-----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 Dear Chris,
did you check the map looks like what you expect it to be? If I remember correctly, I had difficulties covering the Tl+/K+ ions from these data because they lie at the very edge of the asymmetric unit. I used mapmask as in the attached script in order to extend the map to cover the Tl+ atoms. Note that the 1D-profile (as well as the 3D-profile) depends on the B-values of the ions, and a dip in the anomalous signal could be accounted for by an increased vibrational motion. That's why I did not interprete the map but the diffraction data in my re-analysis of these data in http://www.sciencemag.org/content/346/6207/352 with modern means. Kind regards, Tim On 04/14/2015 11:15 PM, Chris K wrote: > Dear all, > > I was trying to generate a one-dimensional electron density > profile along the Z axis from an anomalous difference map (similar > to Fig. 1 of Zhou, Y., & Mackinnon, R. (2003), Journal of Molecular > Biology, 333(5), 965–975) using the program MAPMAN, but I think I’m > missing something. > > This is what I tried: - I’ve generated the anomalous difference > map covering all the atoms in the pdb file using FFT from the CCP4 > gui, doubling the grid space. - I fed MAPMAN with that anomalous > map and ran the command “1d mymap”. - I then selected the Z axis. - > I converted the O2D plot file into a PS file. > > But I think what I’m getting is only noise. Is there a way to plot > the profile only for signals above 4 sigma? > > > Cheers, > > Chris > - -- - -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen phone: +49 (0)551 39 22149 GPG Key ID = A46BEE1A -----BEGIN PGP SIGNATURE----- Version: GnuPG v1 iD8DBQFVLhSCUxlJ7aRr7hoRAhwYAJ9In8VMez0VlZXUba7kajescoeudACg4/Az uBFym57xWQ3itQA66kcOIAI= =UEOO -----END PGP SIGNATURE-----
pha2map.sh
Description: application/shellscript
