Hi Jared, I wrote that code correctly the first time, then someone convinced me I had done it backwards. It was a small snafu that has been fixed. It's now switched in a patch after v1.3, and works as expected in v1.4+.
Cheers, -- Jason On Tue, Apr 12, 2011 at 2:16 PM, Sampson, Jared <jared.samp...@nyumc.org> wrote: > Hello all - > > I have been looking at some electron density from the EDS and wondering why > it didn't appear to match up with the coordinates. Then I found that it > appears PyMOL (v 1.3), when requesting a "2fofc" map, actually reads in the > fofc, and vice versa. Here's a script to illustrate the point (using the > coordinate example from the Fetch page on the wiki, along with the manually > downloaded maps from EDS (saved as *_eds.omap in the same directory). > > ########## start script ########## > > ### Using Fetch from within PyMOL ### > > fetch 1cll, async=0 > as sticks > set stick_radius, 0.12 > > # Fetched "2fofc" > fetch 1cll, type=2fofc, async=0 > isomesh 2fofc_mesh, 1cll_2fofc, 1.5 > color blue, 2fofc_mesh > > # Fetched "fofc" > fetch 1cll, type=fofc, async=0 > isomesh fofc_mesh, 1cll_fofc, 1.5 > color magenta, fofc_mesh > > zoom i. 34-35 > clip atoms, 1, i. 34-35 > png fetch_maps.png > > reinitialize > > ### Using Manually Downloaded Maps ### > > fetch 1cll, async=0 > as sticks > set stick_radius, 0.12 > > # Downloaded "2mFo-DFc" from EDS directly > load 1cll_eds.omap, 1cll_2fofc > isomesh 2fofc_mesh, 1cll_2fofc, 1.5 > color blue, 2fofc_mesh > > # Downloaded "mFo-DFc" from EDS directly > load 1cll_diff_eds.omap, 1cll_fofc > isomesh fofc_mesh, 1cll_fofc, 1.5 > color magenta, fofc_mesh > > zoom i. 34-35 > clip atoms, 1, i. 34-35 > png eds_maps.png > > > ########## end script ########## > > The resulting images can be seen at <http://bit.ly/gPTtbw>. It appears that > PyMOL is switching the 1cll.omap and 1cll_diff.omap somewhere along the way. > Perhaps this has been fixed in v1.4? I couldn't find any mention of this > problem in the wiki/archives. > > Thanks, > Jared > > -- > Jared Sampson > Xiangpeng Kong Lab > NYU Langone Medical Center > New York, NY 10016 > 212-263-7898 > > > ------------------------------------------------------------ > This email message, including any attachments, is for the sole use of the > intended recipient(s) and may contain information that is proprietary, > confidential, and exempt from disclosure under applicable law. Any > unauthorized review, use, disclosure, or distribution is prohibited. If you > have received this email in error please notify the sender by return email > and delete the original message. Please note, the recipient should check this > email and any attachments for the presence of viruses. The organization > accepts no liability for any damage caused by any virus transmitted by this > email. > ================================= > > > ------------------------------------------------------------------------------ > Forrester Wave Report - Recovery time is now measured in hours and minutes > not days. Key insights are discussed in the 2010 Forrester Wave Report as > part of an in-depth evaluation of disaster recovery service providers. > Forrester found the best-in-class provider in terms of services and vision. > Read this report now! http://p.sf.net/sfu/ibm-webcastpromo > _______________________________________________ > 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 > -- Jason Vertrees, PhD PyMOL Product Manager Schrodinger, LLC (e) jason.vertr...@schrodinger.com (o) +1 (603) 374-7120 ------------------------------------------------------------------------------ Forrester Wave Report - Recovery time is now measured in hours and minutes not days. Key insights are discussed in the 2010 Forrester Wave Report as part of an in-depth evaluation of disaster recovery service providers. Forrester found the best-in-class provider in terms of services and vision. Read this report now! http://p.sf.net/sfu/ibm-webcastpromo _______________________________________________ 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
