Hi,
The log file says that you have 112 CA positions which are superposable to better than 4.0A and the RMSD over the equivalent positions is 1.3642.
Eashwar.
Douglas Kojetin wrote: > > Hi- > > I figured out how to get an RMSD fit using the following script (look > correct?): > > ######################################## > # RMSD script > ######################################## > SET OUTPUT_CONTROL = 1 1 1 1 1 > > READ_MODEL FILE = 'B99990100' > SEQUENCE_TO_ALI ATOM_FILES = 'B99990100', ALIGN_CODES = 'B99990100' > READ_MODEL FILE = '../../atom_files/template' > SEQUENCE_TO_ALI ADD_SEQUENCE = on, ATOM_FILES = ATOM_FILES 'template', ; > ALIGN_CODES = ALIGN_CODES 'template' > ALIGN GAP_PENALTIES_1D = -600 -400 > ALIGN3D GAP_PENALTIES_3D = 0 2.0 > WRITE_ALIGNMENT FILE = 'B99990100.ali' > > READ_MODEL FILE = 'sB99990100' > PICK_ATOMS ATOM_TYPES = 'CA' > READ_MODEL2 FILE = '../../atom_files/template' > SUPERPOSE FIT_ATOMS = 'CA' > ######################################## > > This is my output from the .log file > > ######################################## > # output > ######################################## > Least-squares superposition: > > PICKed MODEL atoms are used for superposition if > they have equivalent atoms in MODEL2 > > Superposition done : T > Numb of residues in MODEL : 120 > Numb of atoms/sel atoms in MODEL : 959 120 > Numb of residues in MODEL2 : 122 > Numb of atoms in MODEL2 : 980 > Equivalences refinement : F > Numb of aligned equiv positions : 113 > Numb of aligned equiv distances : 6328 > RMS before superposition : 44.1902 > RMS after superposition : 1.3978 > DRMS : 1.1250 > > Distance cutoff : 3.5000 > Numb of equiv cutoff positions : 112 > Numb of equiv cutoff distances : 6304 > Cutoff RMS after superposition : 1.3642 > Cutoff DRMS : 1.1009 > ######################################## > > My question is -- what exactly do all the categories/listings mean? I > looked (briefly) in the manual for an explanation for each but could not > find one. > > I guess in a round-about way -- which value should I use for my alpha > carbon value RMSD when comparing models? > > Many thanks, > Doug Kojetin > > Bozidar Yerkovich wrote: > > >Hi, > > > >Look at MODELLER commands: SUPERPOSE and COMPARE. > > > >Good luck, > >Bozidar > > > > > > > >On Monday May 20 2002 01:49 pm, Douglas Kojetin wrote: > > > >>Hi- > >> > >>Will modeller perform a calculation of RMSD (Ca, etc) between the target > >>and template and output the RMSD? I'm looking to have a semi-automated > >>(or automatable) method for doing this (to compare 50+ models at once > >>quickly). > >> > >>Many thanks, > >>Doug Kojetin > >>