yes, it is OK.
but if you are interested in subsequently "evaluate" the model you
obtained, you have many different programs that can do that, using
various criteria. Here is a link to collection of links and you can read
more about this in our reviews.
http://salilab.org/modeller/methenz/http://salilab.org/~andras/watanabe/main2.pshttp://salilab.org/modeller/downloads/andras.pdf
Andras
Richard Friedman wrote:
>
> Fellow Modellers,
>
> I ran the first example in the Modeller tutorial, 1fdx,
> and I got several restraint violations in the final structure. I ran the
> diagnostics, and I dod not receive any error messages.
> Is this as it should be?
> Is there anywhere in which one can obtain a standard 1fdx run that can be
> used as a "known"?
>
> I know that, based upon faq #23, interpreting restraint violations is
> something of an art. I am asking to make sure that I ran the program
> correctly, and that the program is running as it should be.
>
> My violated restraints are:
>
> Summary of the restraint violations:
>
> NUM ... number of restraints.
> NUMVI ... number of restraints with RVIOL > VIOL_REPORT_CUT[i].
> RVIOL ... relative difference from the best value.
> NUMVP ... number of restraints with -Ln(pdf) > VIOL_REPORT_CUT2[i].
> RMS_1 ... RMS(feature, minimally_violated_basis_restraint, NUMB).
> RMS_2 ... RMS(feature, best_value, NUMB).
> MOL.PDF ... scaled contribution to -Ln(Molecular pdf).
>
> # RESTRAINT_GROUP NUM NUMVI NUMVP RMS_1 RMS_2 MOL.PDF S_i
> ------------------------------------------------------------------------------------------------------
> 1 Bond length potential : 379 0 0 0.005 0.005 2.8642 1.000
> 2 Bond angle potential : 520 0 0 2.444 2.444 59.089 1.000
> 3 Stereochemical cosine torsion poten: 244 0 10 55.593 55.593 103.81 1.000
> 4 Stereochemical improper torsion pot: 146 0 0 1.474 1.474 6.3455 1.000
> 5 Soft-sphere overlap restraints : 663 0 0 0.002 0.002 0.47318 1.000
> 6 Lennard-Jones 6-12 potential : 0 0 0 0.000 0.000 0.0000 1.000
> 7 Coulomb point-point electrostatic p: 0 0 0 0.000 0.000 0.0000 1.000
> 8 H-bonding potential : 0 0 0 0.000 0.000 0.0000 1.000
> 9 Distance restraints 1 (CA-CA) : 804 0 0 0.344 0.344 30.114 1.000
> 10 Distance restraints 2 (N-O) : 832 0 1 0.467 0.467 37.873 1.000
> 11 Mainchain Phi dihedral restraints : 0 0 0 0.000 0.000 0.0000 1.000
> 12 Mainchain Psi dihedral restraints : 0 0 0 0.000 0.000 0.0000 1.000
> 13 Mainchain Omega dihedral restraints: 53 0 0 4.634 4.634 13.423 1.000
> 14 Sidechain Chi_1 dihedral restraints: 43 0 1 72.693 72.693 11.147 1.000
> 15 Sidechain Chi_2 dihedral restraints: 26 0 1 68.739 68.739 16.513 1.000
> 16 Sidechain Chi_3 dihedral restraints: 9 0 0 37.987 37.987 3.4346 1.000
> 17 Sidechain Chi_4 dihedral restraints: 1 0 0 124.535 124.535 1.0173 1.000
> 18 Disulfide distance restraints : 0 0 0 0.000 0.000 0.0000 1.000
> 19 Disulfide angle restraints : 0 0 0 0.000 0.000 0.0000 1.000
> 20 Disulfide dihedral angle restraints: 0 0 0 0.000 0.000 0.0000 1.000
> 21 Lower bound distance restraints : 0 0 0 0.000 0.000 0.0000 1.000
> 22 Upper bound distance restraints : 0 0 0 0.000 0.000 0.0000 1.000
> 23 Distance restraints 3 (SDCH-MNCH) : 553 0 0 0.540 0.540 18.286 1.000
> 24 Sidechain Chi_5 dihedral restraints: 0 0 0 0.000 0.000 0.0000 1.000
> 25 Phi/Psi pair of dihedral restraints: 52 9 5 29.961 67.309 9.4985 1.000
> 26 Distance restraints 4 (SDCH-SDCH) : 100 0 2 1.196 1.196 15.584 1.000
> 27 Distance restraints 5 (X-Y) : 0 0 0 0.000 0.000 0.0000 1.000
> 28 NMR distance restraints 6 (X-Y) : 0 0 0 0.000 0.000 0.0000 1.000
> 29 NMR distance restraints 7 (X-Y) : 0 0 0 0.000 0.000 0.0000 1.000
> 30 Minimal distance restraints : 0 0 0 0.000 0.000 0.0000 1.000
> 31 Non-bonded restraints : 0 0 0 0.000 0.000 0.0000 1.000
> 32 Atomic accessibility restraints : 0 0 0 0.000 0.000 0.0000 1.000
> 33 Atomic density restraints : 0 0 0 0.000 0.000 0.0000 1.000
>
> openf5__224_> Open 17 UNKNOWN SEQUENTIAL 1fdx.V99990001
> # Heavy relative violation of each residue is written to: 1fdx.V99990001
> # The profile is NOT normalized by the number of restraints.
> # The profiles are smoothed over a window of residues: 1
>
> List of the violated restraints:
> A restraint is violated when the relative difference
> from the best value (RVIOL) is larger than CUTOFF.
>
> ICSR ... index of a restraint in the current set.
> RESNO ... residue numbers of the first two atoms.
> ATM ... IUPAC atom names of the first two atoms.
> FEAT ... the value of the feature in the model.
> restr ... the mean of the basis restraint with the smallest
> difference from the model (local minimum).
> viol ... difference from the local minimum.
> rviol ... relative difference from the local minimum.
> RESTR ... the best value (global minimum).
> VIOL ... difference from the best value.
> RVIOL ... relative difference from the best value.
>
> -------------------------------------------------------------------------------------------------
>
> Feature 25 : Phi/Psi pair of dihedral restraints
> List of the RVIOL violations larger than : 6.5000
>
> # ICSR RESNO1/2 ATM1/2 INDATM1/2 FEAT restr viol rviol RESTR VIOL RVIOL
> 1 1296 7S 8C C N 53 55 -75.51 -117.90 43.16 1.34 -63.00 174.54 20.46
> 1 8C 8C N CA 55 56 133.00 141.10 -41.10
> 2 1297 8C 9I C N 59 61 -109.33 -97.30 83.47 8.55 -63.40 99.45 15.16
> 2 9I 9I N CA 61 62 44.60 127.20 -43.60
> 3 1298 9I 10A C N 67 69 43.10 55.40 23.15 0.89 -62.50 144.55 28.99
> 3 10A 10A N CA 69 70 57.81 38.20 -40.90
> 4 1299 10A 11C C N 72 74 -61.78 -63.00 1.43 0.25 -117.90 -172.86 8.06
> 4 11C 11C N CA 74 75 -40.37 -41.10 141.10
> 5 1310 21N 22I C N 146 148 -109.14 -120.60 69.78 3.55 -63.40 114.60 17.55
> 5 22I 22I N CA 148 149 61.47 130.30 -43.60
> 6 1313 24Q 25G C N 171 173 98.62 78.70 39.64 0.60 82.20 152.01 8.20
> 6 25G 25G N CA 173 174 159.62 -166.10 8.50
> 7 1314 25G 26S C N 175 177 -65.61 -64.10 21.61 1.66 -136.60 167.99 9.49
> 7 26S 26S N CA 177 178 -56.55 -35.00 151.20
> 8 1315 26S 27I C N 181 183 -64.03 -63.40 6.55 1.10 -120.60 -171.73 12.88
> 8 27I 27I N CA 183 184 -50.13 -43.60 130.30
> 9 1316 27I 28Y C N 189 191 104.14 -124.30 131.89 10.18 -124.30 131.89 10.18
> 9 28Y 28Y N CA 191 192 126.16 135.40 135.40
>
> Thanks and best wishes,
> Rich
> --------------------------------------------------------------
> Richard A. Friedman, PhD
> Associate Research Scientist
> Herbert Irving Comprehensive Cancer Center
> Oncoinformatics Core
> Lecturer
> Department of Medical Informatics
> Box 95, Room 130BB or P&S 1-420C
> Columbia University
> 630 W. 168th St.
> New York, NY 10032
> (212)305-6901 (5-6901) (voice)
>
> http://cancercenter.ccc.columbia.edu/~friedman/
>
> In Memoriam, Robert Kanigher
--
,
Andras Fiser, PhD # phone: (212) 327 7216
The Rockefeller University # fax: (212) 327 7540
Box 270, 1230 York Avenue # e-mail:
New York, NY 10021-6399, USA # http://salilab.org/~andras