Hi Matt, The slowness is probably the “chemical perception” rather than the secondary structure stuff. Although Chimera does not have an option to turn this off, ChimeraX does; see ChimeraX command “open” with “atomic false” option: <http://rbvi.ucsf.edu/chimerax/docs/user/commands/open.html#local> ChimeraX is generally better (faster) with large data, and it also has the “molmap” command for transforming atomic coordinates to density: <http://rbvi.ucsf.edu/chimerax/docs/user/commands/molmap.html> Like Chimera, ChimeraX is free for noncommercial use. <http://www.rbvi.ucsf.edu/chimerax/> <http://www.rbvi.ucsf.edu/chimerax/download.html> I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Jul 16, 2018, at 9:47 AM, Mateusz Sikora <masikora@biophys.mpg.de> wrote:
Dear Chimera users, is there any way to turn the secondary structure assignment (kdssp) off?
I am transforming a set of coordinates from a MD trajectory into electron density. I collapsed many frames of the trajectory into a single file, meaning there are many unphysical overlaps (I only care about the density). Problem is, that the PDB file I am opening is rather large (couple of millions of atoms) and kdssp gets absolutely stuck on it.
I would appreciate some help. Best regards, Matt