[PyMOL] scenes and states
Questions: Can two objects be in two different states -- object1 in state 3 and object2 in state 10, for instance, at the same time? If so, how is that set up? How is that then incorporated into a scene? Do CGO, measurements, mesh, and volume objects have states as well? Bob -- Robert M. Hanson Larson-Anderson Professor of Chemistry Chair, Chemistry Department St. Olaf College Northfield, MN http://www.stolaf.edu/people/hansonr If nature does not answer first what we want, it is better to take what answer we get. -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900 -- Get 100% visibility into Java/.NET code with AppDynamics Lite It's a free troubleshooting tool designed for production Get down to code-level detail for bottlenecks, with 2% overhead. Download for free and get started troubleshooting in minutes. http://p.sf.net/sfu/appdyn_d2d_ap2___ 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
Re: [PyMOL] scenes and states
Hi Bob, The answer is yes to all. fetch 1ubq, state=3 fetch 6lzm, state=10 cmd.load_cgo([7.0,0,0,0,2],name=sphere,state=2) The representations (e.g. surface) do have states in the sense that the each state gives a different surface. But whether the surface is shown or not is controlled globally. It is not possible to have the surface representation only in one state, such that looping over the states, the surface would suddenly pop up for one. Hope it helps, Tsjerk On Mon, Jun 3, 2013 at 2:38 PM, Robert Hanson hans...@stolaf.edu wrote: Questions: Can two objects be in two different states -- object1 in state 3 and object2 in state 10, for instance, at the same time? If so, how is that set up? How is that then incorporated into a scene? Do CGO, measurements, mesh, and volume objects have states as well? Bob -- Robert M. Hanson Larson-Anderson Professor of Chemistry Chair, Chemistry Department St. Olaf College Northfield, MN http://www.stolaf.edu/people/hansonr If nature does not answer first what we want, it is better to take what answer we get. -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900 -- Get 100% visibility into Java/.NET code with AppDynamics Lite It's a free troubleshooting tool designed for production Get down to code-level detail for bottlenecks, with 2% overhead. Download for free and get started troubleshooting in minutes. http://p.sf.net/sfu/appdyn_d2d_ap2 ___ 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 -- Tsjerk A. Wassenaar, Ph.D. -- Get 100% visibility into Java/.NET code with AppDynamics Lite It's a free troubleshooting tool designed for production Get down to code-level detail for bottlenecks, with 2% overhead. Download for free and get started troubleshooting in minutes. http://p.sf.net/sfu/appdyn_d2d_ap2___ 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
Re: [PyMOL] scenes and states
[[sorry -- not used to a list that requires reply-all to go back to the list]] What you describe there is a way to load a specific file into a specific state, I think. I meant, once you have a set of multi-state objects, can I select to compare two different states, one from one and one from the other? 1cdr2/10 1sq35/30 and then could I make a scene that does that? -- without viewing all states Bob On Mon, Jun 3, 2013 at 9:07 AM, Tsjerk Wassenaar tsje...@gmail.com wrote: Hi Bob, The answer is yes to all. fetch 1ubq, state=3 fetch 6lzm, state=10 cmd.load_cgo([7.0,0,0,0,2],name=sphere,state=2) The representations (e.g. surface) do have states in the sense that the each state gives a different surface. But whether the surface is shown or not is controlled globally. It is not possible to have the surface representation only in one state, such that looping over the states, the surface would suddenly pop up for one. Hope it helps, Tsjerk On Mon, Jun 3, 2013 at 2:38 PM, Robert Hanson hans...@stolaf.edu wrote: Questions: Can two objects be in two different states -- object1 in state 3 and object2 in state 10, for instance, at the same time? If so, how is that set up? How is that then incorporated into a scene? Do CGO, measurements, mesh, and volume objects have states as well? Bob -- Robert M. Hanson Larson-Anderson Professor of Chemistry Chair, Chemistry Department St. Olaf College Northfield, MN http://www.stolaf.edu/people/hansonr If nature does not answer first what we want, it is better to take what answer we get. -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900 -- Get 100% visibility into Java/.NET code with AppDynamics Lite It's a free troubleshooting tool designed for production Get down to code-level detail for bottlenecks, with 2% overhead. Download for free and get started troubleshooting in minutes. http://p.sf.net/sfu/appdyn_d2d_ap2 ___ 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 -- Tsjerk A. Wassenaar, Ph.D. -- Robert M. Hanson Larson-Anderson Professor of Chemistry Chair, Chemistry Department St. Olaf College Northfield, MN http://www.stolaf.edu/people/hansonr If nature does not answer first what we want, it is better to take what answer we get. -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900 -- Get 100% visibility into Java/.NET code with AppDynamics Lite It's a free troubleshooting tool designed for production Get down to code-level detail for bottlenecks, with 2% overhead. Download for free and get started troubleshooting in minutes. http://p.sf.net/sfu/appdyn_d2d_ap2___ 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
Re: [PyMOL] scenes and states
Hi Bob, it's the object-level state setting: fetch 1nmr 1d7q, async=0 set state, 3, 1nmr set state, 10, 1d7q And since scenes do not store settings, this cannot be stored with a scene. Cheers, Thomas On Jun 3, 2013, at 10:41 AM, Robert Hanson hans...@stolaf.edu wrote: [[sorry -- not used to a list that requires reply-all to go back to the list]] What you describe there is a way to load a specific file into a specific state, I think. I meant, once you have a set of multi-state objects, can I select to compare two different states, one from one and one from the other? 1cdr2/10 1sq35/30 and then could I make a scene that does that? -- without viewing all states Bob On Mon, Jun 3, 2013 at 9:07 AM, Tsjerk Wassenaar tsje...@gmail.com wrote: Hi Bob, The answer is yes to all. fetch 1ubq, state=3 fetch 6lzm, state=10 cmd.load_cgo([7.0,0,0,0,2],name=sphere,state=2) The representations (e.g. surface) do have states in the sense that the each state gives a different surface. But whether the surface is shown or not is controlled globally. It is not possible to have the surface representation only in one state, such that looping over the states, the surface would suddenly pop up for one. Hope it helps, Tsjerk On Mon, Jun 3, 2013 at 2:38 PM, Robert Hanson hans...@stolaf.edu wrote: Questions: Can two objects be in two different states -- object1 in state 3 and object2 in state 10, for instance, at the same time? If so, how is that set up? How is that then incorporated into a scene? Do CGO, measurements, mesh, and volume objects have states as well? Bob -- Thomas Holder PyMOL Developer Schrödinger Contractor -- Get 100% visibility into Java/.NET code with AppDynamics Lite It's a free troubleshooting tool designed for production Get down to code-level detail for bottlenecks, with 2% overhead. Download for free and get started troubleshooting in minutes. http://p.sf.net/sfu/appdyn_d2d_ap2 ___ 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
