les
RE: [PyMOL] Selecting objects to move
Warren, Is 0.73 out? I only see 0.68 on your download site. Thanks, Glen > >It is complete now in version (0.73) but still isn't well documented. > If you provide some more details about how you're planning on doing > this, I could probably post a couple examples for you... > > Warren > > -- > mailto:war...@sunesis.com > Warren L. DeLano, Ph.D. > Informatics Manager > Sunesis Pharmaceuticals, Inc. > 341 Oyster Point Blvd. > S. San Francisco, CA 94080 > (650)-266-3606 fax: (650)-266-3501 > > > ___ > PyMOL-users mailing list > PyMOL-users@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/pymol-users >
RE: [PyMOL] Selecting objects to move
> From: Leslie Hall [mailto:hal...@uthscsa.edu] > I have just started using PyMol and had a question about > moving selected > objects in an animation. > Here is basically what I want to do. > > 1.Load two separate pdb files. > 2.Be able to move the two molecules independently of each other. > 3.Show a conformational change in one of the molecules. > 4.Move the two molecules independently and show them docking with > each other. Leslie, Are you trying to perform these changes manually using the mouse, or automatically using the Python API? The manual approach is documented in the manual, but the Python API approach was neither documented nor complete in 0.68. It is complete now in version (0.73) but still isn't well documented. If you provide some more details about how you're planning on doing this, I could probably post a couple examples for you... Warren -- mailto:war...@sunesis.com Warren L. DeLano, Ph.D. Informatics Manager Sunesis Pharmaceuticals, Inc. 341 Oyster Point Blvd. S. San Francisco, CA 94080 (650)-266-3606 fax: (650)-266-3501
Re: [PyMOL] Selecting objects to move
I'm new too but I think on-line manual can help you. http://pymol.sourceforge.net/html/toc.html Good luck, Ricardo Leslie Hall wrote: > > Hello, > > I have just started using PyMol and had a question about moving selected > objects in an animation. > Here is basically what I want to do. > > 1.Load two separate pdb files. > 2.Be able to move the two molecules independently of each other. > 3.Show a conformational change in one of the molecules. > 4.Move the two molecules independently and show them docking with > each other. > > Thanks, > > Les > > ___ > PyMOL-users mailing list > PyMOL-users@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/pymol-users
[PyMOL] Selecting objects to move
Hello, I have just started using PyMol and had a question about moving selected objects in an animation. Here is basically what I want to do. 1.Load two separate pdb files. 2.Be able to move the two molecules independently of each other. 3.Show a conformational change in one of the molecules. 4.Move the two molecules independently and show them docking with each other. Thanks, Les
