To Everyone: When posting such questions, please always indicate what specific vesion of PyMOL you are using, since the program continues to evolve with every release (to reflect numerous end-user suggestions, as enabled by contributions from our sponsors.)
To Andy: PyMOL version 1.2r1 should symmetry-expand the map assuming that density values have been provided somewhere within the ASU. PyMOL cannot yet render a map straight from a reflection file. Cheers, Warren > -----Original Message----- > From: Andy Torelli [mailto:at...@cornell.edu] > Sent: Thursday, September 17, 2009 11:54 AM > To: pymol-users@lists.sourceforge.net > Subject: [PyMOL] Displaying electron density from maps output by Coot. > > Hi everyone, > > I have a simple problem that has come up before (4/2/2009 post), but > I > haven't found a solution yet. > Maps written out from Coot and display in Pymol seem to be situated > on > a different origin compared to the PDB coordinates. E.g., if I: > load my-structure.pdb > load my-map.map, map1, 1, ccp4 > isomesh msh1,map1,1.0 > A nice electron density map is rendered (no errors), but offset from > the my-structure.pdb coordinates (both map and coords were output from > Coot where they were overlaid correctly). It sometimes works to > explicitly indicate the residues around which to render the map: > isomesh msh1,map1,1.0,(chain a and resi 10),carve=3.0 > In my current case however, an NCS-averaged map output from Coot is > not > displaying at the desired location. To be clear, the map can be > displayed elsewhere in space, but it does not overlap with my > coordinates (these are not symmetry-generated molecules, they're part of > the ASU). As Robert Campbell indicated in response to the earlier post, > Pymol expects maps to be calculated to cover the whole molecule of > interest. My question is why does this map/model pair display correctly > in Coot while Pymol shows the map offset from the model? Is there a way > to tell Pymol to place the map at a different origin (i.e. so that it > overlays with the coordinates)? > > I realize this may also be a Coot question, but I'm not sure of the > source of the problem yet so I'm posting here. I'll try the other bb if > necessary. > > Thanks for your help, > -Andy Torelli > > =========================================== > Andrew T. Torelli Ph.D. > Postdoctoral Associate > Department of Chemistry & Chemical Biology > Baker Laboratory, Cornell University > Ithaca, NY 14853 > =========================================== > > ------------------------------------------------------------------------ -- > ---- > Come build with us! The BlackBerry® Developer Conference in SF, CA > is the only developer event you need to attend this year. Jumpstart your > developing skills, take BlackBerry mobile applications to market and stay > ahead of the curve. Join us from November 9-12, 2009. Register > now! > http://p.sf.net/sfu/devconf > _______________________________________________ > 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 > > > ------------------------------------------------------------------------------ Come build with us! The BlackBerry® Developer Conference in SF, CA is the only developer event you need to attend this year. Jumpstart your developing skills, take BlackBerry mobile applications to market and stay ahead of the curve. Join us from November 9-12, 2009. Register now! http://p.sf.net/sfu/devconf _______________________________________________ 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
