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
