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P!@ %k aH*U % h* ' 4 , @%' 'ɨ H% 8% ' 0X0P! $@X%QP! (%p! p! 4 ׅ $ ( 0%߰ p $p0 %ߵ x߱ 8߲ h߳ `߿ Hߴ P %߶ X߷ @ ' D0 F&( %.3f
Dzz %.3f Dyy %.3f Dxx %.3f DzzC %.3f DyyC %.3f DxxC %.3f Da %.3e Rh %.3f RMS %.4f
Too many iterations in routine jacobi allocation failure for data allocation failure for resp allocation failure for ans Grid point R = %.2f D = %.2f
allocation failure in ivector() allocation failure in vector() allocation failure 1 in matrix() allocation failure 2 in matrix() run-time errror...
'%s' - There is no such file!
...now exiting to system...
'%s' is being read in...
-nofixed -noeuler -thetaMin -thetaMax DYNAMO Error: -saupe option requires 5 values.
DC Error opening output file %s
REMARK Molecular Alignment Simulation.
REMARK Simulation parameters.
(X`T8(D(((
DATA PALES_MODE STERIC
DATA PALES LC_TYPE wall
DATA PALES LC_TYPE rod
DATA PALES LC_CONCENTRATION %.3f
DATA PALES ORIENT_SPHERE %d
DATA PALES ORIENT_PSI %d
DATA PALES GRID_SPACING % .3f
DATA PALES MODEL_RADIUS % .3f
DATA PALES LC_ORDER % .3f
DATA PALES ATOM_RADIUS % .3f
DATA PALES SEL_SIMPLE_FLAG %d
DATA PALES SURF_FLAG %d
DATA PALES_MODE CONV
DATA DCs are normalized.
DATA DCs are not normalized.
DATA Gaussian noise according to DD has been added.
DATA PALES_MODE SAUPE_CP
DATA PALES ACTION max
DATA PALES C1 % .3f
DATA PALES C2 % .3f
DATA PALES ACTION div
DATA PALES ACTION mul
DATA PALES ACTION sub
DATA PALES ACTION add
DATA PALES_MODE DC_CP
DATA PALES_MODE HIST
DATA PALES_MODE DA_ML
DATA PALES DA LOW_GRID % .3f
DATA PALES DA HIGH_GRID % .3f
DATA PALES DA INCREMENT % .3f
DATA PALES R LOW_GRID % .3f
DATA PALES R HIGH_GRID % .3f
DATA PALES R INCREMENT % .3f
REMARK Solving the linear equation system.
DATA EQ Da % .3f
DATA EQ R % .3f
REMARK Maximum Likelihood determination.
DATA ML Da % .3f
DATA ML Da Err % .3f
DATA ML R % .3f
DATA ML R Err % .3f
DATA PALES_MODE CS
DATA PALES_MODE DC
DATA TENSOR_MODE NOFIXED (Variable Da and Dr, Variable Rotations)
DATA DA_RANGE % .4e % .4e
DATA DR_RANGE % .4e % .4e
DATA PSI_RANGE % 8.2f % 8.2f
DATA THETA_RANGE % 8.2f % 8.2f
DATA PHI_RANGE % 8.2f % 8.2f
DATA TENSOR_MODE DADR (Fixed Da and Dr, Variable Rotations)
DATA TENSOR_MODE FIXED (Fixed Da and Dr, Fixed Rotations)
DATA TENSOR_MODE SAUPE (Fixed Saupe Values)
DATA TENSOR_MODE SVD (Order Matrix Method)
DATA PALES_MODE ELECTROSTATIC_GRID
DATA PALES_MODE ELECTROSTATIC_FREE
DATA PALES_MODE ELECTROSTATIC
DATA PALES EL PH % .3f
DATA PALES EL NACL % .3f
DATA PALES EL SURF_CH % .3f
DATA PALES EL DIPOLE on
DATA PALES EL DIPOLE off
DATA PALES EL PKA_DEFAULT on
DATA PALES EL PKA_DEFAULT off
DATA PALES EL CH_TERM on
DATA PALES EL CH_TERM off
DATA PALES EL CUTOFF %e
DATA PALES_MODE STERIC_GRID
DATA PALES_MODE STERIC_FREE
DATA PALES INCLUDE_RIM on
DATA PALES MOLAR_RATIO % .3f
DATA PALES MODEL_LENGTH % .3f
DATA PALES S_DISC_RIM % .3f
REMARK Order matrix.
DATA SAUPE_MATRIX %s %s %s %s %s
S(xx-yy) DATA SAUPE % .4e % .4e % .4e % .4e % .4e
PALES: error occured in analyzeSaupe.
DATA IRREDUCIBLE_REP A0 A1R A1I A2R A2I
DATA IRREDUCIBLE % .4e % .4e % .4e % .4e % .4e
DATA IRREDUCIBLE GENERAL_MAGNITUDE % .4e
REMARK Mapping of coordinates.
DATA MAPPING_COOR Szz_d(x) Szz_d(y) Syy_d(x) Syy_d(y) Sxx_d(x) Sxx_d(y)
DATA MAPPING % .5f % .5f % .5f % .5f
DATA MAPPING INV
REMARK Eigensystem & Euler angles for clockwise rotation about z, y', z''.
DATA EIGENVALUES (Sxx_d,Syy_d,Szz_d) % .4e % .4e % .4e
DATA EIGENVECTORS (x_coor y_coor z_coor)
DATA EIGENVECTORS X_AXIS % .4e % .4e % .4e
DATA EIGENVECTORS Y_AXIS % .4e % .4e % .4e
DATA EIGENVECTORS Z_AXIS % .4e % .4e % .4e
DATA Q_EULER_SOLUTIONS %7s %7s %7s
DATA Q_EULER_ANGLES %2d %7.2f %7.2f %7.2f
REMARK Euler angles (psi/theta/phi) for rotation about x, y, z.
REMARK Dipolar couplings.
DATA N %d
DATA RMS %.3f
DATA Chi2 %.3f
DATA CORR R %.3f
DATA Q SAUPE %.3f
DATA SEQUENCE DATA Q RDC_RMS %.3f
DATA Q STDDEV %.3f
DATA REGRESSION OFFSET %.3f +/- %.3f [Hz]
DATA REGRESSION SLOPE %.3f +/- %.3f [Hz]
DATA REGRESSION BAX SLOPE %.3f +/- %.3f [Hz]
RESID_I RESNAME_I ATOMNAME_I CHAINNAME_I SEGNAME_I RESID_J RESNAME_J ATOMNAME_J CHAINNAME_J SEGNAME_J DI D_OBS D D_DIFF DD W
D DD W
%%4d %%4s %%4s %%9.2f %%9.3f %%9.3f %%9.3f %%.2f %%.2f
%%9.3f %%9.3f %%.2f
%4d %4s %4s % 9.2f % 9.4f % 9.4f % 9.4f %7.4f %.2f
% 9.4f %7.4f %.2f
Error allocating temporary buffers.
REMARK Dipolar Coupling Simulation.
REMARK %s
DATA N %d
DATA RMS %.3f
DATA Chi2 %.3f
pD8τ$TDATA TENSOR_MODE STERIC (Zweckstetter Method)
DATA TENSOR_MODE ELECTROSTATIC DATA SAUPE % .4e % .4e % .4e % .4e % .4e
DI D DD W
%%9.2f %%9.3f %%9.3f %%9.3f %%.2f %%.2f
%%9.2f %%9.3f %%9.3f %%.2f
% 9.2f % 9.4f % 9.4f % 9.4f %7.4f %.2f
% 9.2f % 9.4f %7.4f %.2f
PDB finding |%s|
PDB Error opening PDB file %s
MODEL %d
%s%5d %-4s%1c%-4s%1c%4d%1c % 8.3f% 8.3f% 8.3f%6.2f%6.2f %4s%2s%2s
%s%5d %-3s%1c%-4s%1c%4d%1c % 8.3f% 8.3f% 8.3f%6.2f%6.2f %4s%2s%2s
Utility Error: Aborting.
allocation failure in vector() allocation failure in ivector() allocation failure in dvector() allocation failure 1 in matrix() allocation failure 2 in matrix() allocation failure 1 in dmatrix() allocation failure 2 in dmatrix() allocation failure 1 in imatrix() allocation failure 2 in imatrix() allocation failure in convert_matrix()
---> ERROR when executing line %i in file %s !
---> Execution stopped !
---> WARNING : line %i in file %s
ASIN : invalid argument %f CALLOC : failed in file %s at line %d REALLOC : failed in file %s at line %d divarc: rotation axis of length %f divarc: vector 1 of sq.length %f divarc: vector 2 of sq.length %f ico_dot_arc: error in formula for tessalation level (%d->%d, %d) ico_dot: tn exceeds dimension of xus ico_dot: n_dot(%d) and tn(%d) differ ico_dot_dod: error in formula for tessalation level (%d->%d, %d) make_unsp: mode %c%d not allowed nsc_dclm: no surface atoms selected pdb.list Error allocating DC/PDB/PALES structures.
PALES Error extracting command-line arguments.
??@l??????CPBBT?AAP??@Error reading PDB input %s
%s, %d Atoms, Residues %d to %d.
Error reading DC input %s
%s, %d Couplings, Residues %d to %d.
Error allocating coord buffers.
Error allocating charge and potential buffers.
exclusive inclusive REMARK %d couplings selected (%s%s).
REMARK PDB Selection: All Atoms.
Residues %d to %d Residues: %s Atoms: %s Chains %s Segs: %s.
[1-3]H* H* pales: error in writePDB.
ILLKKJJL pales: error in best-fit of data.
Matrix: error in best-fit of data.
Error reading configuration file %s
WARNING: Error setting up charges!
REMARK %d charges placed, Total charge %.3f [e].
REMARK charges used in simulation:
REMARK ===========================
REMARK chargeID atom serial number charge [e]
REMARK %d: %5d %8.3f %8.3f %8.3f %8.3f
Error allocating grid buffers.
Matrix: unsp error occured.
matrix: error in initOrient.
matrix: error in storePDBCoords.
matrix: setupEnsemble error occured.
REMARK ENSEMBLE MODE.
REMARK STERIC CLASH CHECK ENABLED.
REMARK STERIC CLASH CHECK DISABLED.
REMARK %d states in ensemble.
REMARK Simulated DCs will be appended to %s.
matrix: ensembleAlignment error occured.
Matrix: error in analyzeSaupe.
pales: error in writePales.
Matrix: error in statDC.
DATA SAUPE % .4e % .4e % .4e % .4e % .4e
DATA Da(NH) = %.1f R = Dr/Da = %.3f
Matrix: Error reading selection of atoms.
REMARK %d atoms selected for simulation.
REMARK %d charges selected for simulation.
ERROR: Reading of 3D potential not successful.
REMARK 3D Potential %s, Total # of gridpositions %d (x: %d, y: %d, z: %d).
Matrix: Error simulating alignment.
ERROR Reading of 1D potential not successful.
REMARK 1D Potential %s, Digitization %d, Offset %.1f, Stepsize %.1f [A].
pales: error in iFacePDB.
pales: error reading selection of atoms.
Error allocating potential buffer.
matrix: error in writePDBRot.
pales: error in analysis of PDB.
matrix: error in ssiaFree.
pales: error in conversion of table.
Matrix: error in comparison of order matrices.
pales: error in getHistDabR.
pales: error in getMlDabR.
allocation failure for x_temp allocation failure for y_temp allocation failure for z_temp REMARK Equilibrium density of ion pairs %e [1/nm_3].
REMARK Debye length %e nm.
REMARK Potential at surface %e [e/kB*T].
WARNING: Molecule too close to LC particel ...
Interaction face cannot be determined!
Error allocating temporary buffers.
DATA STATISTICS DC
DATA STATISTICS DC STDDEV_DIFF %.3f [Hz]
DATA STATISTICS DC CORR R %.3f
DATA STATISTICS DC CORNILESCU Q %.3f
DATA STATISTICS DC REGRESSION OFFSET %.3f +/- %.3f [Hz]
DATA STATISTICS DC REGRESSION SLOPE %.3f +/- %.3f [Hz]
DATA STATISTICS DC REGRESSION BAX SLOPE %.3f +/- %.3f [Hz]
resid [DC type] predicted measured pred. - meas.
----- --------- --------- -------- -------------
%d %s p: %8.2f m:%8.2f diff:%7.2f
Error in initOrient: zero atoms selected. initOrient: error in analyzeMatrix3D. initOrient: error in rotateDomain. PALES Error opening ensemble monitoring file %s
setupEnsemble: unsp error occured.
setupEnsemble: ensemble too big.
%.3f %.3f %.3f
% .4e % .4e % .4e
error in readEnsemble.
-stPales -stPalesFree -stPalesGrid -elPales -elPalesFree -elPalesGrid -bestFit -exhaust -exhaustSel -nodcOpt -mcStruc -outFail -nDfixed -nonDfixed -vecNoise -angNoise -stdCone -fixCone -nofixCone -digCone -autoCone -noautoCone -incCone -noautoMc -nAdjustMc -fracAdjustMc -kAdjustMc -kLAdjustMc -incAdjustMc PDBH_DIR PDBH_LIST SURF_DIR HA CA CB C N ALA ARG ASN ASP CYS GLN GLU GLY HIS ILE LEU LYS MET PHE PRO SER THR TRP TYR VAL -csThresh -vcThresh -fixedDI -nofixedDI -noyzInv -rimDisc DYNAMO Error: -cut option requires 1 value only.
-noelInfo -nodipole -nochSel -nopkaDef -charmm22 -nocharmm -nochTerm -unscale -rosetta -dcNoise DYNAMO Error: -inS1 option requires 5 values.
DYNAMO Error: -inS2 option requires 5 values.
DYNAMO Error: -hinge option requires 3 values.
DYNAMO Error: -twist option requires 3 values.
DYNAMO Error: -inS option requires 5 values.
-sdevDzz -sdevDyy -nomapMl pales: error in analyzeSaupe.
pales: error in writePDBRot.
REMARK %d N-HN Unassigned Peaks, Residues %d to %d.
Warning: %d N-HN Unassigned Peaks and %d %s Residues!
REMARK %d N-HN Unassigned Peaks and %d %s Residues.
ranSimDc Error allocating resIdList.
Error allocating rowIdList.
Error allocating bestIdList.
Error allocating rowResList.
Error allocating selIdList.
ranSimDC ranSimDC: error allocating dcMat.
ranSimDC: error allocating diValMat.
ranSimDC: error allocating wMat.
ranSimDC: error allocating sigMat.
ranSimDC: error allocating xMat.
ranSimDC: error allocating yMat.
ranSimDC: error allocating dipo uncertainty matrix.
REMARK Available Types of Unassigned Couplings of SegId %s: REMARK Available Types of Unassigned Couplings: Error in Number of Unassigned N-HN couplings. Error: Degenerate Atoms not implemented yet.
Error: N-HN coupling for PeakID %d not found.
Error: C-N coupling for PeakID %d not found.
Error: C-HN coupling for PeakID %d not found.
Error: CA-C coupling for PeakID %d not found.
Error: CA-HA coupling for PeakID %d not found.
Error: CA-CB coupling for PeakID %d not found.
Error: C-HA coupling for PeakID %d not found.
Error: CA-HN coupling for PeakID %d not found.
REMARK # of coupling types for each SegID: (%s %d) REMARK # of coupling types: %d
REMARK %d x %d Unassigned Coupling Matrix.
allocation failure for xI allocation failure for xJ allocation failure for yI allocation failure for yJ allocation failure for zI allocation failure for zJ allocation failure for dcList allocation failure for diList allocation failure for ddList allocation failure for wList allocation failure for dcOrigList allocation failure for diOrigList allocation failure for ddOrigList REMARK Peak exhaustively searched.
REMARK Couplings of type %s for residue REMARK No couplings for residue. are fixed.
REMARK %d couplings fixed in total.
Error in Number of assigned couplings. REMARK No couplings are fixed.
REMARK Sampled %d of %d
Warning: no assignment was found for Da [%.3f,%.3f] R [%.3f %.3f]!
PALES Error opening log file for error space mapping %s
PALES Error opening log file for Da distribution mapping %s
PALES Error opening log file for Saupe distribution %s.
# SVD_ID Aa R
PALES Error: Only %d couplings available. Exiting ....
REMARK Adjusting DC error bars ...
REMARK DC Error Scaling factor %.1f
REMARK DC error bars automatically adjusted by factor of %.1f.
REMARK DC error bars scaled by user supplied factor of %.1f.
%6d %e %.3f %9.3f %9.3f
%f %f %f %f
%f %f # SVD_ID ANGLE_X ANGLE_Y ANGLE_Z ANGLE_5D COLL_5D
VARS ID S_ZZ S_XXYY S_XY S_XZ S_YZ
FORMAT %%5d %%e %%e %%e %%e %%e
%5d %e %e %e %e %e
pales: error in compareSaupe.
%8.3f %8.3f %8.3f %8.3f %e
REMARK Mapping Statistics.
DATA STATISTICS MAPPING NUMBER OF SUCCESFUL STEPS %d
DATA STATISTICS MAPPING G_MAG (AVERAGE/STD_DEV/MIN/MAX) % .4e % .4e % .4e % .4e
DATA STATISTICS MAPPING Da_HN (AVERAGE/STD_DEV/MIN/MAX) % .4e % .4e % .4e % .4e
DATA STATISTICS MAPPING ANGLE_5D (AVERAGE/STD_DEV/MIN/MAX) %.4e % .4e % .4e % .4e
DATA STATISTICS MAPPING SZZ (AVERAGE/STD_DEV/MIN/MAX) % .4e % .4e % .4e % .4e
DATA STATISTICS MAPPING SAUPE AVERAGE % .4e % .4e % .4e % .4e % .4e
DATA STATISTICS MAPPING SAUPE STD_DEV % .4e % .4e % .4e % .4e % .4e
DATA STATISTICS MAPPING SAUPE MIN % .4e % .4e % .4e % .4e % .4e
DATA STATISTICS MAPPING SAUPE MAX % .4e % .4e % .4e % .4e % .4e
DATA STATISTICS MAPPING Da (AVERAGE/STD_DEV/MIN/MAX) % .4e % .4e % .4e % .4e
DATA STATISTICS MAPPING Dr (AVERAGE/STD_DEV/MIN/MAX) % .4e % .4e % .4e % .4e
DATA STATISTICS MAPPING Phi (MIN/MAX) % .2f % .2f
DATA STATISTICS MAPPING Psi (MIN/MAX) % .2f % .2f
DATA STATISTICS MAPPING Theta (MIN/MAX) % .2f % .2f
REMARK Failure Statistics.
DATA STATISTICS MAPPING NUMBER OF SUCCESFUL STEPS %d
PALES Error opening log file for Da distribution mapping %s.
PALES Error opening log file for Angular distribution %s.
pales: error in storePDBCoords.
REMARK Experimental DC and structure have %.3f Hz DC Rms.
REMARK Adjusting amount of structural noise ...
REMARK Amount of structural noise automatically determined.
REMARK Width of Gaussian cone %.2f degree and %.3f Hz DC Rms.
REMARK Amount of structural noise by user specified.
REMARK Width of Gaussian cone %.2f degree.
REMARK %d SVD runs of %d succesful.
%5d %e %e %e %e %e
WARNING %d SVD runs of %d succesful.
REMARK %d DC of %d picked.
allocation failure for indexList allocation failure for indexTab pales: error in addSaupe.
REMARK %.2f degree between input hinge and twist axis.
REMARK This corresponds to %.2f %% closure motion.
get_euler: error occured
REMARK Input order matrices.
DATA SAUPE 1 % .4e % .4e % .4e % .4e % .4e
DATA SAUPE 2 % .4e % .4e % .4e % .4e % .4e
DATA SAUPE RESULT % .4e % .4e % .4e % .4e % .4e
REMARK Relative orientation of alignment tensors.
DATA ANGLE_3D_AXES (X/Y/Z) %.2f %.2f %.2f
DATA ANGLE_5D_SPACE %.2f
DATA COLL_5D %.5f
REMARK Hinge rotation between Saupe frames.
DATA HINGE_ANGLES %7.2f %7.2f %7.2f %7.2f
DATA CLOSURE_ANGLES %7.2f %7.2f %7.2f %7.2f
DATA CLOSURE_PERCENTAGE %7.2f %7.2f %7.2f %7.2f
DATA HINGE_AXIS (X/Y/Z) %2d %6.3f %6.3f %6.3f
REMARK Euler rotation between Saupe frames.
DATA Q_EULER_SOLUTIONS REL %5s %7s %7s
DATA Q_EULER_ANGLES %2d %7.2f %7.2f %7.2f
DATA EULER_SOLUTIONS REL %5s %7s %7s
DATA EULER_ANGLES %2d %7.2f %7.2f %7.2f
REMARK Closure/twist/bend rotation between Saupe frames.
DATA EULER_SOLUTIONS REL %5s %7s %7s
DATA CTB_ANGLES %2d %7.2f %7.2f %7.2f
REMARK Closure, twist, bend frame.
DATA CTB_FRAME X_AXIS (X/Y/Z) % .4e % .4e % .4e
DATA CTB_FRAME Y_AXIS (X/Y/Z) % .4e % .4e % .4e
DATA CTB_FRAME Z_AXIS (X/Y/Z) % .4e % .4e % .4e
Error allocating DC structures.
REMARK %d couplings combined (%s%s).
getHistDabR Error: Too many folders (%d) for histogram.
Measurement error too small.
==> 3-parameter fit not possible.
Error: No single most populated coupling value.
Warning: No single most populated coupling value.
allocation failure for dots PALES Error opening output file %s
motionHist motionHist: error allocating dipo matrix.
motionHist: error allocating dipo uncertainty matrix.
motionHist: error allocating nDcType.
motionHist: error allocating arrays for jackknifing.
motionHist: unsp error occured.
REMARK %d simulated couplings (isotropic).
REMARK Histogram %d of %d
pales: error in histoExtFit.
# nDots = %d
%d %.3f %.3f %4d %8.3f %8.3f %8.3f
# DATA MAX_MIN Da %.3f %.3f
# DATA MAX_MIN R %.3f %.3f
# DATA MAX_MIN Score %.3f %.3f
%.3f %.3f %4d getMlDabR Error in mlMagTensor.
Error in errorIso.
Error in mapMagToDc.
VARS DA R SCORE
FORMAT %%3.1f %%1.2f %%e
%3.1f %1.2f %e
convertTab ! Normalized dipolar couplings from %s.
%3d %s HN %9.2f %7.2f %5.1f
Normalized dipolar couplings from %s.
Dipolar couplings from %s.
Gaussian noise has been added.
No Gaussian noise has been added.
comment
%s %4d %4s %4d %4s %10.2f
%4d %4s %4s ! Dipolar couplings from %s.
! Gaussian noise has been added.
assign ( resid %3d and name OO )
( resid %3d and name Z )
( resid %3d and name X )
( resid %3d and name Y )
( resid %3d and name %s and not segid REF )
( resid %3d and name %s and not segid REF ) %.4f %.4f
iFacePDB pales: error in rotateDomain. pales: error in shiftMol2Domain.
pales: error determining interaction face.
REMARK Probability of initial orientation %e.
REMARK Probability of 180 deg. rotated orientation %e.
pales: error in restorePDBCoords.
analyzePDB Error in analyzePDB: allocating coord buffers.
pales: error in calcInertia. pales: error in analyzeMatrix3D. eigVec2euler: error occured!
REMARK Molecular Alignment Simulation.
REMARK Simulation parameters.
REMARK Inertia tensor.
REMARK Dipole tensor.
DATA PDB_EL MONOPOL % e
DATA PDB_EL SUM_POS % e
DATA PDB_EL SUM_NEG % e
DATA PDB_EL LOC (x,y,z)
DATA PDB_EL LOC_NEG % e % e % e
DATA PDB_EL LOC_POS % e % e % e
DATA PDB_EL DIPOL % e
REMARK Input tensor.
REMARK Relative orientation of two coordinate systems.
DATA DCOS_DEG (x/y/z) %.3f %.3f %.3f
palesFit PALES Error (Fit) allocating workspaces.
stericAlignment Error allocating coord buffers.
WARNING: concentration too low - magnitude of alignment tensor incorrect
REMARK Orientation %d of %d
macroAlignment @@2: ddots[0] = %e
characteristics of electrostatic potential:
===========================================
equilibrium density of ion pairs [1/nm_3]: %e
Debye length [nm]: %e
potential at surface [e/kB*T]: %e
warning: potential of neighbouring liquid crystal particles overlapping! There is a atom of unknown type: %s
There is a residue of unknown type: %s
PALES Error opening file for pka output %s
chargeSetup File open error: %s.
%d %s %s %f Error: wrong format of pka file.
terminus WARNING: There is no residue %d or the proper atom in the given PDB file!
Too many pKa values were supplied ... REMARK %s, %d Charges/pka Values, Net Charge %.3f Residues %d to %d.
%d %s %s %.3f
pka Default Values, %d Charges/pka Values, Net charge %.3f Residues %d to %d.
pka Default Values, %d Charges/pka Values Net Charge %.3f, Residues %d to %d.
Numerical Recipes run-time error...
...now exiting to system...
shiftMol2Domain Error in shiftMol2Domain: allocating coord buffers.
Error in positionDomain: zero atoms selected. Error allocating coord buffers.
PALES Error opening log file for grid search %s
matrix: error in storePDBCoords.
ensembleAlignment: error in chkDomClash.
pales: error in rotateDomain.
[%d] domain rotation angle [deg.]: %e %e %e
ENSEMBLE ID %d
REMARK ENSEMBLE Q_EULER_ANGLES %7.2f %7.2f %7.2f
pales: error in rotateDomain. matrix: error in shiftMol2Domain.
REMARK X Y Z %.3f %.3f %.3f
rotEns.pdb matrix: error in calcInertiaSel. REMARK steric clash of domains in state %d.
matrix: error in analyzeMatrix3D. inter helix angle (x/y/z) [deg.]: %.3f %.3f %.3f
Matrix: Error reading selection of atoms.
Matrix: Error simulating alignment.
Matrix: error in analyzeSaupe.
Da(NH) = %.1f [Hz] R = Dr/Da = %.3f
Euler angles (alpha/beta/gamma) [deg.]: %7.2f %7.2f %7.2f
REMARK allowed state %d.
matrix: zero number of ensemble states.
REMARK Molecule shifted to geometric center.
simulateAlignment: error in stericAlignment. SaupeSteric gMag %e
SaupeEl gMag %e
SaupeSum gMag %e
Error in chkDomClash: zero atoms selected.
REMARK steric clash of %5d %6s %6s and %5d %6s %6s : %6.2f A
chCoorSelect chCoorSelect: Error allocating coord buffers.
Error reading selection of atoms.
Error in calcInertia: allocating coord buffers.
WARNING: Zero atoms for inertia tensor selected. calcInertia calcInertiaSel Error in calcInertiaSel: allocating coord buffers.
Error in positionDomain: zero atoms selected. REMARK Total positive charge %.3f [e], Total negative charge %.3f [e].
REMARK Monopol charge at (%.3f,%.3f,%.3f) [A] of %.3f [e].
REMARK Dipol at (%.3f,%.3f,%.3f) [A] of %.3f [Debye].
REMARK Dipol direction (%.3f,%.3f,%.3f).
REMARK Sampled %d
PALES Prediction of ALignmEnt from Structure.
ARGUMENTS FOR STERIC PALES
-stPales [on] Steric PALES Mode.
-pdb pName [None] PDB Input (Required).
-inD dName [None] Dipolar Coupling (Input).
-outD dName [None] Dipolar Coupling (Output).
-pdbRot pRotName [None] PDB rotated (Output).
-rotID rotID [0] Index of Rotation of PDB.
Simulation Parameters:
-bic [on] Wall LC Model.
-pf1 [off] Rod LC Model.
-wv conc [0.05] Liquid Crystal Concentration [mg/ml].
-dot density [100] Orientation Density (Sphere).
-digPsi digPsi [18] Orientation Density (3rd angle).
-dGrid dGrid [0.2] Grid Spacing [A].
-rM radius [20.0] Half Model Thickness [A].
-lcS order [0.8] Liquid Crystal Order [0-1].
-surf [on] Select Surface Accessible Atoms.
-nosurf [off] Don't Select Surface Accessible Atoms.
-rA radius [0.0] Atom radius [A].
PDB Selection Flags:
-H [off] Simple PDB Selection (all Atoms).
-noH [on] Simple PDB Selection (all Atoms except H).
-res resID Single Residue for Selection.
-r1 res1 [0] First Residue in Segment.
-rN resN [0] Last Residue in Segment.
-atom aList [*] Atom Name List.
-resName rList [*] Res Name List.
-chain cList [*] Chain Name List.
-seg sList [*] Seg Name List.
-id sID [*] Selection ID.
-inv Invert Selection.
PDB Special Selection; No Other Selection Performed:
-clear Clear Selection for All Atoms.
-set Set Selection for All Atoms.
PDB Name Matching Modes:
-exact Match Names Exactly (Default).
-regex Regular Expression Pattern Matching.
-glob Glob-style Pattern Matching.
-aExact Match Atom Names Exactly.
-aRegex Atom Regular Expression Pattern Matching.
-aGlob Atom Glob-style Pattern Matching.
-rExact Match Res Names Exactly.
-rRegex Res Regular Expression Pattern Matching.
-rGlob Res Glob-style Pattern Matching.
-cExact Match Chain Names Exactly.
-cRegex Chain Regular Expression Pattern Matching.
-cGlob Chain Glob-style Pattern Matching.
-sExact Match Seg Names Exactly.
-sRegex Seg Regular Expression Pattern Matching.
-sGlob Seg Glob-style Pattern Matching.
DC Selection Flags:
-a1 aRes1 [0] First Res in PDB.
-s1 res1 [0] First Res in Segment.
-sN resN [0] Last Res in Segment.
-aD1 atom {All} DC Atom Type 1 used.
-aD2 atom {All} DC Atom Type 2 used.
ARGUMENTS FOR ELECTROSTATIC PALES
-elPales [off] Electrostatic PALES Mode.
-pot potName [None] Electrostatic Potential (Input).
-pot3D pot3DName [None] 3D Electrostatic Potential (Input).
-pka pkaName [None] Charge Info (Input).
-outPka pkaName [None] Res Charge Info (Output; optional).
-wv sim [0.05] Liquid Crystal Concentration [mg/ml].
-3D [off] General 3D Potential.
-vol sim [515.0] Sample Volume [ul].
-mwLC sim [268e+3] Liquid Crystal Molecular Weight [g/mol].
-massLC sim [0.05] Liquid Crystal Mass [g].
-unitLC sim [1.574] Liquid Crystal Unit Height [A].
-polyLC sim [1707] Polymerisation Degree.
-dot sim [100] Orientation Density (Sphere).
-digPsi sim [18] Orientation Density (3rd angle).
-nX nGrid [1] Gridposition Counts along X.
-nY nGrid [1] Gridposition Counts along Y.
-nZ nGrid [1] Gridposition Counts along Z.
-dX dGrid [0.2] 3D Grid Spacing along X [A].
-dY dGrid [0.2] 3D Grid Spacing along Y [A].
-dZ dGrid [0.2] 3D Grid Spacing along Z [A].
-rM sim [20.0] Half Model Thickness [A].
-lcS sim [0.8] Liquid Crystal Order [0-1].
-rA sim [0.0] Atom radius [A].
Electrostatic Simulation Parameters:
-pH simEl [7.0] pH.
-nacl simEl [0.2] NaCl Concentration [M].
-chSurf simEl [-0.47] Surface Charge Density [e/nm2].
-cut simEl [400.0] Cutoff for Electrostatics [A].
-maxPot simEl [5.0] Maximum (+/-) Used Potential [kT/e].
-z1 posZ1 [0] First Z Position in 3D Grid.
-zN posZN [0] Last Z Position in 3D Grid.
-pkaDef [on] Use Pka Defaults.
-nopkaDef [off] Don't Use Pka Defaults.
-nocharmm [on] Don't Apply CHARMM Partial Charges.
-charmm [off] Apply CHARMM19 Partial Charges.
-charmm22 [off] Apply CHARMM22 Partial Charges.
-chTerm [on] Put Charges at Termini.
-nochTerm [off] Don't Put Charges at Termini.
-kEne scale [1.0] Scaling of Energy.
-kPot scale [1.0] Scaling of Potential.
-kMono scale [1.0] Scaling of Monopole Charges ch[1].
-kDipo scale [1.0] Scaling of Dipole Charges ch[9,10].
-kQuad scale [1.0] Scaling of Quadrupole Charges ch[2-8].
-temp simEl [298.15] Boltzmann Temperature.
-dIFace simEl [50.0] Surface Distance for Interaction Face [A].
-noelInfo [on] Report Electrostatic Info.
-elInfo [off] Report Electrostatic Info.
-nodipole [on] Consider Full Charge Distribution.
-dipole [off] Consider Molecule as Dipole.
-nochSel [on] Use Uncharged and Charged Atoms.
-chSel [off] Use Charged Atoms only.
ARGUMENTS FOR FREE FORMAT, STERIC PALES
-stPalesFree [off] Free Format Steric PALES Mode.
-pdbF pdbFName [None] PDB Input (free format) (Required).
-outA outAName [None] Predicted Saupe Matrix (Output).
-dGrid gridSpac [0.2] Grid Spacing [A].
ARGUMENTS FOR BEST-FIT (SVD/POWELL)
-bestFit [off] Pure Best-Fit Mode.
-single eMode [on] Perform Single Best-Fit.
-jack eMode [off] Error Estimation using Jackknifing
-mcDc eMode [off] Monte-Carlo Error Estimation
by Addition of DC Noise.
-mcStruc eMode [off] Monte-Carlo Error Estimation
by Addition of Strctural Noise.
-outD dName [None] Best-fit Coupling (Output).
Error Mapping Specifications:
-map mapCount [0] # of Best-Fits in Error Mapping.
-outDa daName [None] Da & R Distribution. (Output).
-outMap mName [None] World Map Coordinates (Output).
-outAng mName [None] Angular Deviation from Average (Output).
-outFail dName [None] Mapping Fail Statistics (Output).
-err [on] Use only Best-Fit Predictions within
Experimental Errors in Mapping (Default).
-noerr [off] Use All Best-Fit Predictions in Mapping.
-vecNoise [on] Structural Noise: Perturbation of Internuclear Vectors.
-angNoise [off] Structural Noise: Perturbation of Dihedral Angles.
-stdCone [10.0] StdDev of Cone Angle Distribution [Hz].
-nofixCone [on] Don't Fix Size of Cone.
-fixCone [off] Fix Size of Cone.
-digCone [360] Digitization of Cone.
-autoCone [on] Automatically Adjust Structural Noise.
-noautoCone [off] Don't Automatically Adjust Structural Noise.
-lCone [0.0] Starting value of Structrual Noise.
-incCone [0.25] Increment of Structrual Noise.
-nCone [100] # of Steps in Structural Noise Determination.
-kAdjustMc [1.0] Scaling Factor of Experimental DC Errors.
-autoMc [on] Automatically Adjust Scaling of DC Errors.
-noautoMc [off] Don't Automatically Adjust Scaling of DC Errors.
-nAdjustMc [1000] # of Steps in Determination of DC Error Scaling.
-fracAdjustMc [0.7] Required Fraction of Self-consistent Best-Fits.
-kLAdjustMc [1.0] Starting Scaling Factor of DC Errors.
-incAdjustMc [0.2] Increment of Scaling Factor of DC Errors.
-dFrac dFrac [0.2] Fraction of Total DC Data.
-nDfixed [off] Use Fixed # of DC in Jackknifing.
-nonDfixed [on] Dont't Use Fixed # of DC in Jackknifing.
Alignment Tensor Specification Methods:
-svd SVD Calc of Saupe Matrix (Default).
-saupe sList List of 5 Saupe Values (also: -align).
-fixed Fixed Da, Dr, and Rotations.
-nofixed Variable Da, Dr, and Rotations.
-dadr Fixed Da and Dr, Variable Rotations.
Alignment Tensor Magnitude and Rhombicity Limits:
-da [1.0e-3] Initial DA Value.
-daMin [-1.0e-2] Minimum Initial DA Value.
-daMax [1.0e-2] Maximum Initial DA Value.
-dr [1.0e-4] Initial DR Value.
-drMin [-1.0e-2] Minimum Initial DR Value.
-drMax [1.0e-2] Maximum Initial DR Value.
Rotation Angle Starting Values and Limits:
-psi [45.0] Initial X-Axis Rotation.
-psiMax [360.0] Maximum X-Axis Rotation.
-psiMin [-360.0] Minimum X-Axis Rotation.
-theta [45.0] Initial Y-Axis Rotation.
-thetaMax [360.0] Maximum Y-Axis Rotation.
-thetaMin [-360.0] Minimum Y-Axis Rotation.
-phi [45.0] Initial Z-Axis Rotation.
-phiMax [360.0] Maximum Z-Axis Rotation.
-phiMin [-360.0] Minimum Z-Axis Rotation.
-a1 aRes1 [0] First Res in PDB.
-s1 res1 [0] First Res in Segment.
-sN resN [0] Last Res in Segment.
-aD1 atom {All} DC Atom Type 1 used.
-aD2 atom {All} DC Atom Type 2 used.
ARGUMENTS FOR UNASSIGNED BEST-FIT (exhSVD)
-bestFit [on] Pure Best-Fit Mode.
-exhaust eMode [off] Exhaustive Best-Fit.
-fixAa aaList List of # Peaks of Each Amino Acid Type.
-fixRes rIdList List of Peaks/Residues IDs with Fixed Assignment.
-dcID sList List of Alignment Media ID (Seg Name in PDB).
-exhaustSel [off] Exhaustive Best-Fit on Subset of Available Peaks.
-nSel [0] # of Peaks to select for ExhausSel.
-dcOpt [on] Optimize Peak Selection.
-nodcOpt [off] Use first rowId Peaks in inD.
-rand eMode [off] Random Best-Fit.
-map mapCount [0] # of Random Best-Fits.
Limits for Alignment Magnitude and Rhombicity:
-lDa simMag [-25.0] Minimal possible Da.
-hDa simMag [-3.0] Maximal possible Da.
-lR simMag [0.0] Minimal possible R.
-hR simMag [0.7] Maximal possible R.
ARGUMENTS FOR ADDITiON OF STRUCTURAL NOISE
-struc [off] Addition of Noise to PDB.
-pdbRot pRotName [None] PDB with Noise (Output).
-idum [-1] Seed for Random Numbers.
-nofixCone [on] Fix Size of Cone.
-fixCone [off] Don't Fix Size of Cone.
ARGUMENTS FOR ANALYSIS OF ORDER MATRIX
-anA [off] Analysis of 2 Saupe matrices.
-inS1 sList List of 5 Saupe Values (Input).
-inS2 sList List of 5 Saupe Values (Input).
-outA outAName [None] Saupe Analysis (Output).
Action Flags:
-add Action: inS1 + inS2
-sub Action: inS1 - inS2 (Default)
-mul Action: inS1 * inS2
-div Action: inS1 / inS2
-max Action: Max(inS1, inS2)
(Tests general magnitude)
Other Options:
-c1 scale [1.0] Scale factor for inS1
-c2 scale [1.0] Scale factor for inS2
-twist Coordinates (X Y Z) of Twist Axis.
-rotID rotID [0] Index of Calculated Hinge Axis.
-hinge Coordinates (X Y Z) of User Hinge Axis.
ARGUMENTS FOR ANALYSIS OF DIPOLAR COUPLINGS
-anDc [off] Analysis of 2 Sets of Dipolar Couplings.
-inD1 d1Name [None] Dipolar Coupling Set 1 (Input).
-inD2 d2Name [None] Dipolar Coupling Set 2 (Input).
-outD outDName [None] DC Analysis (Output).
Selection Flags:
-add Action: d1Name + d2Name (Default)
-sub Action: d1Name - d2Name
-mul Action: d1Name * d2Name
-div Action: d1Name / d2Name
-c1 scale [0.0] Scale factor for d1Name
-c2 scale [1.0] Scale factor for d2Name
ARGUMENTS FOR ANALYSIS OF PDB FILE
-anPdb [off] Analysis of PDB file.
-inS sList List of 5 Saupe Values (Input).
-outP outPName [None] PDB Analysis (Output).
Electrostatic Parameters:
-charmm22 [off] Apply CHARMM Partial Charges.
-user [off] Use User Saupe Matrix.
-ster [on] Uncharged PDB file.
-el [off] Charged PDB file.
ARGUMENTS FOR Da & R HISTOGRAM DETERMINATION
-daHist [off] Da-R Histogram Mode.
-outD dName [None] Histogram Results (Output).
Histogram Parameters:
-bin simMag [0] Number of Bins (zero=automatic).
-nFit simMag [3] Degree of Nonlinear Fit.
-sdevDzz simMag [0.4] Scaling of Dzz Error.
-sdevDyy simMag [0.9] Scaling of Dyy Error.
-daLo simMag [-1000.0] Minimal Da in Histo Fit.
-daHi simMag [1000.0] Maximal Da in Histo Fit.
-rhLo simMag [0.0] Minimal R in Histo Fit.
-rhHi simMag [0.667] Maximal R in Histo Fit.
-noave [off] Don't Average Min & Max DC.
-ave [on] Average Min & Max DC.
ARGUMENTS FOR Da & R LIKELIHOOD DETERMINATION
-daMl [off] Da-R Likelihood Mode.
-outD dName [None] Likelihood Results (Output).
-outSc scName [None] Scoring Statistics (Output).
Maximum Likelihood Parameters:
-lDa simMag [-25.0] Minimal Da in Grid Search.
-hDa simMag [-3.0] Maximal Da in Grid Search.
-incDa simMag [0.1] Da Increment in Grid Search.
-lR simMag [0.0] Minimal R in Grid Search.
-hR simMag [0.7] Maximal R in Grid Search.
-incR simMag [0.01] R Increment in Grid Search.
-nomapMl [on] Don't Transform DC.
-mapMl [off] Transform DC.
ARGUMENTS FOR CONVERSION OF DIPOLAR COUPLING TABLE
-conv [off] Conversion of DC Input.
Conversion parameters:
-xplor [off] Xplor DC Format.
-cns [off] Cns DC Format.
-dyana [off] Dyana DC Format (only HN-N).
-tbl [on] Residue Spefic Listing.
-pales [off] PALES DC FORMAT.
-rosetta [off] Rosetta DC Format.
-tensID [500] Tensor Molecule ID.
-scale [off] Normalize Dipolar Couplings.
-unscale [on] Don't Normalize Dipolar Couplings.
-dcNoise [off] Add Noise to Dipolar Couplings.
-nodcHH [on] Exclude 1H-1H DCs in Conversion.
-dcHH [off] Include 1H-1H DCs in Conversion.
COMMOM ARGUMENTS
-euler Solve for Euler Angles, Da, Dr (Default).
-noeuler Don't Solve for Euler Angles.
-qDa [on] Calculate Q using Order matrix (Default).
-qRms [off] Calculate Q using rDC Rms.
-qStd [off] Report Standard Deviation instead of Q.
-w wList List of Weights for Segment.
-excl Exclude Outside Range.
-incl Include Any Within Range.
-verb [on] DC Output in Extended Format.
-noverb [off] DC Output in Format of DC Input.
-yzInv [off] Exchange Ordering of y and z axis.
-noyzInv [on] Don't Exchange Ordering of y and z axis.
-rem remTxt PDB Remark Text.
Dipolar Interaction Value Calculation:
-fixedDI Use Fixed Values When Possible (Default).
-nofixedDI Always Use Values from PDB Distances.
*--------------------------------------------------------------------*
| PALES (C) M. Zweckstetter 2000 |
*--------------------------------------------------------------------*
DATA IRREDUCIBLE REPRESENTATION (A0,A1R,A1I,A2R,A2I) % .4e % .4e % .4e % .4e % .4e
DATA IRREDUCIBLE GENERAL_MAGNITUDE % .4e
REMARK Eigensystem & Euler angles for clockwise rotation about z, y', z''.
DATA EIGENVALUES (Axx,Ayy,Azz) % .4e % .4e % .4e
DATA EIGENVECTORS
DATA EIGENVECTORS XAXIS % .4e % .4e % .4e
DATA EIGENVECTORS YAXIS % .4e % .4e % .4e
DATA EIGENVECTORS ZAXIS % .4e % .4e % .4e
DATA Q_EULER_SOLUTIONS %7s %7s %7s
DATA Q_EULER_ANGLES %2d %7.2f %7.2f %7.2f
pales: error in storePDBCoords.
pales: error in rotateDomain. pales: error in shiftMol2Domain.
6L 7T I F C A ?l ?4 > ;\ ;T 6L ;H :x 9 9p
DATA PALES_MODE STERIC
DATA PALES LC_TYPE wall
DATA PALES LC_TYPE rod
DATA PALES LC_CONCENTRATION %.3f
DATA PALES ORIENT_SPHERE %d
DATA PALES ORIENT_PSI %d
DATA PALES GRID_SPACING % .3f
DATA PALES MODEL_RADIUS % .3f
DATA PALES LC_ORDER % .3f
DATA PALES ATOM_RADIUS % .3f
DATA PALES SEL_SIMPLE_FLAG %d
DATA PALES SURF_FLAG %d
DATA PALES_MODE PDB
DATA PALES_MODE SAUPE_CP
DATA PALES ACTION max
DATA PALES ACTION div
DATA PALES ACTION mul
DATA PALES ACTION sub
DATA PALES ACTION add
DATA PALES C1 % .3f
DATA PALES C2 % .3f
DATA PALES_MODE DC_CP
DATA PALES_MODE DA_HIST
DATA DC MIN_MAX % .3f % .3f
DATA FIT_PAR % d
DATA AVE_EXTREM NO
DATA AVE_EXTREM YES
DATA SDEVDZZ %.3f
DATA SDEVDYY %.3f
DATA nBINS %d
DATA BINWIDTH %.3f
REMARK Solving the linear equation system.
DATA EQ Da % .3f
DATA EQ R % .3f
REMARK Nonlinear least-square opimization.
DATA Dzz_Dyy_Dxx % .3f % .3f % .3f
DATA Da % .3f
DATA Da_ERR % .3f
DATA R % .3f
DATA R_ERR % .3f
DATA PALES_MODE CS
DATA PALES_MODE DC
DATA PALES_MODE ELECTROSTATIC_GRID
DATA PALES_MODE ELECTROSTATIC_FREE
DATA PALES_MODE ELECTROSTATIC
DATA PALES EL PH % .3f
DATA PALES EL NACL % .3f
DATA PALES EL SURF_CH % .3f
DATA PALES EL PKA_DEFAULT on
DATA PALES EL PKA_DEFAULT off
DATA PALES EL CH_TERM on
DATA PALES EL CH_TERM off
DATA PALES EL CUTOFF % e
DATA PALES_MODE STERIC_GRID
DATA PALES_MODE STERIC_FREE
DATA PALES INCLUDE_RIM on
DATA PALES MOLAR_RATIO % .3f
DATA PALES MODEL_LENGTH % .3f
DATA PALES S_DISC_RIM % .3f
RdTable File open error: %s.
%lf %lf %lf Error: Input data in file with measured dipolar couplings have wrong format
error in readEnsemble: digitization of ensemble too high.
readConfig File open error: %s.
Error: Input data in auto file have wrong format
CENTER_PIVOT: OUTPUT_ENSEMBLE: ALIGN_ALONG_Z: FIX_POSITION_DOM1: ENSEMBLE_CLASH: CLASH_DISTANCE: ENSEMBLE_DENSITY: ENSEMBLE_GAMMA: DOMAIN_ANGLE_VAR: DOM_ANG_ALPHA: DOM_ANG_BETA: DOM_ANG_GAMMA: ORIGIN_DOM1: ORIGIN_DOM2: START_RESID_1: END_RESID_1: START_RESID_2: END_RESID_2: ALPHA_CENTER: ALPHA_WIDTH: START_RES_ANGLE_1: END_RES_ANGLE_1: START_RES_ANGLE_2: END_RES_ANGLE_2: Error: Wrong input parameter in auto file readPotential File open error: %s.
Error: The potential must be supplied with a uniform stepsize
%e %e ==> diff = %e
Error in readPotential: digitization of potential too high. read3DPotential File open error: %s.
REMARK Reading values of 3D potential %d of %d
%lf %lf %lf WARNING: File with 3D Potential may contain line with wrong input format!
ERROR: Total size of 3D grid not as specified.
readPDBfree File open error: %s.
%d %s %s %d %f %f %f error in readPDBfree: too many atoms.
allocation failure for x_temp allocation failure for y_temp allocation failure for pot_dist allocation failure for grid_el allocation failure for total WARNING: concentration too low - magnitude of alignment tensor incorrect
allocation failure for totalNew allocation failure for pCount allocation failure for potentialRef allocation failure for gridOk o_pts: %d saupe_dev[%d]: %e
deviation from uniform distribution: %e %e
palesInfo->elInfo.kPot: %.1f
REMARK Minimum molecule dimension %.3f [A].
REMARK Maximum molecule dimension %.3f [A].
REMARK palesInfo->elInfo.kAtt = %.3f [A].
@@@ offset_grid = %.3f [A] t_pts = %d.
@@@ REMARK grid_el[0] = %.3f [A].
@@@ REMARK grid_el[%d] = %.3f [A].
REMARK Equilibrium density of ion pairs %e [1/nm_3].
REMARK Debye length %e nm.
REMARK Potential at surface %e [e/kB*T].
Warning: Potential drops within clash region to below %e!
---> Magnitude of alignment tensor wrong!
REMARK Value of potential at cutoff: %e
REMARK # of translational points for EL: %d
REMARK Maximum distance: %e
Warning: Potentials between neighbouring cells overlapping, cutoff %e!
@@ palesInfo->elInfo.cutoffPot: %e
@@ palesInfo->radiusModel: %f
@@ palesInfo->concentration: %f
@@ density: %f
@@ end_dist: %f
@@ beta: %f
@@ no_pt_ph: %d
@@ lengthGrid: %d
digPsi = %d dots = %d inc_psi = %.1f
total_ph: %e test: %e p: %e ln(p): %e
grid_el[0] = %.1f grid_el[lengthGrid %d] = %.1f d = %.1f
%6.1f %6.1f %e
%6.1f %6.1f %e %e
allocation failure for nGridX allocation failure for nGridY allocation failure for nGridZ allocation failure for z_temp allocation failure for pot3DAtom REMARK o_pts: %d saupe_dev[%d]: %e
REMARK deviation from uniform distribution: %e %e
WARNING: Potentials between neighbouring cells overlapping!
---> Magnitude of alignment tensor might be wrong!
REMARK palesInfo->volSample: %f
REMARK palesInfo->mwLC: %f
REMARK palesInfo->massLC: %f
REMARK palesInfo->unitLengthLC: %f
REMARK palesInfo->polymerDeg: %f
REMARK palesInfo->rSingleCell: %e
REMARK palesInfo->elInfo.maxPot: %e
REMARK palesInfo->grid3DdeltaX: %e
REMARK palesInfo->grid3DdeltaY: %e
REMARK palesInfo->grid3DdeltaZ: %e
REMARK palesInfo->grid3DnX: %d
REMARK palesInfo->grid3DnY: %d
REMARK palesInfo->grid3DnZ: %d
REMARK palesInfo->elInfo.z1: %d
REMARK palesInfo->elInfo.zN: %d
REMARK lengthGrid: %d
REMARK nZGridSel: %d
REMARK Digitization of orientations: digPsi = %d dots = %d inc_psi = %.1f
REMARK nX2 nY2 nZ2: %d %d %d
REMARK startGrid (x,y,z): %f %f %f
WARNING: Error in simulation
ssiaFree Error allocating coord buffers.
Matrix: Error reading PDB file in free format.
%s, %d Atoms, Free format.
Matrix: unsp error occured.
PALES: error - zero atoms remain after surface selection!
REMARK %d atoms selected for simulation.
simulateAlignment: error in stericAlignment. pales: error in analyzeSaupe.
allocation failure for dcAList allocation failure for dcBList allocation failure for xK allocation failure for yK allocation failure for zK allocation failure for dcListK allocation failure for diListK allocation failure for ddListK allocation failure for wListK visitAll Error allocating rowIdList.
Error allocating dcIdList.
Error allocating bestSelIdList.
Error allocating matIdList.
Error allocating selDcList.
visitAll: error allocating dcMatSel.
visitAll: error allocating diValMatSel.
visitAll: error allocating wMatSel.
visitAll: error allocating sigMatSel.
visitAll: error allocating xMatSel.
visitAll: error allocating yMatSel.
visitAll: error allocating dipo uncertainty MatSelrix.
Error allocating cColList.
Error allocating cColListB.
REMARK Maximum of %d available RDCs per peak.
REMARK %d peaks with RDCs will be selected.
REMARK %d peaks with %d RDCs in total will be selected.
REMARK Smallest and largest normalized RDC: %.3f %.3f [Hz].
Warning: only subset of 2 to 7 peaks allowed! Error selecting RDCs!
REMARK DC Peaks have been selected.
. Error: # of selected peaks != %d.
Error allocating coord buffers.
REMARK Sampled %d
Error: Error in length of permutation.
REMARK %d N-HN Unassigned Peaks, Residues %d to %d.
Warning: %d N-HN Unassigned Peaks and %d %s Residues!
REMARK %d N-HN Unassigned Peaks and %d %s Residues.
ranSimDc Error allocating resIdList.
Error allocating rowIdList.
Error allocating bestIdList.
Error allocating rowResList.
Error allocating selIdList.
ranSimDC ranSimDC: error allocating dcMat.
ranSimDC: error allocating diValMat.
ranSimDC: error allocating wMat.
ranSimDC: error allocating sigMat.
ranSimDC: error allocating xMat.
ranSimDC: error allocating yMat.
ranSimDC: error allocating dipo uncertainty matrix.
REMARK Available Types of Unassigned Couplings: Error in Number of Unassigned N-HN couplings. Error: Degenerate Atoms not implemented yet.
Error: N-HN coupling for PeakID %d not found.
Error: C-N coupling for PeakID %d not found.
Error: C-HN coupling for PeakID %d not found.
Error: CA-C coupling for PeakID %d not found.
Error: CA-HA coupling for PeakID %d not found.
Error: CA-CB coupling for PeakID %d not found.
Error: C-HA coupling for PeakID %d not found.
Error: CA-HN coupling for PeakID %d not found.
REMARK %d x %d Unassigned Coupling Matrix.
allocation failure for xI allocation failure for xJ allocation failure for yI allocation failure for yJ allocation failure for zI allocation failure for zJ allocation failure for dcList allocation failure for diList allocation failure for ddList allocation failure for wList allocation failure for dcOrigList allocation failure for diOrigList allocation failure for ddOrigList REMARK Peak exhaustively searched.
REMARK Couplings for residue are fixed.
Error in Number of assigned couplings. REMARK No couplings are fixed.
REMARK Sampled %d of %d
Warning: no assignment was found for Da [%.3f,%.3f] R [%.3f %.3f]!
pales: error in analyzeSaupe.
pales: error in writePDBRot.
ANGLE_HI ANGLE_LO DYN Error Allocating Angle Values.
Angle Error opening file %s
REMARK Angle Table.
REMARK %s
DATA N %d
DATA RMS %.3f
DATA Chi2 %.3f
VARS INDEX RESID_I RESNAME_I ATOMNAME_I CHAINNAME_I SEGNAME_I RESID_J RESNAME_J ATOMNAME_J CHAINNAME_J SEGNAME_J RESID_K RESNAME_K ATOMNAME_K CHAINNAME_K SEGNAME_K ANGLE ANGLE_LO ANGLE_HI ANGLE_VIO S W FC STATUS
ANGLE ANGLE_LO ANGLE_HI S W FC STATUS
FORMAT %%4d %%4d %%4s %%4s %%9.2f %%9.2f %%9.2f %%9.2f %%.2f %%.2f %%.2f %%s
%%9.2f %%9.2f %%9.2f %%.2f %%.2f %%.2f %%s
%4d %4s %4s % 9.2f % 9.2f % 9.2f % 9.2f % 9.2f % 9.2f % 9.2f %6.2f %6.2f %6.2f %s
DYNAMO Warning: No Atom Map for Angle:
ResIDI: %4d ResNameI: %4s AtomNameI: %4s SegI: %4s ChainI: %4s
ResIDJ: %4d ResNameJ: %4s AtomNameJ: %4s SegJ: %4s ChainJ: %4s
ResIDK: %4d ResNameK: %4s AtomNameK: %4s SegK: %4s ChainK: %4s
APOD-> Code: %d
APOD-> tSize: %d aStart: %d aSize: %d mSize: %d
APOD-> SW: %f Def: %f Q1: %f Q2: %f Q3: %f
APOD-> Inv: %s
Apodize Warning: %d Negative Window Points.
\
4
NMRCHECK Program %s, argument checking enabled.
Warning from %s: not all arguments will be checked.
Debug Info from %s. Original Checksum: %d Final Checksum: %d.
%3d. %c %3d Characters: '%s'
Warning from %s: argument checking may not be valid.
Warning from %s:
Arguments %d to %d may be unknown or unused:
Argument %d may be unknown or unused:
strListArg StrList Error allocating string.
Code allocation error. Frame allocation error. Stack allocation error. Stack overflow. Stack underflow. Call nested too deeply: PROC should not return a value. FUNC returns no value. Not enough arguments. Attempt to reference non-variable: Undefined variable: Attempt to reference non-array: Re-allocating array: Attempt to dereference null pointer: Array index out of bounds: Division by zero. Modulus Division by zero. Assignment to non-variable: Array Assignment to non-variable: >h@@@@D??AlCCC\CBBlProgram too big. Compile overflow. DYNAMO Error allocating CS table header.
DYNAMO Error Allocating CS-Observed Values.
DYNAMO Error Allocating CS SeqInfo Structure.
DYNAMO Error Allocating PCS Structure.
DC Error Allocating CS Workspaces.
DYNAMO Error opening output file %s
REMARK DYNAMO Chemical Shift Simulation.
REMARK %s
DATA N %d
DATA RMS %.3f
DATA Chi2 %.3f
DATA WChi2 %.3f
RESID RESNAME ATOMNAME CHAINNAME SEGNAME CS_OBS SHIFT RC_SHIFT CS_DIFF SIGMA W
SHIFT SIGMA W
%%4d %%4s %%4s %%9.3f %%9.3f %%9.3f %%9.3f %%9.3f %%.2f
%%9.3f %%9.3f %%.2f
%4d %4s %4s % 9.3f % 9.3f % 9.3f % 9.3f %9.3f %.2f
% 9.3f % 9.3f %.2f
DYNAMO Warning: No Res Map for CS (offset %d):
ResID: %4d ResName: %4s AtomName: %4s Seg: %4s Chain: %4s
HA HA2 HA3 CA CB C N ALA ARG ASN ASP CYS cys GLN GLU GLY HIS his ILE LEU LYS MET PHE PRO SER THR TRP TYR VAL %s/%s.%s.dat %s/%s.dat DYNAMO Error Allocating Surface List.
DYN Error reading conformation surface %s
%s/zero.dat DYN Error reading null surface %s
CS Error reading random coil table %s
CS Error reading homology table %s
ATOMNAME DYNAMO RC Error: missing RESNAME/ATOMNAME.
DYNAMO RC Error: missing SHIFT/TYPE/OFFSET.
CSURF Error creating secondary shift table.
%s,%s,%s,%d HOMO Error: missing RESNAME.
HOMO Error creating homology table.
DYNAMO Error reading shift surface %s
%s/%s.d.dat DYNAMO Error reading density surface %s
%s/%s.q.dat DYNAMO Error reading dev surface %s
DYNAMO Reading surface %s
CS Error opening Phi/Psi Surface %s
CS Error reading header in Phi/Psi Surface %s
CS Notice: Error testing header in %s CS Error allocating Phi/Psi Surface %s
CS Error reading data in Phi/Psi Surface %s
DYNAMO Writing surface %s
CS Error writing header to Phi/Psi Surface %s
CS Error writing data to Phi/Psi Surface %s
CS Scan Error: no zero surface.
CS Scan Error: zero surface is not 361x361 points.
DYNAMO Shift Count Too Large, Residue %d.
NMR_IO_SELECT NMR_IO_TIMEOUT CreateKeep Read/Write DATAIO SYSOPEN Error %d:
File: %s Access: %s
SYSOPEN Message DATAIO POPEN Error %d:
Cmnd: %s Access: %d
DataOpen2 Error DATAIO File Read Error %d.
Request: %d Actual: %d.
SYSREAD Message DATAIO File Write Error %d.
SYSWRITE Message DATAIO File Seek error %d.
DATAIO File Close Error %d.
DATAIO File Create Error %d.
DATAIO Error Creating Directory %s
MKDIR Message DATAIO Error Deleting File DATAIO Error opening dir %s
System Message DC Error Reading PDB File %s
exclusive inclusive REMARK %d couplings selected (%s%s).
%s(%d->%d of %d)
REMARK %s(%d->%d of %d)
REMARK D_N: %d D_RMS: %.3f D_CHI2: %.3f
REMARK CS_N: %d CS_RMS: %.3f CS_CHI2: %.3f CS_WCHI2: %.3f
VARS %s %s %s
SEGID INDEX D_RES1 D_RESN D_COUNT CS_COUNT P_NAME P_RES1 P_RESN P_MAXRES DA DR THETA PHI PSI D_N D_RMS D_CHI2 CS_N CS_RMS CS_CHI2 A_RMS HOMO_N HOMO SURF_N SURF FORMAT %s %s %s
%5d %5d %3d %3d %4d %4d %-18s %3d %3d %3d %.4e %.4e %7.2f %7.2f %7.2f %3d %10.3f %7.3f %3d %10.3f %10.3f %10.3f %3d %10.3f %3d %10.3f %5d %5d %3d %3d %4d %4d %-12s %3d %3d %3d % .4e % .4e %7.2f %7.2f %7.2f %4d %7.3f %10.2f %4d %7.3f %10.2f %10.3f
%-12s %4d %4d %4d %4d %4d % .4e % .4e %8.2f %9.4f %9.4f %9.4f %9.4f
DC Error Allocating DC Values. DC Error Allocating DC Workspaces.
DC Error opening output file %s
REMARK DYNAMO Dipolar Coupling Simulation.
REMARK %s
DATA N %d
DATA RMS %.3f
DATA Chi2 %.3f
DATA Q_FACTOR %.3f
DATA CORR_R %.3f
DATA TENSOR_MODE FIT_NONLIN (Variation of Da, Dr or Rh, or Rotations)
(Variation of Da, Dr or Rotations)
DATA DA_RANGE % .4e % .4e
DATA RH_RANGE % .3f % .3f
DATA DR_RANGE % .4e % .4e
DATA PSI_RANGE % 8.2f % 8.2f
DATA THETA_RANGE % 8.2f % 8.2f
DATA PHI_RANGE % 8.2f % 8.2f
DATA TENSOR_MODE FIXED (Fixed Da and Dr, Fixed Rotations)
(Fixed Da and Rhombicity, Fixed Rotations)
DATA TENSOR_MODE SAUPE (Fixed Saupe Values)
DATA TENSOR_MODE SVD (Order Matrix Method)
DATA TENSOR_MODE ELECTROSTATIC (Zweckstetter Method)
DATA TENSOR_MODE STERIC DATA SAUPE % .4e % .4e % .4e % .4e % .4e
RESID_I RESNAME_I ATOMNAME_I CHAINNAME_I SEGNAME_I RESID_J RESNAME_J ATOMNAME_J CHAINNAME_J SEGNAME_J DI D_OBS D D_DIFF DD W
DI D DD W
%%4d %%4s %%4s %%9.2f %%9.3f %%9.3f %%9.3f %%.2f %%.2f
%%9.2f %%9.3f %%9.3f %%.2f
%4d %4s %4s % 9.2f % 9.4f % 9.4f % 9.4f %7.4f %.2f
% 9.2f % 9.4f %7.4f %.2f
DYNAMO Warning: No Atom Map for DC, offset %d:
ResIDI: %4d ResNameI: %4s AtomNameI: %4s SegI: %4s ChainI: %4s
ResIDJ: %4d ResNameJ: %4s AtomNameJ: %4s SegJ: %4s ChainJ: %4s
0TTlllTTl Dipolar Interaction - Unknown atom %s.
DYNAMO Error Allocating Dipolar Workspace.
Alignment Tensor Specification Methods:
-svd SVD Calc of Saupe Matrix (Default).
-saupe sList List of 5 Saupe Values (also: -align).
-fit Nonlinear Fit with Variation of one or
more of: Da, Dr or Rh, and Rotations.
-fixed Fixed Da, Dr or Rh, and Rotations.
-nofixed Same as -fit.
Predefined Nonlinear Fitting Modes (Use Only One):
-dadr Fixed Da and Dr, Variable Rotations.
-rot Fixed Rotations, Variable Da and Dr.
-rotdr Fixed Dr and Rotations, Variable Da.
-rotrh Fixed Rh and Rotations, Variable Da.
Alignment Tensor Magnitude (Da) Limits:
-da [1.0e-3] Initial Da Value.
-daMin [-1.0e-2] Minimum Da Value.
-daMax [1.0e-2] Maximum Da Value.
Alignment Tensor Dr or Rhombicity Limits:
-dr [1.0e-4] Initial Dr Value.
-drMin [-1.0e-2] Minimum Dr Value.
-drMax [1.0e-2] Maximum Dr Value.
-rh [0.5] Initial Rhombicity Value.
-rhMin [0.0] Minimum Rhombicity Value.
-rhMax [0.6666] Maximum Rhombicity Value.
Rotation Angle Starting Values and Limits:
-psi [45.0] Initial X-Axis Rotation.
-psiMax [360.0] Maximum X-Axis Rotation.
-psiMin [-360.0] Minimum X-Axis Rotation.
-theta [45.0] Initial Y-Axis Rotation.
-thetaMax [360.0] Maximum Y-Axis Rotation.
-thetaMin [-360.0] Minimum Y-Axis Rotation.
-phi [45.0] Initial Z-Axis Rotation.
-phiMax [360.0] Maximum Z-Axis Rotation.
-phiMin [-360.0] Minimum Z-Axis Rotation.
Extraction of Da, Dr Etc (for -svd and -saupe):
-euler Solve for Euler Angles, Da, Dr (Default).
-noeuler Don't Solve for Euler Angles.
-nofixed -noeuler DC Tensor Warning: mixed use of Dr and Rhombicity arguments.
-thetaMin -thetaMax DYNAMO Error: -saupe option requires 5 values.
DYNAMO Error Allocating Distance Values.
Dist Error opening output file %s
REMARK Distance Table, %d restraints.
REMARK %s
VARS INDEX RESID_I RESNAME_I ATOMNAME_I CHAINNAME_I SEGNAME_I RESID_J RESNAME_J ATOMNAME_J CHAINNAME_J SEGNAME_J D D_LO D_HI D_VIO S W FC STATUS
D D_LO D_HI S W FC STATUS
FORMAT %%5d %%4d %%4s %%4s %%9.3f %%9.3f %%9.3f %%9.3f %%.2f %%.2f %%.2f %%s
%%9.3f %%9.3f %%9.3f %%.2f %%.2f %%.2f %%s
%4d %4s %4s VIOLATED % 9.3f % 9.3f % 9.3f % 9.3f % 9.3f % 9.3f % 9.3f %6.2f %6.2f %6.2f %s
DYNAMO Error Allocating Distance Pair Values.
DYNAMO Error Allocating AC Values.
AC Error opening file %s
REMARK AC Table.
DATA N %d
DATA RMS %.3f
DATA Chi2 %.3f
VARS INDEX FIXED RESID RESNAME ATOMNAME CHAINNAME SEGNAME D_LO D_HI D_DIFF D_VIO S W FC STATUS
FORMAT %%4d %%d %%9.3f %%9.3f %%9.3f %%9.2f %%9.2f %%9.2f %%9.2f %%.2f %%.2f %%.2f %%s
% 9.2f % 9.2f % 9.2f % 9.2f NOE Error opening output file %s
REMARK NOE Table, %d complex constraints.
VARS INDEX GROUP FORMAT %%5d %%2d %5d %2d DYNAMO building bond matrix.
DYNAMO %d bonds.
DYNAMO building VDW exclusion matrix.
DYNAMO %d VDW exclusions.
DYNAMO Warning: No Atom Map for Distance:
ResIDI: %4d ResNameI: %4s AtomNameI: %4s SegI: %4s ChainI: %4s
ResIDJ: %4d ResNameJ: %4s AtomNameJ: %4s SegJ: %4s ChainJ: %4s
DYNAMO Warning: No Atom Map for Coord:
ResID: %4d ResName: %4s AtomName: %4s Seg: %4s Chain: %4s
DYNAMO Warning: No Atom Map for Distance Pair: ResIDK: %4d ResNameK: %4s AtomNameK: %4s SegK: %4s ChainK: %4s
ResIDL: %4d ResNameL: %4s AtomNameL: %4s SegL: %4s ChainL: %4s
DYNAMO Error Allocating NOE List.
DYNAMO Error Allocating NOE Values.
NOE Table %d complex contstraints:
ID %d, %d groups:
Group %d, %d entries:
%4d %6s %6s -> %4d %6s %6s
DYNAMO updating VDW neighbor matrix.
DYNAMO VDW Matrix used %d exclusions.
DMUSIC Error allocating DMUSIC structure.
DMUSIC Error: unsupported dimension count.
%s Error allocating memory.
DMUSIC Warning: Max signal count exceeded.
%d. %f %f %f
DYNAMO_KEY DYNAMO Error: Bad Initialization Environment.
DYNAMO Error: Missing Initialization Environment.
SURF_DIR homo.tab DYNAMO Error Reading Phi/Psi Surfaces.
DYNAMO Error (Energy) allocating workspaces.
DATA EULER_SOLUTIONS %d
DATA EULER_ANGLES % 7.2f % 7.2f % 7.2f
DATA Da % e
DATA Dr % e
DATA Aa % e
DATA Ar % e
DATA Da_HN % 8.6e
DATA Rhombicity % 8.6e
REMARK S %f %f %f %f %f
************** FATAL ERROR *************
GetParm Error: bad code %d.
GetParm Error: bad dim %d.
:?>>>p>D>====h=<=<< %f
*** Math Library Error: %s
%-6s %dx%d Variable Count
%-6s %dx%dx%d
%-6s %6d
%-6s %6d of %d
xNotify -label %s %s & NMRPipe Error Status: %d
NMRPipe Function %s
NMRPipe Exiting, Status: %d
NMRPipe Aborting with null header.
NMRPipe Client Error writing header to %s.
NMRSocket Client Error reading server list %s
NMRSocket Client Error in Server List.
NMRSocket Client Name Memory Error.
NMRSocket Client Error: Null Server List.
NMRSocket Client Error in Server Speeds.
NMRSocket Client Error starting server.
NMRSocket Server %s waiting to close connection.
NMRSocket Server %s closed connection.
rsh -n %s "kill -9 %d" & NMRSocket Kill Command: %s
NMRSocket Client Error finding unique port file.
rsh -n %s "%s -server %s -sID %d -buff %d NMRSocket Client starting server %s.
Command: %s
NMRSocket Client Error starting shell NMRSocket Client Error reading port file %s
NMRSocket Client assigned port %d.
NMRSocket Client Error connecting to server %s
NMRSocket Client connected on port %d.
NMRSocket Client Error opening socket NMRSocket Client Error finding host %s
NMRSocket Client Error connecting to socket NMRSocket Client Warning setting SO_KEEPALIVE NMRSocket Client Warning setting SO_SNDBUF NMRSocket Client Warning setting SO_RCVBUF NMRSocket Server %s initializing.
NMRSocket Server Error opening socket NMRSocket Server Error binding to socket NMRSocket Server Error getting socket name NMRSocket Server Error writing port number.
NMRSocket Server %s accepted connection.
NMRSocket Server Warning setting SO_LINGER NMRSocket Server Error opening port file 1 NMRSocket Server Error writing port file 1 NMRSocket Server Error opening port file 2 NMRSocket Server Error writing port file 2 NMRSocket Client Error opening port file NMRSocket Client Error reading port ID.
%s/%s%d.%03d NOSA Error allocating bit value list.
NOSA Error allocating bit correspondance list.
NOSA Error allocating new variable list.
NOSA Error: integer bit allocation overflow.
NOSA Error: floating point bit allocation overflow.
Clipping bit from %u to %d.
Clipping value from %f to %f
%m %d %Y %d %d %d DYNAMO Error opening output file %s
REMARK DYNAMO Pseudo-Contact Shift Simulation.
REMARK %s
DATA N %d
DATA RMS %.3f
DATA Chi2 %.3f
RESID RESNAME ATOMNAME CHAINNAME SEGNAME CS_OBS SHIFT CS_DIFF SIGMA W
SHIFT SIGMA W
%%4d %%4s %%4s %%9.3f %%9.3f %%9.3f %%9.3f %%.2f
%%9.3f %%9.3f %%.2f
%4d %4s %4s % 9.3f % 9.3f % 9.3f %9.3f %.2f
% 9.3f % 9.3f %.2f
DYNAMO Warning: No Atom Map for PCS:
ResID: %4d ResName: %4s AtomName: %4s Seg: %4s Chain: %4s
PARAMAGNETIC DATA PARAMAGNETIC %3d %-4s %-4s %-4s %-4s
DATA PCS_TENSOR % .3e % .3e % .3e % .3e % .3e
DATA PCS_DADR % .4e % .4e
DATA PCS_EULER % 7.2f % 7.2f % 7.2f
PDB Error Allocating VDW coords.
DYNAMO Error Allocating Bond/Neighbor memory.
-res resID Single Residue for Selection.
-r1 res1 First Residue in Segment.
-rN resN Last Residue in Segment.
-atomName aList Atom Name List (also -atom).
-resName rList Res Name List (Default: *).
-chain cList Chain Name List (Default: *).
-seg sList Seg Name List (Default: *).
-id sID Selection ID.
-inv Invert Selection.
Special Class Selection:
-protein Select Only Canonical Amino Acids.
Reset Selection; No Other Selection Performed:
-clear Clear Selection for All Atoms.
-set Set Selection for All Atoms.
Name Matching Modes:
-exact Match Names Exactly (Default).
-regex Regular Expression Pattern Matching.
-glob Glob-style Pattern Matching.
PDB Input Options:
-hetatm Interpret HETATM records as ATOMs.
-nohetatm -protein -atomName -resName PDB Selection: All Atoms.
%d to %d Atoms: %s Residues: %s Chains %s Segs: %s.
PDB Error opening PDB file %s
REMARK %s
PDB Error creating object tables.
PDB Error Indexing PDB File %s
PDB Error Allocating PDB coords.
PDB Error Allocating Chain Residue Array.
PDB Error Allocating Seg Residue Array.
REMARK Expanding Atom List: %d atoms max.
PDB Error Allocating Atom memory.
REMARK Expanding Atom Index List: %d atoms max.
PDB Error Allocating Atom Index memory.
REMARK Expanding Res Index List: %d residues max.
PDB Error Allocating Residue Index memory.
REMARK Expanding Res List: %d residues max.
PDB Error Allocating Residue memory.
REMARK Expanding Chain List: %d chains max.
PDB Error Allocating Chain memory.
REMARK Expanding Seg List: %d segs max.
PDB Error Allocating Seg memory.
DYNAMO updating VDW coords.
Error (PDBCopy): Null PDB Data.
Error (PDBCopy): Atom Count Mismatch.
Error (PDBCopy): Residue Count Mismatch.
PDB finding |%s|
alpha error at %d
kappa error at %d
omega error at %d
DynSetChi Error finding %d %s
DYNAMO Info: Simple Selection.
DYNAMO Info: Complex Selection Atom %d Res %d Seg %d Chain %d
%d %-2s %-4s %-2s %-4s %-4s %-2s PDB Warning: Redundant Atom Specification.
ResID: %d AtomName: %s Chain: %s Segment: %s
PDB inserting atom |%s|
PDB Atom Symbol Table Error.
PDB inserting residiue |%s|
PDB Residue Symbol Table Error.
PDB inserting chain |%s|
PDB Chain Symbol Table Error.
PDB inserting segment |%s|
PDB Seg Symbol Table Error.
PDB Error: string item too long: %s
PDB Error: name item too long: %s
ATOMNAME OCCUPANCY TEMPFACTOR ATOMNAME CHAINNAME FIRST_RESID SEQUENCE DYNAMO Error Allocating SEQUENCE info.
DATA FIRST_RESID %d
DATA SEQUENCE POLY Error allocating fit mask.
POLY Error allocating sub mask.
POLY Error allocating P Data.
POLY Error allocating X Data.
POLY Error allocating Y Data.
POLY Error allocating coefficients.
POLY Error fitting polynomial/series.
SVDFUNC Error performing SVD.
SVDPOLY Error performing SVD.
QMIX: Complex mixing of N inputs to M outputs.
-ic n [1] Input Channel Count.
-oc m [1] Output Channel Count.
-cList cList [0.0 ...] N by M Coefficient Matrix.
QMIX Error: bad in/out count.
QMIX error allocating input buffer.
QMIX error allocating output buffer.
QMIX error allocating real coefficients.
QMIX error allocating imaginary coefficients.
QMIX Error: bad coefficient count.
RG_TARGET DYN Error Allocating Radius of Gyration Values.
DYN Notice: Radius of Gyration ID too large.
DYNAMO Warning: No Atom Map for Rad Gyr:
ResID: %4d ResName: %4s AtomName: %4s Seg: %4s Chain: %4s
RdTable File open error: %s.
TOLERANCE NULLSTRING NULLVALUE RdTable Error: no entries in %s
RdTable Error: no variables found.
RdTable Error: VARS/FORMAT mismatch:
RdTable Error: VARS/TOLERANCE mismatch:
RdTable Error allocating variable info.
RdTable Error allocating var name.
Name: %s
RdTable Error allocating var format.
Format: %s
RdTable Error: bad format %s
RdTable error allocating data matrix.
RdTable Error: bad vartype.
RdTable Warning: Bad T-Item %d:
%s
RdTable Error mapping text.
RdTable Warning: Bad F-Item RdTable Warning: Bad I-Item Read1D Error Opening File %s
Read1D Error Positioning File %s
Read1D Error Reading Header In %s
Read1D Error Allocating Data.
SASE Error optimizing variables.
%4d. SIGNAL %2d HI: % e %c0: %8.4f %cDAMP: %6.4f SASE Enhance Error: dim count too high.
SASE Error allocating amplitude workspace.
SASE Error allocating input workspace.
SASE Error allocating amplitude memory.
SASE Error allocating input memory.
SASE Error allocating output memory.
SASE Error allocating workR memory.
SASE Error allocating workI memory.
SASE Error allocating variables.
SASE Error initializing optimization.
%dD-SASE, %d Bits, %d T Steps, %d Ops/Step, %.2f MBytes
SASE: Simulated Annealing Spectral Enhancement:
-nsig [8] Number of Model Signals.
-ndim [1] Dimension Count of Model.
-sigma [1.0] Std Dev of Time Domain Noise.
-report [0] Report Level.
-iter [1] Iteration Count.
-replace Replace Original with Model.
Axis-Specific Parameters (Use -x -y -z -a...):
-xSize [2*SIZE] Final Size, Pts.
-xFreqTol [0.01] Freq Tolerance, Pts.
-xDampMin [0.00] Min Dampening Factor.
-xDampMax [2.00] Max Dampening Factor.
-xDampTol [0.01] Dampening Factor Tolerance.
-xDampInit [0.00] Initial Dampening Factor.
-xP0 [0.0] Required Zero-Order Phase.
-xP1 [0.0] Required First-Order Phase.
-xModel [Exp] Signal Model Type; Keywords:
Exp Gauss CT.
Simulated Annealing Parameters:
-scale [100.0] Energy Scale Factor.
-tInit [100.0] Initial Temperature.
-tFinal [1.0] Final Temperature.
-oc [0] Operations Per Temperature;
Use 0 for Auto.
-tc [100] Temperature Step Count.
-gc [20] Greedy Optimization Count.
-rand [54321] Random Number Seed.
-replace -%cModel -%cFreqTol -%cDampMin -%cDampMax -%cDampTol -%cDampInit N: %6d T: %9.4f E: %9.4f CHI/N: %9.4f
Server Error reading server list %s
Server Error in Server List.
Server Name Memory Error.
Server Command Memory Error.
Server Error in List Length.
Server Error: Null Server List.
Server Error in Server Speeds.
Server Error adjusting partitions.
Host %2d: %10s CPU=%d Partition=%d Speed=%g
FdI(I HHHHhHTFTHGGG`G4GFF SHUF Error: unknown code %d.
SPLINE Error allocating memory.
SOLVENT Error: unknown type.
SOLVENT Error allocating memory.
SOLVENT Error generating filter.
SOLVENT Error: POLY mode is not supported yet.
SPLINE Error: null/bad solution
SOLVENT Error extrapolating head.
SOLVENT Error evaluating head.
SOLVENT Error extrapolating tail.
SOLVENT Error evaluating tail.
SOLVENT Error: unknown shape.
SpecUnit Error: bad units.
pP4StrCatAlloc Error: Null pointer.
StrCatAlloc Error: alloc failed.
StrCatAlloc Error: realloc failed.
StrCpyAlloc Error: Null pointer.
FGetSAlloc Error: Null pointer.
FGetSAlloc Error: Buffer too small.
Expanding to %d
CTempAlloc memory allocation error.
out of memory NULL argument Regexp too big out of space too many () unmatched () junk on end *+ operand could be empty nested *?+ ,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,pp,,@,,,,,,,,,,,,,,,,p,,,,,,,,,,,,,,,,,,,,,,,,,,,T,4,,,,,,,,,,,,,,,,,,,,,,,,,,,,, trailing \ invalid [] range unmatched [] ?+* follows nothing internal urp ^$.[()|?+*\ internal disaster NULL parameter corrupted program ȀɴǴɄT< ȘȘ,,,,,,,,,,,,,,,,,,,,PPPPPPPPPmemory corruption corrupted pointers internal foulup SVD Error: bad matrix size.
Bad Type for User Variable: Re-allocating array: Name: %12s Type: %d Size: %3d
File open error: %s
TOLERANCE NULLVALUE %d
NULLSTRING %s
WrTable Error: bad type.
Entry %d, %d
_NULLTXT WrTable Error: bad text.
Entry %d, ID %d
WrTableN Error allocating variable info.
WrTableN Error allocating variable name.
WrTableN Error allocating variable format.
Error reallocating table variables.
AddTabVar Error reallocating variable name.
AddTabVar Error reallocating variable format.
ChTabVar Error allocating NAME.
ChTabVar Error allocating FMT.
AddHdrLine Error allocating header line.
AddHdrLine Error allocating header item.
File Size Check Error: Insufficient Data in %s
Predicted Size: %d bytes.
Available Size: %d bytes.
Predicted Size: %.0f bytes.
Available Size: %.0f bytes.
File Status Notice GetToken: Memory Allocation Failure.
ANGLE_HI ANGLE_LO DYN Error Allocating Torsion Values.
Torsion Error opening file %s
REMARK Torsion Table.
REMARK %s
DATA N %d
DATA RMS %.3f
DATA Chi2 %.3f
VARS INDEX RESID_I RESNAME_I ATOMNAME_I CHAINNAME_I SEGNAME_I RESID_J RESNAME_J ATOMNAME_J CHAINNAME_J SEGNAME_J RESID_K RESNAME_K ATOMNAME_K CHAINNAME_K SEGNAME_K RESID_L RESNAME_L ATOMNAME_L CHAINNAME_L SEGNAME_L ANGLE ANGLE_LO ANGLE_HI ANGLE_VIO S W FC STATUS
ANGLE ANGLE_LO ANGLE_HI S W FC STATUS
FORMAT %%4d %%4d %%4s %%4s %%9.2f %%9.2f %%9.2f %%9.2f %%.2f %%.2f %%.2f %%s
%%9.2f %%9.2f %%9.2f %%.2f %%.2f %%.2f %%s
%4d %4s %4s VIOLATED % 9.2f % 9.2f % 9.2f % 9.2f % 9.2f % 9.2f % 9.2f %6.2f %6.2f %6.2f %s
DYNAMO Warning: No Atom Map for Torsion (offset %d):
ResIDI: %4d ResNameI: %4s AtomNameI: %4s SegI: %4s ChainI: %4s
ResIDJ: %4d ResNameJ: %4s AtomNameJ: %4s SegJ: %4s ChainJ: %4s
ResIDK: %4d ResNameK: %4s AtomNameK: %4s SegK: %4s ChainK: %4s
ResIDL: %4d ResNameL: %4s AtomNameL: %4s SegL: %4s ChainL: %4s
slevmar_bc_der(): cannot solve a problem with fewer measurements [%d] than unknowns [%d]
No function specified for computing the jacobian in slevmar_bc_der().
If no such function is available, use slevmar_bc_dif() rather than slevmar_bc_der()
slevmar_bc_der(): at least one lower bound exceeds the upper one
slevmar_bc_der(): memory allocation request failed
Warning: component %d of starting point not feasible in slevmar_bc_der()! [%g projected to %g]
slevmar_bc_dif(): memory allocation request failed
dlevmar_bc_der(): cannot solve a problem with fewer measurements [%d] than unknowns [%d]
No function specified for computing the jacobian in dlevmar_bc_der().
If no such function is available, use dlevmar_bc_dif() rather than dlevmar_bc_der()
dlevmar_bc_der(): at least one lower bound exceeds the upper one
dlevmar_bc_der(): memory allocation request failed
Warning: component %d of starting point not feasible in dlevmar_bc_der()! [%g projected to %g]
dlevmar_bc_dif(): memory allocation request failed
slevmar_chkjac(): memory allocation request failed
memory allocation in slevmar_pseudoinverse() failed!
LAPACK error: illegal value for argument %d of sgesvd_"/" sgesdd_ in slevmar_pseudoinverse()
LAPACK error: dgesdd (dbdsdc)/dgesvd (dbdsqr) failed to converge in slevmar_pseudoinverse() [info=%d]
dlevmar_chkjac(): memory allocation request failed
memory allocation in dlevmar_pseudoinverse() failed!
LAPACK error: illegal value for argument %d of dgesvd_"/" dgesdd_ in dlevmar_pseudoinverse()
LAPACK error: dgesdd (dbdsdc)/dgesvd (dbdsqr) failed to converge in dlevmar_pseudoinverse() [info=%d]
memory allocation in dAx_eq_b_QR() failed!
LAPACK error: illegal value for argument %d of dgeqrf_ in dAx_eq_b_QR()
Unknown LAPACK error %d for dgeqrf_ in dAx_eq_b_QR()
LAPACK error: illegal value for argument %d of dorgqr_ in dAx_eq_b_QR()
Unknown LAPACK error (%d) in dAx_eq_b_QR()
LAPACK error: illegal value for argument %d of dtrtrs_ in dAx_eq_b_QR()
LAPACK error: the %d-th diagonal element of A is zero (singular matrix) in dAx_eq_b_QR()
Normal equations require that the number of rows is greater than number of columns in dAx_eq_b_QRLS() [%d x %d]! -- try transposing
memory allocation in dAx_eq_b_QRLS() failed!
LAPACK error: illegal value for argument %d of dgeqrf_ in dAx_eq_b_QRLS()
Unknown LAPACK error %d for dgeqrf_ in dAx_eq_b_QRLS()
LAPACK error: illegal value for argument %d of dtrtrs_ in dAx_eq_b_QRLS()
LAPACK error: the %d-th diagonal element of A is zero (singular matrix) in dAx_eq_b_QRLS()
memory allocation in dAx_eq_b_Chol() failed!
LAPACK error: illegal value for argument %d of dpotf2_ in dAx_eq_b_Chol()
LAPACK error: the leading minor of order %d is not positive definite,
the factorization could not be completed for dpotf2_ in dAx_eq_b_Chol()
LAPACK error: illegal value for argument %d of dtrtrs_ in dAx_eq_b_Chol()
LAPACK error: the %d-th diagonal element of A is zero (singular matrix) in dAx_eq_b_Chol()
LAPACK error: illegal value for argument %d of dtrtrs_in dAx_eq_b_Chol()
memory allocation in dAx_eq_b_LU() failed!
argument %d of dgetrf_ illegal in dAx_eq_b_LU()
singular matrix A for dgetrf_ in dAx_eq_b_LU()
argument %d of dgetrs_ illegal in dAx_eq_b_LU()
unknown error for dgetrs_ in dAx_eq_b_LU()
memory allocation in dAx_eq_b_SVD() failed!
LAPACK error: illegal value for argument %d of dgesvd_"/" dgesdd_ in dAx_eq_b_SVD()
LAPACK error: dgesdd (dbdsdc)/dgesvd (dbdsqr) failed to converge in dAx_eq_b_SVD() [info=%d]
memory allocation in sAx_eq_b_QR() failed!
LAPACK error: illegal value for argument %d of sgeqrf_ in sAx_eq_b_QR()
Unknown LAPACK error %d for sgeqrf_ in sAx_eq_b_QR()
LAPACK error: illegal value for argument %d of sorgqr_ in sAx_eq_b_QR()
Unknown LAPACK error (%d) in sAx_eq_b_QR()
LAPACK error: illegal value for argument %d of strtrs_ in sAx_eq_b_QR()
LAPACK error: the %d-th diagonal element of A is zero (singular matrix) in sAx_eq_b_QR()
Normal equations require that the number of rows is greater than number of columns in sAx_eq_b_QRLS() [%d x %d]! -- try transposing
memory allocation in sAx_eq_b_QRLS() failed!
LAPACK error: illegal value for argument %d of sgeqrf_ in sAx_eq_b_QRLS()
Unknown LAPACK error %d for sgeqrf_ in sAx_eq_b_QRLS()
LAPACK error: illegal value for argument %d of strtrs_ in sAx_eq_b_QRLS()
LAPACK error: the %d-th diagonal element of A is zero (singular matrix) in sAx_eq_b_QRLS()
memory allocation in sAx_eq_b_Chol() failed!
LAPACK error: illegal value for argument %d of spotf2_ in sAx_eq_b_Chol()
LAPACK error: the leading minor of order %d is not positive definite,
the factorization could not be completed for spotf2_ in sAx_eq_b_Chol()
LAPACK error: illegal value for argument %d of strtrs_ in sAx_eq_b_Chol()
LAPACK error: the %d-th diagonal element of A is zero (singular matrix) in sAx_eq_b_Chol()
LAPACK error: illegal value for argument %d of strtrs_in sAx_eq_b_Chol()
memory allocation in sAx_eq_b_LU() failed!
argument %d of sgetrf_ illegal in sAx_eq_b_LU()
singular matrix A for sgetrf_ in sAx_eq_b_LU()
argument %d of sgetrs_ illegal in sAx_eq_b_LU()
unknown error for sgetrs_ in sAx_eq_b_LU()
memory allocation in sAx_eq_b_SVD() failed!
LAPACK error: illegal value for argument %d of sgesvd_"/" sgesdd_ in sAx_eq_b_SVD()
LAPACK error: dgesdd (dbdsdc)/dgesvd (dbdsqr) failed to converge in sAx_eq_b_SVD() [info=%d]
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* H* CA -help -csSim -daHist -daFlex -daMl -asRan -anA -anDc -anPdb -conv -struc -idum -rand -dcOpt -single -jack -mcDc -map -dFrac -nCone -lCone -autoMc -pdb -dbg -verb -noverb -qDa -qRms -qStd -err -noerr -w -in -inD -inCS -out -outD -outS -outPka -outCS -ref -path -list -sPath -sList -rList xPRO -dStep -sStep -d1 -dN -s1 -sN -sID -a1 -excl -inc -fit -nofit -rem -yzInv -inp -outDa -outMap -outAng -pot -pot3D -pka -inE -outE -flex -dcEns -ave -pdbF -pdbRot -rotID -outEAx -aD1 -aD2 -inD1 -inD2 -bic -pf1 -3D -wv -vol -mwLC -massLC -unitLC -polyLC -dot -digPsi -dGrid -dX -dY -dZ -nX -nY -nZ -maxPot -z1 -zN -rM -lcS -H -noH -surf -nosurf -rA -rim -pRatio -lM -pH -nacl -chSurf -dIFace -cut -elInfo -dipole -chSel -pkaDef -charmm -chTerm -kEne -kPot -kMono -kDipo -kQuad -temp -kAtt -pow -dcHH -nodcHH -scale -xplor -cns -tbl -dyana -pales -tensID -inS1 -inS2 -hinge -twist -outA -add -sub -mul -div -max -c1 -c2 -outP -inS -user -ster -el -noave -bin -nFit -daLo -daHi -rhLo -rhHi -nSel -nRun -outCol -outSc -lDa -hDa -incDa -lR -hR -incR -mapMl -fixAa -fixRes -dcID HN H N C HA CB N-HN C-N C-HN CA-C CA-HA CA-CB C-HA CA-HN .
%d %f %f
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%d
a %4s %.3f %8.3f 1+ 0+ 1- %s
C C1 C1' C1'A C1'C C1'N C10 C11 C12 C13 C14 C15 C16 C17 C18 C19 C1A C1B C1C C1D C1M C2 C2' C2'A C2'C C2'N C20 C21 C210 C211 C212 C213 C214 C215 C216 C22 C23 C24 C25 C26 C27 C28 C29 C2A C2B C2C C2D C2N C3 C3' C3'A C3'C C3'N C30 C31 C310 C311 C312 C313 C314 C315 C316 C32 C33 C34 C35 C36 C37 C38 C39 C3A C3B C3C C3D C3N C4 C4' C4'A C4'C C4'N C40 C41 C42 C43 C44 C45 C46 C4A C4B C4C C4D C4N C5 C5' C5'A C5'C C5'N C5A C5C C5M C5N C6 C6A C6C C6N C7 C7M C7N C8 C8A C8M C9 C9A CA CAA CAB CAC CAD CAL CAY CB CB1 CB2 CBA CBB CBC CBD CC CD CD1 CD2 CE CE1 CE2 CE3 CED CF CF3 CG CG1 CG2 CG3 CGA CGD CH2 CH3 CHA CHB CHC CHD CL CL1 CLP CM CM1 CM10 CM2 CM3 CM4 CM5 CM6 CM7 CM8 CM9 CMA CMB CMC CMD CP1 CP10 CP11 CP12 CP13 CP14 CP15 CP16 CP17 CP18 CP19 CP2 CP20 CP3 CP4 CP5 CP6 CP7 CP8 CP9 CR CRP CT CY CZ CZ2 CZ3 Cl FC1 FC2 FC3 N1C N3C N4C NC O2'C O2C O3'C O4'C O5'C 1NE2 1ZN N N1 N10 N1A N1N N2 N3 N3A N4 N5 N6 N6A N7 N7A N7N N9 N9A NA NB ND ND1 ND2 NE NE1 NE2 NH1 NH2 NL NR NT NZ NZ1 Na O1PN O2'N O2PN O3'N O4'N O5'N O7N PN ZN O O1 O10 O11 O12 O13 O14 O1A O1B O1D O1P O1PA O2 O2' O2'A O21 O22 O2A O2D O2P O2PA O3 O3' O3'A O31 O32 O3P O4 O4' O4'A O5 O5' O5'A O6 O7 O8 O9 OBB OBD OD1 OD2 OE1 OE2 OF OF1 OF2 OF3 OG OG1 OG2 OG3 OH OH1 OH2 OH3 OL OM OR OS1 OS2 OS3 OS4 OY SOD S S2 S3 SD SG FE MG P P1 PA PF YB H H1 H1' H10 H101 H102 H10R H10S H10X H10Y H11 H111 H112 H113 H11A H11B H11R H11S H11X H11Y H12 H121 H122 H123 H12A H12B H12R H12S H12T H12X H12Y H12Z H13 H13A H13B H13C H13R H13S H13X H13Y H14A H14B H14C H14R H14S H14T H14X H14Y H14Z H15A H15B H15C H15R H15S H15X H15Y H16R H16S H16T H16X H16Y H16Z H2 H2' H2'' H2'A H2'C H2'N H21 H211 H212 H213 H22 H23 H2R H2S H2X H2Y H3 H3' H3'A H3'N H31 H32 H33 H3R H3S H3T H3X H3Y H4 H4' H41 H41C H42 H42C H43 H4R H4S H4X H4Y H5 H5' H5'' H51 H52 H53 H5R H5S H5T H5X H5Y H6 H61 H61A H62 H62A H63 H6R H6S H6X H6Y H7 H71 H71N H72 H72N H73 H7R H7S H7X H7Y H8 H81 H82 H83 H8R H8S H8X H8Y H9 H91 H92 H9R H9S H9X H9Y HA HA1 HA2 HA3 HAA1 HAA2 HAB HAC HAD1 HAD2 HB HB1 HB2 HB3 HBA1 HBA2 HBB1 HBB2 HBC1 HBC2 HBD1 HBD2 HC HC1 HC2 HC3 HD HD1 HD11 HD12 HD13 HD2 HD21 HD22 HD23 HD3 HE HE1 HE2 HE21 HE22 HE3 HG HG1 HG11 HG12 HG13 HG2 HG21 HG22 HG23 HG31 HG32 HH HH11 HH12 HH2 HH21 HH22 HL HL1 HL2 HL3 HMA1 HMA2 HMA3 HMB1 HMB2 HMB3 HMC1 HMC2 HMC3 HMD1 HMD2 HMD3 HN HN1 HN2 HN3 HN5 HO HO1 HO2 HO3 HO4 HO6 HO7 HO8 HO9 HR HR1 HR2 HR3 HS HT HT1 HT2 HX HY HY1 HY2 HY3 HZ HZ1 HZ11 HZ12 HZ13 HZ2 HZ3 1HG 1HG1 2HG 2HG1 OXT OT1 OT2 OT3 1HA 2HA 1HB 2HB 3HB 3HG1 1HG2 2HG2 3HG2 1HE 2HE 3HE 1HE2 2HE2 1HD 2HD 1HD1 2HD1 3HD1 1HD2 2HD2 3HD2 1HZ 2HZ 3HZ 1HH1 2HH1 1HH2 2HH2 1HT 2HT 3HT 1H 2H 3H X QB 1MA 1MC 1MT 2'OM 2AMP 2END 2M2G 3PHO 3TER 3UMP 5MC 5MET 5PHO 5TER 7MG 9EG 9MA 9MG A12 A13 A13L A14 A16 A16L A23 A26 ACE ACEH ACEM ACET ACHO ACP ADE AIB ALA ALAD AMG AMX AP2 ARG ASN ASP ASPP AZID B12 B14 B1N BCB BCHC BCL BENZ BMPP BPB BPH BPHC BUTA BtoA CA++ CA2 CBX CCMP CHL CHOL CMP CO COH CPA CPR CT1 CT2 CT3 CTEG CTER CTN CYS CYT DEO1 DEO2 DEOT DEOX DHU DISU DLPE DMDS DMPA DMPC DPPC EIMI EIMM EMS ES1 ETAC ETAM ETH ETHA ETO ETOH ETSH FC FE1 FEGL FEOX FHEM FMA FME FMN FORM FUC GAL GCM GLC GLN GLU GLUA GLUP GLY GLYP GMG GMP GMX GNP GOM GPC GPE GUA GUAN HEM HEME HIBD HID HIP HIS HISD HISE HISH HIST HISU HS2 HSD HSE HSP HYL HYP IBUT ILE IMIA IMIM INDO LDA LEU LIG1 LIG2 LIG3 LINK LPPC LYS LtoD M2G MAMI MAMM MAN MAS MEOH MES1 MESH MET METO MGUA MIMI MIP MPRO MP_0 MP_1 MP_2 MQ7 MSO4 NAD NAF NAG NAH NAP NAX NC4 NC5 NH4 NMA NMG NMX NS1 NTEG NTER NUC PBCL PC PCYB PCYC PEN PENT PEPP PEPT PFE PHE PHEM PHEN PHEO PLIG PLO2 PLWA PMET PPG1 PPG2 PPGG PPGP PRO PRO2 PROP PSI PUR PURA PURG PYR PYRC PYRU RIBN RIBT RMHB SDS SER SIA SO4 TFE TFME THE THR THY TIP3 TP2 TRP TYR UNPR UQ1 URA URE URI VAL WAT WYE XCM XMG XMP XMX XNP XOM XXX XYL YB3 ZN2 ZNK w r Line:%s N pKa OT1 OT2 O OXT ARG default NH1 NH2 LYS NZ HIS ND1 NE2 TYR OH GLU OE1 OE2 ASP OD1 OD2 charge ADE GUA CYT THY A G C U 2MG H2U M2G OMC OMG YG PSU 5MC 5MU 1MA 7MG O1P O2P HT1 HT2 HT3 CA ALA HN H CD NE HE CZ HH11 HH12 HH21 HH22 ASN ND2 HD21 HD22 CB CG CYS SG GLN HE21 HE22 GLY HSD HD1 CD2 CE1 HSC HE2 ILE LEU CE HZ1 HZ2 HZ3 MET SD PHE PRO SER OG HG THR OG1 HG1 TRP CE2 CE3 CD1 NE1 HE1 HH VAL HEME FE NA NB NC ND C1A CHA C4D C1B CHB C4A C1C CHC C4B C1D CHD C4C C2A CAA C3A CMA CBA CGA O1A O2A C2B CMB C3B CAB CBB C2C CMC C3C CAC CBC C2D CMD C3D CAD CBD CGD O1D O2D ACE SO4 O1 O2 O3 O4 P O5' C5' H5' H5'' C4' H4' O4' C1' H1' N9 C4 N3 C2 N1 H1 N2 H21 HN' H22 HN'' C6 O6 C5 N7 C8 H8 C2' H2'' O2' H2' C3' H3' O3' H2 N6 H61 H62 H6 N4 H41 H42 H5 H3 C5M CM H51 H52 H53 URA DMPA P1 C1 H11 H12 H13 H23 MP_0 MP_1 MP_2 TIP3 OH2 SOD MG RIBT HN1 HN2 H3T DEOT HA HB1 HB2 HB3 HG2 HD2 HA1 HA2 HSE HSP HB CG2 HG21 HG22 HG23 CG1 HG11 HG12 HD3 HD11 HD12 HD13 HD23 HE3 HZ CZ2 CZ3 CH2 HH2 HG13 %s
matrix w rot.pdb %s a %e
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ALPHA BETA GAMMA %s.%d r Line:%s %s %f Pmax: BETA_L: BETA_H: %lf %lf
%s ATOM END
w %d
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HN H N C CA HA CB N-HN C-N C-HN CA-C CA-HA CA-CB C-HA CA-HN .
%d
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%%4s %4d %4s
Yes No apod ALL FLAGS DEBUG -help (None) ' %s '
program %f listArg M %.8g
_result %.8g None SHIFT INDEX SIGMA FC W cs G GLY HA2 HA3 w VARS FORMAT %%4s %4s HA CA CB C N xPRO PRO dyn %s.%s %s zero %s/%s RESNAME TYPE OFFSET %s,%s CS HA1 RC ADJ ??? Create Write Read w r W %s/%s max
None _I _J INDEX ABS D DI DD S W FC dc w
VARS FORMAT %%4s %4s HN N H HA CA HA# HA1 HA2 C dipolar -help -svd -saupe -align -fit -fixed -euler -da -dr -rh -psi -theta -phi -dadr -rot -rotdr -rotrh -daMin -daMax -drMin -drMax -rhMin -rhMax -psiMin -psiMax -phiMin -phiMax None _I _J D D_HI D_LO S W FC INDEX TYPE GROUP FIXED dist NONE w %%4s %5d %4s UNUSED OK _K _L ds X Y Z ac
X Y Z %4d %d dmusic DMUSIC %d rc.tab energy
%s
%s %s
TPPI States Image Complex Real Freq Time Unknown None SP EM GM TM ZE TRI GMB align nls align X Y Z A net r %f hsym NULL %lu %d %f r ./ ipl REMARK FORMAT VARS DATA END r None _I _J _K _L ABS A B C PHASE DA DB DC DPHASE OBSJ J FC S W INDEX jcoup w
%%4s %4d %4s % 9.2f * lp2d
mapText strDup mat2ptr matFree DEALLOC NOOP_AL ml '%s'
-fn -select -fdata
%s
nmr
%s: %s
%s %f sock pipe -in -out -buff -ibuff -obuff -client %s " & w %d %d %s. READY r pid %d nosa w VARS FORMAT %%4s None %4s DATA cs
pdb * -help -dbg -verb -hetatm -id -inv -res -r1 -rN -atom -chain -seg -clear -set -exact -regex -glob -aExact -aRegex -aGlob -rExact -rRegex -rGlob -cExact -cRegex -cGlob -sExact -sRegex -sGlob w ATOM END
r %s ATOM HETATM (stdin) ? None GLY HA3 HA1 HA C N CA HN H O CO {} none (Null)
%9.4f ATOMID LOCID RESNAME CHAINID RESID ICODE X Y Z SEGID ELEMENT CHARGE RESID RESNAME SEGNAME DATA seq
?
None ps poly -help -ic -oc -defR -defI qmix -cList %f,%f %f None FC S W INDEX radgyr r %s FORMAT VARS %s
%s
table %f DATA REMARK strDup mapText ??? r rdText %s strDup 1d
sase -help -report -nsig -iter -ndim -sigma -scale -%cSize -%cP0 -%cP1 -tInit -tFinal -oc -tc -gc -rand Exp Gauss CT %s %f server spline solv spline %f%s ppm Hz WN WL-nm % cm mm mic nm Pts spec str M BUFLEN %lf - w %s
VARS FORMAT %5.2f
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%f %d token %s%n None _I _J _K _L ANGLE FC S W INDEX torsion NONE w
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