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Re: RMSD calculation



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