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