CEDAR: Crystallographic, Energy and Dynamics Refinement

Authors: KeithWatenpaugh, Michael Carson & Jan Hermans

Contact: Keith Watenpaugh, Physical and Analytical Chemistry,

7255-209-1, The Upjohn Company, Kalamazoo, MI 49007, USA

CEDAR refines molecular structures using energy minimization, dynamics and crystallographic techniques either separately or together. Forces that may enter into the calculations include those from target atoms, bondlengths, bondangles, dihedral angles, interatomic distances, van der Waals interaction and partial ionic charges. In addition, least-squares refinement against the crystallographic data; symmetrically related and lattice related forces; and solvent molecules may be included in the calculations and minimization procedure.

Calculations Performed

Based on the dictionary of bonding forces entered onto the bdf by PRECED, a process of minimizing a non-linear function of the following form is performed.

Φ = Σφi

where φ1a = Σ(||-||)2 Structure factors

φ1b = Σ(∊p)2 Parameter shifts

φ2 = 1/2Σ(-)2 Bond lengths

φ3 = 1/2Σ(-)2 Bond angles

φ4 = Σ(-)2 Fixed dihedral angles

φ5 = Σ(1-cos(nx))2 Flexible dihedral angles

φ6 = Σ(/-/+/ Non-bonded

φ7 = Σ(/-/ 1-4 distances

p = shift in atomic positions from crystallographic terms

L = interatomic distance

T = interatomic bond angles

D = fixed torsion angles

nX = flexible torsion angle with "n" minimum positions

and = van der Waals terms between non-bonded atoms

and = partial charges on atoms "i" and "j"

d = dielectric constant

= interatomic distance of non-bonded atoms

and = van der Waals terms 1-4 interactions (i.e. separated by two bonds)

Any member of the set of functions may be weighted from 0.0 upwards. If all the energy terms are weighted at 0.0, then the program is doing a conventional crystallographic unrestrained refinement. If the crystallographic refinement is weighted at 0.0, then the program is doing an energy minimization of the terms selected without using any crystallographic structure factors. Likewise, dynamics simulation or combined dynamics and crystallographic refinement may be turned on.

During the calculation of the crystallographic shifts, a block diagonal matrix is used, each block consisting of the variable parameters for each atom. The shifts of the parameters, adjusted or weighted by user defined parameters are combined with the other terms of Φ. Φ is then solved by an interative conjugate gradient method. In other words φ1b rather than φ1a is used. If φ1b is applied using only the diagonal terms as is the case with other restrained refinement programs (e.g. PROLSQ), then it reduces to φ1a. The advantage of φ1b is that bad or large shifts may adjusted to reasonable values or weighted by their e.s.d.'s before applying the conjugant gradient step. The block diagonal calculation also takes into account correlation between atom parameters. In addition, shifts calculated in other programs may be used in place of the internal crystallographic least-squares routines. The most frequently used is CRYLSQ in order to do rigid body refinement at early stages of refinement.

When non-bonded energy terms are incorporated into the minimization process, the symmetry related atoms are also included in the calculations. The neibor option must have been used in PRECED previously to put the necessary symmetry and translational operators on the bdf.The number of interatomic interactions can become quite large and thus computing time can increase greatly. Turning on the dynamics simulations allows for complete subversion of a computer for vast amounts of time.

Description of Some Input Lines

mode line:

The mod option sets weights 1-5 to 1.0, and weights 6-8 to 0.0. The ene option sets weights 1-7 to 1.0 and the target weight on hydrogen (weight 8) to a pseudo sigma of 25.0 or a weight of 1.0/25.0. xta turns on crystallographic least-squares cycle while ext uses the previously calculated shifts and sigmas. The previously calculated shifts could be from CEDAR (see the xmode line) or CRYLSQ. Target atoms with larger estimated standard deviations can be down weighted using the sig option.

weight, initwt and finlwt lines:

If a finlwt line is included in addition to the weight (initwt) line, the the weights will change from the initial weighting to the final weighting in the number of conjugate gradient refinement cycles requested. For example, a large target weighting may be used initially and small target weighting at the end.

xmode line:

Only the isotropic B factor option works; anisotropic B factors have been coded in but not activated and tested. The pre option puts the input atomic coordinates into the previous atomic coordinate fields on the output bdf and the currently refined coordinates in the current coordinate fields. A similar option exists on some versions of CRYLSQ. The ext option on the mode line uses the previous and current coordinates to calculate shifts. The fca, fxe and fxa options allow inclusion but no refinement of additional atoms, for example, hydrogens. fca uses the A(calc) and B(calc) stored on the bdf and adds them into the terms calculated in this run. The fixed A and B are over-written and lost. In the fxe option the A(calc) and B(calc) are strored for future use in the fields reserved for them on the bdf and also applied. The fxa option used the valued stored in the fixed atom contribution fields on the bdf, but doesn't modifiy them. The ski option calculates the FC and partial derivatives for every nth reflection. This allows for an estimate of the R-factor to be calculated with the FC option. It is not recommended for the least-squares refinement.

xlimit line:

B factors are reset to be between the minimum and maximum limits before each cycle of refinement. At the same time, the bch option allows B's to change by a maximum amount between connected atoms. For example, if bch=2., and atom1 has a B of 5.0, then atom2 that is bonded to atom1 will be reset to be between 5.0/2.0 or 2.5 and 5.0*2.0 or 10.0. I don't defend this a the best way of maintaining reasonable B's and I am open to other suggestions. I don't beleive the "riding motion" restraint in PROLSQ is a correct way to handle it.

scale line:

In the current version, a scale line should always be included if the scale is not unity.

Refinement Strategies

Normal combined crystallographic and energy minimization refinement usually consists of refinement with the input lines


mode xtal model

weight 100. 1 1 4 1 0 0

refine 4

In this case the crystallographic shifts are weighted 100.0 times the default weight. Frequently even a weighting of 1000.0 can be used to place more importance on the crystallographic terms. In later stages of refinement the crystallographic weighting may be dropped to reduce deviations from the standard bonding parameters. In addition, the fixed torsion angles are weighted more heavily to force peptides and aromatics to maintain greater planarity than their nornal forces parameters suggest. Four complete cycles of refinement will be carried out. As with other restrained refinement programs, the decrease of R-factors usually greatly slows down after a few cycles of refinement. An unconstrained refinement cycle followed by idealization in a separate step using the input lines


mode xtal

weight 1 0 0 0 0 0 0


mode model


can sometimes get regions out of local minima. Otherwise, more drastic methods such as rebuilding with computer graphics, non-bonded energy terms or dynamic simulations are required to correct areas of a structure. Turning on the listing of bad energy terms (weight line, field 9) helps identify bad inter-atomic parameters (lengths, angles, dihedrals).

Including the non-bonded terms is much more compute-intensive, but may help in the refinement process. It especially helps in keeping non-bonded atoms from getting too close and helps form hydrogen-bonding networks. The pseudo energy terms for chirality can help low resolution refinements from flipping to a wrong hand. A typical combined non-bonded energy refinement with crystallographic refinement could include the input lines.


mode xtal energy

weight 100.


The energy option on the mode line automatically places unit weight on weigths 1-6. The weight line changes weight of crystallographic shifts to 100. without changing the others. The non-bonded terms tend to push inter-atomic parameters slightly away from the standard values in systematic and hopefully in realistic ways depending on secondary structure or neighbouring contacts. In this mode, the non-bonded energy for each residue is listed after each cycle of refinement. Limited experience has shown that residues with positive energies are suspect and should be checked. It is also good to check graphically where the hydrogens are and to adjust them to give more reasonable H-bonds sometimes. Be default, the hydrogen positions are weighted down by 1/25.0 relative to other atoms (weight line, field 8)=25.), but they still don't always move from their initially calculated postions very well.

One can further play around with trying to get the best set of refinement parameters by breaking the process up into the computing crystallographic step and the energy minimization step by first doing and storing the results of the crystallographic calculations using the input lines


mode xtal

weight 1 0 0 0 0 0

xmode previous


This will store the shifts and e.s.d.s on the output bdf for input into the energy minimization step. Then by using a set of input lines such as


mode external

weight 1000 1 1 1 1 0 0


xmode skip 50



the effect of different weighting schemes can be tested quickly and usually interactively on the computer.

Externally calculated shifts can be used in another and sometimes powerful way by using CRYLSQ to do rigid-body refinement coupled with CEDAR doing restrained refinement. As yet a program to conveniently set-up the sometimes extensive control lines for many rigid groups does not exist and needs to be written. A sample input could be:

title crylsq refinement cycle 1

CRYLSQ iso fu .75 cy 1 ms pp

scale 1.00 1

maxhkl *4 0.05 0.35

select o n c

group *6 -1

atomgr c001_a-c002_a

group *6 -1

atomgr c002_b-c002_z

group *6 -1

atomgr c002-n003

group *6 -1

atomgr c003_a-o003_xt

noref pop

title cedar refinement cycle 2


scale 1.00 1

mode model

weight 1 1 1 1 1 0


maxhkl *4 0.05 0.3333


Debugging dictionary entries

It is not always possible to generate a new residue dictionary correctly the first time. A way to see if connectivity, bond angle, torsion angles, etc are correct is to let CEDAR either put out bad energy terms using the weight line or print out all observed and calculated values of bond lengths, angles, dihedrals using printer priority of 4 on the reset line. The number of lines output can be controled by just putting a range of residues of interest into the calculations by using a reszon line. Any new residue dictionary entries should be checked before refining a structure.


The currently distributed version of CEDAR does not contain the dynamics routines. The dynamics version can be obtained by communication directly with the author.


Use of PRECED and CEDAR should be referenced as:

K.D. Watenpaugh, "Conformational Energy as a Restraint in Refinement", In: **

Molecular Dynamics and Protein Structure (ed. J. Hermans), Polycrystal Book,

Yellow Springs, OH, 77-80, 1985.


PROATM must have been run to load atom parameters

PRECED must have been run after any loading of atoms

File Assignments

Read input from input archive bdf

Write output to the output archive bdf



mode sigma xtal

weight 8 1 1 1 1 1 0 1

scale 8.4

maxhkl *4 0.05 0.27

xlimit bmin 3.0 bmax 50.0 bchange 1.5 damp .8 sft .4

refine 1

CEDAR will be run with crystallographic refinement. During the energy minimization step the target atomic postions will be given a weighting proportional to the inverse of the least-squares derived standard deviations weighted up by a factor of 8. The F(obs) will be scaled by a factor of 8.4 and only reflections between sinθ/λ limits of 0.05 and 0.27 will be used in the refinement. During the least-squares refinement B-factors will be restrained to be between 3.0 and 50.0. In addition, B-factors can only vary by af factor of 1.5 from the previous atom to which an atom is bound. The least-squares calculated shifts will be damped by 0.8 and the maximum shift of an atomic positional coordinate is 0.4 Angstroms. One pass will be made through the procedure set-up with the current options and parameters.


mode energy

weight 0 1 1 1 1 1 0 0

mmode 50


This is a straight energy refinement. Starting with an initial set of coordinates, both the bonded and non-bonded energies are minimized. All interatomic interactions are included, including those to symmetry related molecules.


mode model

weight 1 1 2 8 1 0 1 0

reszon 1 24

refine 50

In this refinement, non-bonded energies are ignored, while bond angles are given double weight and torsion angles eight times their normal weight. This will force them to be more ideal than the normal weighting would have done. Only residues 1 through 24 will be shifted.


Molecular Mechanics Calculations

U. Burkert and N.L. Allinger, Molecular Mechanics, Amer. Chem. Soc., Washington,D.C., 1982.

S.J. Weiner, P.A.Kollman, D.A. Case, U.C. Singh, C Ghio, G. Alagona, S. Profeta, Jr and P.Weiner, "A New Force Field for Molecular Simulations of Nucleic Acids and Proteins", J. Amer. Chem. Soc., 106, 765-784, 1984.

Molecular Dynamics Simulations

J.A. McCammon and S.C. Harvey, Molecular Dynamics of Proteins and Nucleic Acids, Cambridge Univ. Press, NY, 1987.

M. Karplus, B.M. Pettit and C. A. Brooks, Proteins: Dynamics, Academic Press, NY, 1988.

Combined Crystallographic and Molecular Mechanics/Dynamics

K.D. Watenpaugh, "Conformational Energy as a Restraint in Refinement", In: Molecular Dynamics and Protein Structure (ed. J. Hermans), Polycrystal Book, Yellow Springs, OH, 77-80, 1985.

A.T. Brunger, G.M. Clore, A.M. Gronenborn and M. Karplus, "Three dimensional structures of proteins determined by molecular dynamics with interproton distance restrainsts: Application to crambin", Proc. Natl Acad Sci, USA, 83, 3801-3805, 1986.