I have a structure with some Zn fingers. How can I describe the Zn2+ tetrahedral environment for Isolde? Cryo EM density is less than spectacular... Thanks. Fred ******************************************************************************* Fred Dyda, Ph.D. Phone:301-402-4496 Laboratory of Molecular Biology Fax: 301-496-0201 NIDDK Bldg. 5. Room 338 e-mail: Fred.Dyda@nih.gov Bethesda, MD 20892-0560 URGENT message: 2022476710@msg.fi.google.com Google map: 39.001168, -77.102048 http://www-mslmb.niddk.nih.gov/dyda/dydalab.html *******************************************************************************
There's currently no "real" definition for this in ISOLDE, but I find the following works for all but the worst density: - deprotonate the cysteine residues (i.e. delete their HG atoms). If histidine residues are involved, make sure they're deprotonated on the zinc-facing nitrogen (select the His, and do "isolde mod his sel {ND|NE|both}" where the last argument defines the protonated nitrogen(s)). If your density is remotely reasonable I'd suggest giving it a try after doing just this. - if it's still recalcitrant, try adding distance restraints. Ctrl-click on the ZN, ctrl-shift-click on an adjacent sulfur or nitrogen, and use the Simple Distance Restraints widget to add a restraint (set the target distance to 2.35 A for sulfur, 2.05 for nitrogen). Consider increasing the spring constant from the default 50 to 250 or so. - if it still misbehaves after that (i.e. the local density is truly awful) then consider adding distance restraints between the coordinating atoms (i.e. sulfur-sulfur, sulfur-nitrogen etc.). I'm afraid ISOLDE doesn't currently implement manually-added angle restraints. Hope this helps! Tristan On Fri, May 24, 2024 at 3:20 PM Dyda, Frederick (NIH/NIDDK) [E] via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
I have a structure with some Zn fingers.
How can I describe the Zn2+ tetrahedral environment for Isolde? Cryo EM density is less than spectacular...
Thanks.
Fred
******************************************************************************* Fred Dyda, Ph.D. Phone:301-402-4496 Laboratory of Molecular Biology Fax: 301-496-0201 NIDDK Bldg. 5. Room 338 e-mail: Fred.Dyda@nih.gov Bethesda, MD 20892-0560 URGENT message: 2022476710@msg.fi.google.com Google map: *39.001168, -77.102048* http://www-mslmb.niddk.nih.gov/dyda/dydalab.html
******************************************************************************* _______________________________________________ ChimeraX-users mailing list -- chimerax-users@cgl.ucsf.edu To unsubscribe send an email to chimerax-users-leave@cgl.ucsf.edu Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/
-- Altos Labs UK Limited | England | Company reg 13484917 Registered address: 3rd Floor 1 Ashley Road, Altrincham, Cheshire, United Kingdom, WA14 2DT
participants (2)
-
Dyda, Frederick (NIH/NIDDK) [E] -
Tristan Croll