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
> >>
--
Eashwar Narayanan
Research Associate (Sali Lab)
The Rockefeller University
1230 York Avenue, New York, NY 10021-6399
Phone: +1 212 327 7757 ; Fax +1 212 327 7540
E-mail: