The results are saved in the sscache_data array.
# routine to evaluate the secondary structure based on the new # the data to redefine the "structure" keyword values (but only for # exists in the Tcl array sscache_data(molecule,frame). # structure definition for the given molecule number and frame already Whenever the frame for that molecule changes, the # saved (the default is "top", which gets converted to the correct # molecule number of the molecule whose secondary structure should be So all you’d need to do in Pymol > is a simple loop over all residues to get their secondary structure > designation and write the corresponding character to a text file. # It is turned on with the command "start_sscache> followed by the sscache Automatically stores secondary structure information for animations sscachebunch FAST storage of secondary structure information for animations trajectoryanalyze An example of an efficient way to analyze large trajectories within VMD while they load. VMD gets/sets secondary structure as a simple Tcl > array of characters, one per residue. PyMOL Tutorial (2) Animations & Scripts 5. Sketch a topology diagram on paper (use the open structure 4AKE for analysis): number helices H1 - H8 (ignore short helices < 4 residues, count all helices as helix ( -helix, -helix, 3 10 -helix)) label the -sheets A, B, C, number individual strands A1-A5, B1-B2, C1-C3. As it turns out, the other tools necessary. Create Scene 1: a cartoon representation colored by secondary structure. Identify secondary structure and topology. This lets you see how the secondary structure Ill be using the built-in tcl interpreter to automate generating geometry for each frame in the dynamics animation.
# Calculates and stores the secondary structure assignment for # sscache - internal function used by trace # start_sscache molid - start caching the given molecule # Automatically stores secondary structure information for animations Secondary structure attributes helix : G,H,I If the atom is part of a helix alphahelix : H If the atom is part of an alpha helix helix310 : G If the atom. # Cache secondary structure information for a given molecule Identify secondary structure and topology.
ANIMATE SECONDARY STRUCTURE VMD PLUS
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