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.
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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) friedman@cancercenter.ccc.columbia.edu http://cancercenter.ccc.columbia.edu/~friedman/
In Memoriam, Robert Kanigher
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.ps http://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) > friedman@cancercenter.ccc.columbia.edu > http://cancercenter.ccc.columbia.edu/~friedman/ > > In Memoriam, Robert Kanigher
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Andras Fiser -
Richard Friedman