[PyMOL] ccp4 map sigma setting
Hi, When I display ccp4 maps in pymol they look a bit larger than I am used to seeing in coot for a given sigma setting. Is it common for users to increase the sigma setting when displaying maps in pymol? -- Yarrow Madrona Graduate Student Molecular Biology and Biochemistry Dept. University of California, Irvine Natural Sciences I, Rm 2403 Irvine, CA 92697 -- Everyone hates slow websites. So do we. Make your web apps faster with AppDynamics Download AppDynamics Lite for free today: http://p.sf.net/sfu/appdyn_d2d_feb ___ 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] ccp4 map sigma setting
On Wed, Feb 20, 2013 at 2:21 PM, Yarrow Madrona wrote: > When I display ccp4 maps in pymol they look a bit larger than I am used to > seeing in coot for a given sigma setting. Is it common for users to > increase the sigma setting when displaying maps in pymol? Have you tried: set normalize_ccp4_maps = 0 ? -Nat -- Everyone hates slow websites. So do we. Make your web apps faster with AppDynamics Download AppDynamics Lite for free today: http://p.sf.net/sfu/appdyn_d2d_feb ___ 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] ccp4 map sigma setting
Unless the values have changed since I last checked the documentations, by default pymol contours maps at 1.0 sigma and coot defaults to 1.5 sigma (for non-difference maps). Pete Yarrow Madrona wrote: > Hi, > > When I display ccp4 maps in pymol they look a bit larger than I am used to > seeing in coot for a given sigma setting. Is it common for users to > increase the sigma setting when displaying maps in pymol? > > > -- Everyone hates slow websites. So do we. Make your web apps faster with AppDynamics Download AppDynamics Lite for free today: http://p.sf.net/sfu/appdyn_d2d_feb ___ 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
[PyMOL] constant distances over states
Hi everyone, I was wondering if there is an easy way to show distances as a function of state. As you show each state (using the play button or mplay), can you show the distance measurement changing? For now it just keeps the distance of the first state shown. I could script this but first would like to ask the users group if there is an easier alternative. Jordan -- Everyone hates slow websites. So do we. Make your web apps faster with AppDynamics Download AppDynamics Lite for free today: http://p.sf.net/sfu/appdyn_d2d_feb ___ 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] constant distances over states
Hi Jordan, distance measurements actually should be multistate by default. Do you create those with a script and provide the state argument? # create multi-state measurement (default) distance test, pk1, pk2, state=0 # create only for state 1 distance test, pk1, pk2, state=1 Cheers, Thomas Jordan Willis wrote, On 02/21/13 06:46: > Hi everyone, > > I was wondering if there is an easy way to show distances as a > function of state. As you show each state (using the play button or > mplay), can you show the distance measurement changing? For now it > just keeps the distance of the first state shown. I could script > this but first would like to ask the users group if there is an > easier alternative. > > Jordan -- Thomas Holder PyMOL Developer Schrödinger Contractor -- Everyone hates slow websites. So do we. Make your web apps faster with AppDynamics Download AppDynamics Lite for free today: http://p.sf.net/sfu/appdyn_d2d_feb ___ 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
