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 >>