[PyMOL] Symmetry expanding electron density maps
Hi everyone, I am trying to expand a map beyond the full asymmetric unit cell to display electron density in pymol. I thought there might be a way to use symmetry operators to expand the map range within pymol (I don't think symexp works for maps, but maybe I'm messing it up) . I will be displaying several asu. I would also appreciate to learn if there is an easy way to reproduce a map to cover many as. unit cells in a program like mapman. Thanks, Engin Ozkan --- Postdoctoral Fellow Stanford University
Re: [PyMOL] Symmetry expanding electron density maps
Engin, This is one of the improvements present in the current open-source code and our latest PyMOL 1.1 builds. PyMOL will nowadays automatically expand the map based on the symmetry defined for the molecule(*) containing the target atoms about which the map is being drawn. Also, if you ask for a buffer which extends beyond the map, then it will be automatically generated based on symmetry. One potential gotcha is that the target atom selections cannot span multiple objects when symmetry expansion is being relied upon. Cheers, Warren (*) NOTE: not the map -- PyMOL maps don't have symmetry records at present -- DeLano Scientific LLC Subscriber Support Services mailto:supp...@delsci.com -Original Message- From: pymol-users-boun...@lists.sourceforge.net [mailto:pymol-users-boun...@lists.sourceforge.net] On Behalf Of Engin Ozkan Sent: Thursday, June 19, 2008 4:34 PM To: pymol-users@lists.sourceforge.net Subject: [PyMOL] Symmetry expanding electron density maps Hi everyone, I am trying to expand a map beyond the full asymmetric unit cell to display electron density in pymol. I thought there might be a way to use symmetry operators to expand the map range within pymol (I don't think symexp works for maps, but maybe I'm messing it up) . I will be displaying several asu. I would also appreciate to learn if there is an easy way to reproduce a map to cover many as. unit cells in a program like mapman. Thanks, Engin Ozkan --- Postdoctoral Fellow Stanford University - Check out the new SourceForge.net Marketplace. It's the best place to buy or sell services for just about anything Open Source. http://sourceforge.net/services/buy/index.php ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users
Re: [PyMOL] Symmetry expanding electron density maps
This sounds more like a testimonial, but 1.1 did seemlessly and exactly what I wanted, so thanks a bunch. Engin DeLano Scientific wrote: Engin, This is one of the improvements present in the current open-source code and our latest PyMOL 1.1 builds. PyMOL will nowadays automatically expand the map based on the symmetry defined for the molecule(*) containing the target atoms about which the map is being drawn. Also, if you ask for a buffer which extends beyond the map, then it will be automatically generated based on symmetry. One potential gotcha is that the target atom selections cannot span multiple objects when symmetry expansion is being relied upon. Cheers, Warren (*) NOTE: not the map -- PyMOL maps don't have symmetry records at present -- DeLano Scientific LLC Subscriber Support Services mailto:supp...@delsci.com -Original Message- From: pymol-users-boun...@lists.sourceforge.net [mailto:pymol-users-boun...@lists.sourceforge.net] On Behalf Of Engin Ozkan Sent: Thursday, June 19, 2008 4:34 PM To: pymol-users@lists.sourceforge.net Subject: [PyMOL] Symmetry expanding electron density maps Hi everyone, I am trying to expand a map beyond the full asymmetric unit cell to display electron density in pymol. I thought there might be a way to use symmetry operators to expand the map range within pymol (I don't think symexp works for maps, but maybe I'm messing it up) . I will be displaying several asu. I would also appreciate to learn if there is an easy way to reproduce a map to cover many as. unit cells in a program like mapman. Thanks, Engin Ozkan --- Postdoctoral Fellow Stanford University - Check out the new SourceForge.net Marketplace. It's the best place to buy or sell services for just about anything Open Source. http://sourceforge.net/services/buy/index.php ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users
