Docstoc

Acorn 6

Document Sample
Acorn  6 Powered By Docstoc
					                           ACORN (CCP4: Supported Program)

NAME

   acorn - ab initio procedure for the determination of protein structure
   using atomic resolution data or artificially extended data to atomic
   resolution, and for finding sub-structures from anomalous or
   isomorphous differences.

SYNOPSIS

   acorn hklin foo_in.mtz hklout foo_out.mtz [xyzin foo_in.pdb]
   [Keyworded input]

CONTENTS

       1. DESCRIPTION
             + General Description
             + ACORN-MR
             + ACORN-PHASE
             + SCENARIOS
       2. KEYWORDED INPUT
             + General Keywords to select data, select model and preform
               miscellaneous functions
             + Keywords Specific for ACORN-MR
             + Keywords Specific for ACORN-PHASE
       3. INPUT AND OUTPUT FILES
       4. PRINT OUTPUT
       5. EXAMPLES

       a. Examples starting from some known atomic coordinates.
             + Example 1: Use a constellation of correctly placed atoms as
               the starting point. For example, a Zn atom placed from
               sharpened atomic resolution Patterson.
             + Example 2: Use a constellation of correctly placed anomalous
               scatterers as the starting point. These may be sulphurs found
               from the anomalous diffraction data.
             + Example 3: Use a fragment already positioned by some other MR
               procedure (e.g. AMoRe).
             + Example 4: Test for the best result from 10 possible heavy
               atoms positioned from the Harker vectors alone, i.e. they are
               not necessarily on the same origin or hand.

       b. Examples starting from a large set of randomly positioned atoms.
             + Example 5: Use a randomly placed single atom as a starting
               point for a complete structure solution. This is usually
               successful for metallo-proteins, for finding substructures
               from isomorphous or anomalous difference data and for solving
               small molecular structures.
             + Example 6: Use a randomly placed single atom as a starting
               point to determine the position of heavy atoms in a protein
               structure from the anomalous differences only.
             + Example 7: Use a randomly placed single atom as a starting
               point to determine the position of the sub-structure of
            anomalously scattering atoms in a protein structure from both
            the anomalous and isomorphous differences.
          + Example 8: Use a randomly placed single atom as a starting
            point to solve a small molecular structure.

    c. Examples starting from a molecular replacement search.
          + Example 9: Use standard alpha helices as search models for a
            complete molecular replacement (MR) search.
          + Example 10: Use standard alpha helices as search models for
            random MR search.
          + Example 11: Use a fragment from a similar structure for MR
            search.

    d. Examples (re)starting using previously determined results.
          + Example 12: Use externally determined phases and weights as a
            starting point.
          + Example 13: Restart using results from previous run of ACORN.
          + Example 14: Use the results from AMoRe given as Euler angles
            and translation components to position the model atoms
            correctly.

    e. Examples extending data resolution to 1.0 Å and starting with
       positioned fragments or experimental phases.
          + Example 15: Use all extended reflections in the file and
start
            from a heavy atom.
          + Example 16: Use the extended reflections within 50.0 to 1.0 Å
            and start from Molecular Replacement model.
          + Example 17: Use the extended reflections within 50.0 to 1.0 Å
            and start from experimental phases.

     AUTHOR

     REFERENCES

     SEE ALSO

DESCRIPTION

   ACORN [1] [2] [3] [4] is a flexible and fast ab initio procedure to
   solve a structure when the data are sufficient to separate atom sites
   in the E maps. There are three catagories where this holds:
    a. proteins with diffraction data to 1.2Å or artificially extended
       data to 1.0Å with observed data as low as 1.7Å;
    b. small molecules where the data clearly reach to atomic resolution;
    c. well-separated sub-structures such as Se or S atoms, or other
       anomalous/isomorphous scatterers, where even low resolution data
       will suffice.

   The initial phase sets are generated from the atomic coordinates of a
   putative structural fragment. The fragment can be made up in various
   ways. Firstly, in simple cases, such as metalloproteins, small
   molecules or for finding sub-structures, it is sufficient to make many
   tests starting from a single randomly placed atom. Secondly, complete
   proteins can certainly be solved starting from their sub-set of
   correctly positioned heavier atoms, such as the sulphur sites which
can
   be found from their anomalous contributions. Thirdly, a molecular
   replacement solution will provide a good starting set of phases for a
   protein which diffracts to high resolution. The starting model may
   consist of the whole contents of the asymmetric unit, a domain, or a
   smaller fragment such as a standard alpha helix. The size of the
   fragment can be less than 5% of the scattering matter of the unit
cell.
   The fragments can in principle be positioned using MR searches with
   normalised data within ACORN.

   Alternatively phase information from other procedures, for instance
low
   resolution phases previously determined for a protein for which there
   is now atomic resolution data available, can be used to initiate the
   procedure.

   The starting phase sets are refined primarily using Dynamic Density
   Modification (DDM), supplemented by Patterson superposition (SUPP),
   real space Sayre Equation Refinement (SER) and weak density
enhancement
   (ENHS).

   The observed reflections are divided into three groups: strong, medium
   and weak reflections according to their normalized structure factors
   (E-values). Correlation coefficients (CCs) between the observed and
   calculated E-values for each class are used in different ways
   throughout the procedures. All reflections are used to select likely
   trial sets; the strong and weak reflections are used in the phase
   refinement and the CC for the medium reflections acts as the figure of
   merit. This is a major strength of ACORN: this CC provides a simple
and
   unequivocal criterion of correctness for a phase set.

   When the   resolution for observed reflections is only between 1.2Å and
   1.7Å the   UNIQUE procedure has to be run first to extend data
resolution
   to 1.0Å.   Then in ACORN an expected value of E=1.0 will be given to all
   extended   reflections using keyword EXTEND.

   The program has two main parts: ACORN-MR and ACORN-PHASE.

  ACORN-MR:

   ACORN-MR allows the evaluation of multiple starting models. These are
   required
    a. for the MR positioning of small fragments of a protein; such as an
       idealised alpha helix or a well characterised domain
    b. for the use of a single atom as a model, useful for a
       metalloprotein
    c. to position sub-substructures where starting from a single
randomly
         placed atom is the essence of the application.

     In all applications where a previously positioned fragment is
     available, ACORN-MR is not required.

   Furthermore, ACORN-MR provides an alternative molecular replacement
   search procedure using normalised structure factors generated from the
   observed data and the model. When the data are of a sufficiently high
   resolution and the fit between model and structure is very good, this
   works well. The best results have been obtained using idealised alpha
   helices which may make up only a small part of the new structure but
   which fit exactly. When searching for domains or whole molecules using
   ACORN-MR it is not necessary to use atomic resolution data. In fact
the
   results from other MR programs using lower resolution data may be
   obtained more quickly, and be more reliable.

   If the "model" is a single atom, a rotation function search is not
   required, and the MR "translational" search allows the systematic
trial
   of all starting points in the Cheshire Cell. This procedure can be
used
   to find anomalous scatterers from anomalous data where the resolution
   can be as low as 3Å to 4Å. The grid needs to be about max_resln/3.0

     The results are scored using the highest CCs for all reflections, and
     typically the best 100 or so are tested as starting sets for phase
     refinement using ACORN-PHASE.

     The solutions from the rotation function are given in terms of the
     Eulerian angles: alpha, beta and gamma using the convention described
     by Tony Crowther as in all CCP4 programs, e.g. ALMN, LSQKAB, PDBSET,
DM
     and AMoRe. The required ranges for the translational search are
     governed by the space group and will be chosen by the program.

     ACORN-PHASE:

     ACORN-PHASE refines a starting set of phases using DDM taking the CC
     for the medium E-values to indicate a likely solution. There are four
     phase refinement procedures in the suite, of which DDM is the most
     important:
       * Dynamic Density Modification (DDM) eliminates the negative
         densities, and truncates the highest density (for the first cycle
         this will be at the sites of the starting coordinates). The rest
of
         density is modified according to a formula based on the standard
         deviation of the map and the cycle number. There are three kinds
of
       map coefficients used in DDM and called DDM0, DDM1 and DDM2, see
       DDMK.
     * Patterson superposition (SUPP) generates a semi-sharpened
Patterson
       sum-function map from the starting fragment.
     * Sayre Equation Refinement (SER) is carried out in real space using
       Fast Fourier Transforms instead of working directly with the phase
       relationships; the equations are identical but the real space
       formulation is much faster.
     * Weak density enhancement (ENHS) is used to find an envelope and
       raise the weak densities within the envelope.

   ACORN-PHASE first uses DDM. If no solution can be found, a few cycles
   of Sayre Equation Refinement or one cycle of enhancement may modify
the
   phase set sufficiently to allow the DDM algorithm to function more
   effectively. The number of trials can be set by the user. See NTRY.

   ACORN will stop automatically if the value of CC for the medium
   E-values in DDM becomes greater than a preset value. The default value
   is determined by ACORN, but this value needs to be adjusted according
   to the data quality, particularly when determining anomalous
scatterers
   from SAD or MAD data. Maps calculated from the refined phases are
   normally excellent; proteins can be built automatically and for
   sub-structures the highest peaks indicate the true sites.

    Reflection input:

   ACORN reads pre-calculated E-values and amplitudes. Within CCP4
   E-values can be generated by ECALC. The data resoluton can be extended
   using CCP4 program UNIQUE and then ACORN uses keyword EXTEND to
control
   how to use the extended reflections. Known phases and weights can be
   input and refined by ACORN-PHASE directly. Only the best set of phases
   and weights, that with the highest CC for the medium reflections, is
   output to the foo_out.mtz file.

  SCENARIOS:

    Solving an atomic resolution protein structure with a known starting
    fragment:

   Some known atom positions are available. These may be:
    a. anomalous scatterers such as a metal site found in a
       metallo-protein. Example 1.
    b. a sub-structure such as the sulphurs or seleniums. Example 2.
    c. a model obtained from some MR search. Example 3.

   ACORN-PHASE will refine the initial phases calculated from these known
   atom positions and produce an unbiased map.
    d. If a set of possible atom sites is available which are not
       necessarily consistent, and which may not be on the same origin or
       hand, ACORN-PHASE can test each site in turn and select the best
       phase set. For instance they may be solutions to a Patterson
       superposition search of the Harker sections. Example 4.

    Solving an atomic resolution metallo-protein structure or finding the
    sub-structure or solving a small molecule structure by testing many
randomly
    placed atoms:

      e. It is expected that the structure contains a heavy atom: many
         randomly positioned single atom sites are checked, the best 100 or
         so sets refined, and the best phase set of these output. Example
5.
         Example 6. Example 7. Example 8.
      f. Solving a small molecule structure:
         Again, many randomly positioned single atom starting sites are
         checked and refined, and the best phase set output. The default
         parameters are set for the determination of a macromolecular
         structure, so it is best to set the resolution to the highest
         avalable, and to make sure the grid sampling is about 0.3Å. The
         CONTENTS list should also be given if the Sayre Equation is to be
         used. Example 8.
      g. To determine a sub-structure:
         Many randomly positioned single atom starting sites are checked
and
       refined, and the best phase set output. Of course atomic
resolution
       data is not required to find the sub-structure sites. Example 6.
       Example 7.

      Carrying out a MR search as a preliminary to phase refinement:

    h. Most proteins contain some standard fragments such as Alpha
helices
       or Beta sheets. There is a coordinate library for such standard
       fragments available in $CLIBD/fraglib/. Good results have been
       obtained searching for the correct position of idealised Alpha
       helices (main chain plus CB) which then provide the starting
       fragment for ACORN-PHASE. Other motifs or standard fragments can
be
       used in the same way. Example 9. Example 10. Example 11.

      Using some prior phase information:

      i. Some known phase information is available: use ACORN-PHASE to
         refine it. Example 12.

      There is an option to restart the procedure:

      j. ACORN can be restarted using likely solutions from a previous run
         or using solutions from AMoRe. Example 13. Example 14.

      Using extended reflections:

      k. Use a known heavy atom position with all extended reflections.
         Example 15.
      l. Use MR model from MOLREP with the extended reflections from 50.0
to
        1.0 Å. Example 16.
       m. Use experimental phases from SAD with the extended reflections
from
         50.0 to 1.0 Å. Example 17.

KEYWORDED INPUT

   The data control is keyworded. Only the first 4 characters of a
keyword
   are significant. They can be in any order, except END (if present)
   which must be last. Numbers and characters in "[ ]" are optional.
   Anything input on a line after an exclamation mark or hash ("!" or
"#")
   is ignored and lines can be continued by using a minus sign.

   It is essential to give LABIN to describe and define the input data,
   and one keyword to direct the mode of ACORN (either to phase, restart
   or do a MR search). Most other keywords are optional.

   The   keywords can be subdivided into groups:
     *   General Keywords to select data and model
     *   Keywords for miscellaneous functions
     *   Keywords Specific for ACORN-MR
     *   Keywords Specific for ACORN-PHASE

  General keywords to select the data and model:

       * Reflection Selection Keywords

       LABIN, ECUT, ESTRONG or NSTRONG, EWEAK or NWEAK, EXCLUDE,
       RESOLUTION, EXTEND NOEXTEND
       * Atom Selection Keywords

       NAFRAG, NSTART, POSI, RATM

  Keywords to restart the procedure, and for miscellaneous functions:

       * Restart the program using results from a previous run

       INITIAL
       * Keywords for miscellaneous functions

       CONTENT, GRID, LABOUT, SEED, TITLE, END.

  Keywords to Select reflections, and organise input data:

  LABIN <program label>=<file label>...

   (COMPULSORY)

   This keyword defines which items are to be used in the calculation.
The
   following program labels can be assigned, of which the first three are
   essential. E is the normalised amplitude used as the target for the
   structure solution. It may be based on the amplitude for a whole
 structure or on an anomalous or isomorphous difference, or an estimate
 of FH or FA derived from both disperive and anomalous differences. See
 ECALC.
E     FP     SIGFP   [PHIN]     [WTIN]    [FCIN]    [FT]   PHIFT]
E     Normalized structure factors.
FP    Observed structure factors.
SIGFP Sigma of FP.
PHIN Known phases.
WTIN Weights of known phases.
FCIN Calculated magnitudes with the known phases.
FT    Amplitudes from final structure model.
PHIFT Phases from final structure model.

If PHIFT is assigned ACORN will calculate phase error with proper
origin shifts for both enantiomorphs.

 Example: To calculat phase errors.
LABI E=EO FP=FP SIFFP=SIGFP FT=FC PHIFT=PHIC

If PHIN and WTIN are assigned they are used as the set of initial
phases with weights for ACORN-PHASE. If WTIN is not given, all weights
default to 1.0. If FCIN is given ACORN will calculate the weights from
the magnitudes.

 Example: Use the experimental phases PHIB and FOM as the initial phase
 set.
LABI E=EO FP=FP SIFFP=SIGFP PHIN=PHIB WTIN=FOM
LABI E=EO FP=FP SIFFP=SIGFP PHIN=PHIB FCIN=FCcal

ECUT <ecut>

(optional) - Default: <ecut> = 5.0

The observed reflections with E-values greater than <ecut> will be
rejected and treated as extended reflections. This can be used to
exclude outliers.

Example: ECUT 4.5

ESTRONG <estrong>

(optional - alternative to NSTRONG) - Default: <estrong> = value
determined by ACORN.

The lower limit of E-values for the "strong" class of observed
reflections. These are used in the phase refinement, but ACORN will
calculate final phases and weights for all reflections and output them
to foo_out.mtz.

Example: ESTRONG 1.0

NSTRONG <nstrong>

(optional - alternative to ESTRONG) - Default: use value of <estrong>
   and derive <nstrong> as the number of observed reflections this
   selects.

   The number of strong observed reflections to be used. The program will
   set <estrong> appropriately.

   Example: Use 25000 strong reflections.
  NSTRONG 25000

  EWEAK <eweak>

   (optional - alternative to NWEAK) - Default: <eweak> = 0.1

   The upper limit of E-values for the "weak" class of observed
   reflections. These are only used in the SER refinement of phases.

   Example: The reflections with E-values less than 0.2 make up the
"weak"
   class of reflections.
  EWEAK 0.2

  NWEAK <nweak>

   (optional - alternative to EWEAK) - Default: use EWEAK 0.1 and derive
   <nweak> as the number of observed reflections this selects.

   The number of weak reflections to be used. The program will set
<eweak>
   appropriately.

   Example: Use 500 weak reflections.
  NWEAK 500

  The "medium" class of reflections

   The medium observed reflections are all those with E-values between
   <eweak> and <estrong>. These reflections are not used for phase
   refinement and provide the cross validation set. If the CC for this
   class increases to a reasonable value, it indicates a solution.

  EXCLUDE <sigcut>

   (optional) - Default: <sigcut>=0.0. Use all the observed reflections.

   The reflections with FP less than <sigcut>*SIGFP will be rejected and
   treated as the extended reflections.

   Example: The reflections with FP less than 2.0*SIGFP will be rejected.
  EXCL 2.0

  RESOLUTION <res_low> <res_high>

   (optional) - Default: Use all observed reflections in the file.
     The resolution range of the observed reflections to be used -
     resolution limits are given in Å in either order.

      Example: Use observed reflections from 20.0 to 1.5 Å.
     RESO 20.0 1.5
or
     RESO 1.5 20.0

     EXTEND <res_low> <res_high>

     (optional) - Default: Use all extended reflections.

     Giving EXTE without other parameters: to use all extended reflections
     in the file that is pre-provided by CCP4 program UNIQUE.

     <res_low> and <res_hight> give the resolution range of the extended
     reflections to be used - resolution limits are given in Å in either
     order.

      Example: Use extended reflections from 50.0 to 1.0 Å.
     EXTE 50.0 1.0
or
     EXTE 1.0 50.0

     NOEXTEND

     (optional) - Do not use any extended reflections.

      Example:
     NOEXTE

     Keywords to Select atoms for initial fragment

   The coordinates given in XYZIN can be used in various ways; the
default
   option is to use them all as input for a MR search or for phase
   refinement.

     If no control keyword is given, the program defaults to doing phasing
     refinement with all atoms, equivalent to NAFRAG ALL and POSI 1.

     It is also possible to use only some of them beginning from different
     starting points in the file. This is controlled by combinations of the
     keywords NAFRAG, NSTART and POSI.

     NAFRAG <nafrag> [ALL]

     (optional) - Default: ALL i.e. use all atoms in XYZIN (assigned to
     foo_in.pdb)

     Pick up <nafrag> atoms from foo_in.pdb.

     Example: The fragment uses 50 atoms starting from the first from
     foo_in.pdb file.
     NAFRAG 50

     NSTART <nstart>

     (optional) - Default: <nstart> = 1

     The fragment runs from the <nstart>th atom in foo_in.pdb with a length
     of <nafrag>.

      Example: The fragment consists of atom 5 to 14 from foo_in.pdb.
     NAFRAG 10
     NSTART 5

     POSI [<nrand>]

     (optional) - Default: <nrand> = 1

     <nrand> randomly selected starting points will be chosen from
     foo_in.pdb file, each with length <nafrag>. For example if there are
10
     possible heavy atom sites in foo_in.pdb, you can use the following
     input to test all ten of the positions one by one.

      Example: Use 10 sets of one atom fragments.
     NAFRAG 1
     POSI 10

     RATM [<nratm>] [<percentage>]

     (optional) - Default: <nratm> = 50000. <percentage> = 20%. No XYZIN
     required.

     This keyword can be used without assigning XYZIN. ACORN generates
     <nratm> sets of single random atoms as starting fragments. The CC will
     be calculated for [<percentage>]% of all reflections and sorted. Then
     for the top 1000 sets the CC for all reflections is calculated and
     again sorted. The phases from the top sets are then generated and
     refined. For space group P1 two atoms are required; one at the origin
     and another randomly placed one.

      Example: Generate 5000 sets of single random atom fragments and test
      them against 10% of reflections.
     RATM 5000 10.0

     Restart the program using results from a previous run

  INITIAL <mesg> <numb1> [<numb2>] [<numb3>] [<numb4>] [<numb5>]
[<numb6>]

     (optional) - No Defaults

     The keyword allows the user to input some of the output from the log
     file generated by a previous run of ACORN. All useful information is
     flagged by the word INITIAL.
  <mesg>
            indicates which method was used to provide the initial output.
            It must be one of POSI, RATM, RROT, ROTF, TRAN and RTRA.

  <numb1>
            For POSI <numb1> defines the starting atom number in the XYZIN
            file. The foo_in.pdb file should be the same as that in the
            previous run.

  <numb1> <numb2> <numb3>
         For RROT, ROTF, TRAN and RTRA these define the Eulerian angles
         ALPHA, BETA and GAMMA.
         For RATM these are the fractional coordinates X_f, Y_f and Z_f.

  <numb1> <numb2> <numb3> <numb4> <numb5> <numb6>
         FOR TRAN and RTRA these define the Eulerian angles and the
         fractional translation. ALPHA, BETA and GAMMA Tx Ty Tz .

  Default: Do not use the results from previous run of ACORN.

    Examples:
   INITIAL TRAN 117.07 48.00 141.00 0.05 0.00     0.19   !! ALPHA BETA
GAMMA Tx Ty
 Tz
or
   INITIAL RATM 0.27304  0.09822   0.62551               !! X_f   Y_f    Z_f


 Miscellaneous Rarely used Keywords:

 LABOUT <program label>=<file label>...

  (optional)

  This keyword allows the user to assign their own labels for the final
  phase and weight written to the output file foo_out.mtz. It is useful
  if you want to restart ACORN to test a different starting model; the
  output phases can be grouped in the same mtz file. All columns in the
  input file foo_in.mtz will be copied to the output file foo_out.mtz.
  The following <program label>s can be assigned:
 EOEXT PHIOUT WTOUT ECOUT
 EOEXT E value for observed reflections plus extended reflections.
 PHIOUT The final phases from the last cycle of DDMK.
 WTOUT The final weights from the last cycle of DDMK.
 ECOUT Map coefficients from the last cycle of DDMK.

  Example: Use labels PHIOUTse17 and WTOUTse17 instead of default PHIOUT
  and WTOUT in foo_out.mtz.
 LABO PHIOUT=PHIOUTse17 WTOUT=WTOUTse17

 CONTENT <symbol1> <number> <symbol2> <number> ...

  (optional) - Default: ACORN estimates the numbers for elements C, N, O
   and S assuming the molecule is a protein and the solvent content is
   50%.

   NB1: It is only used for the Sayre Refinement of phases.

   NB2: It takes no account of anomalous signal.

   For small molecules or if there is some unusual feature such as a Fe-S
   cluster in a small protein it might be sensible to specify the
contents
   more precisely.
   <symbol>
          element symbol.
   <number>
          number of <symbol> in UNIT CELL.

   Example: To use ACORN to solve rubredoxin.
  CONT C 256 N 61 O 88 S 5 FE 1

  TITLE <title>

   (optional)

   80 character title to replace old title in MTZ file.

  GRID <grid>

   (optional) - Default: <grid> = 0.3333 Å

   A factor in Å controlling the sampling along cell edge for FFT.

   Example: Use 0.5 Å grid for speed up ACORN process, but lose the
   accuracy.
  GRID 0.5

  SEED <iseed>

   (optional) - Default: <iseed> = 1

   Integer seed for random number generater. This keyword allows the user
   to obtain a different set of random numbers.

   Example: To obtain second set of random numbers.
  SEED 2

  END

   of input. If present, this must be the last keyword.

  Keywords for ACORN-MR to do fragment selection and molecular
replacement
  searches:

   For each case ACORN tests many solutions by first calculating the CC
   for a given percentage of all reflections, to a limited resolution.
   These are sorted and for the top 1000 solutions, the CC is
recalculated
   for all reflections for the full resolution range. The best 100 of
   these solutions are used as starting points for further refinement.

     ROTF, RROT, RTRA, TRAN, SOLUTION.

  ROTF [<step>] [<percentage>] [<resoR>]

   (optional) - Default: <step> = 3.0; <percentage> = 20%; <resoR> =
   <res_high>

   The rotation function.

   <step>
             The step size of rotation in degrees for Eulerian angles ALPHA,
             BETA and GAMMA.

   <percentage>
          <percentage>% of reflections to be used in first stage of ROTF.

   <resoR>
             The resolution limit for the first stage of ROTF.

   In the first stage of ROTF ACORN will rotate the model <step> degrees
   at a time and calculate the CC for each step for <percentage>% of the
   reflections to a resolution of <resoR>. The CCs are then recalculated
   with all data to the full resolution range for the best 1000
solutions.
   These are again ranked according to CC and translation function
   searches done for a chosen rotation solution specified by <nsrot> (see
   TRAN). The default is to use the top solution only.

   Example: Use 2.0 degrees rotation step with 100% reflections in 2.0 Å
   resolution in first stage.
  ROTF 2.0 100.0 2.0

  RROT [<nrot>] [<percentage>] [<resoR>]

   (optional) - Default: <nrot> = 50000; <percentage> = 20%; <resor> =
   <res_high>

   The random rotation function.

   <nrot>
             The number of sets of random orientations.

   <percentage>
          <percentage>% of reflections to be used in first stage of RROT.

   <resoR>
             The resolution limit for the first stage of RROT.
   ACORN will generate <nrot> sets of random orientations rather than
   doing a systematic search.

   Example: Generate 10000 random orientations and check the CC for 100%
   of reflections to 2.0 Å resolution in first stage.
  RROT 10000 100.0 2.0

  TRAN [<nsrot>]

   (optional) - Default: <nsrot> = 1

   The translation function.

   <nsrot>
             The solution number from the results of rotation function
             (maximum 50).

   ACORN will carry out translational searches for <nsrot> results of
   rotation function using FFT techniques based on fitting between
   observed and calculated intensities. Then CCs for structure factors
are
   calculated and the final solutions are sorted on CCs. The best 1000
   solutions are saved and ACORN-PHASE will refine the phases according
to
   this order.

   Example: Use 10 solutions from rotation function.
  TRAN 10

  RTRA [<ntran>] [<percentage>] [<nsrot>]

   (optional) - Default: <ntran> = 50000; <percentage> = 20%; <nsrot> = 1

   The random translation function.

   <ntran>
             The number of sets for random shifts on X, Y and Z.

   <percentage>
          <percentage>% of reflections to be used in first stage of RTRA.

   <nsrot>
             The solution No. from the results of rotation function.

   ACORN will generate and rank <ntran> sets of random translation shifts
   for <nsrot>th solution from the rotation function. ACORN-PHASE will
   refine the phases according to the final order.

   Example: Generate 5000 sets of random shifts using 10% reflections for
   solution 2 from rotation function.
  RTRA 5000 10.0 2

  SOLUTION <nset> <alpha> <beta> <gamma> [<X_f>] [<Y_f>] [<Z_f>]
    (optional)

    The keyword allows the user to input the results of AMoRe to generate
a
    starting fragment. The foo_in.pdb, to which the rotation and
    translations are applied must be the XYZOUT produced by the AMoRe
    TABFUN.

    This is NOT recommended. A better procedure is to generate the output
    model from AMoRe or MOLREP, then input this as foo_in.pdb, using the
    ACORN-PHASE option NAFRAG ALL.

    The lines starting with the word SOLUTION in the .log or .mr files can
    be included in the ACORN script.

    <nset>
             set number.

    <alpha> <beta> <gamma>
           Eulerian angles of rotation function.

    <X_f> <Y_f> <Z_f>
           shifts from translation function in fractions of the observed
           unit cell edges.

    Default: Do not use AMoRe result.

     Example: Use one solution from AMoRe.
    SOLUTIONTF1_1   1 271.99    90.00   35.68   0.4500   0.0000   0.2794

    Keywords for ACORN-PHASE:

      CUTDDM, CCFINISH, PSFINISH, MAXSET, NTRY, NCDDM, NCSER, SUPP, ENHS,
      RADIUS, SOLVENT, DDMK, CCDDM1.

    CUTDDM <cutd>

    (optional) - Default: <cutd> = 3.0

   The factor to select the upper cut off value for density during the
DDM
   cycles.

   The upper cut off is set to <ncycle>*<cutd>*<sigro> for first 5
cycles,
   where
   <ncycle>
           is the cycle number of DDM.
   <sigro>
           is the standard deviation of the density map.

    and for subsequent cycles is held as 5*<cutd>*<sigro>. The final upper
    cut off value will be not less than 0.1*<nct>*<romax> and not greater
    than 0.8*<romax> where <romax> is the maximum density in the map and
   <nct> is the cycle number in each try.

   When there are some atoms much heavier than others, and especially
when
   searching for sub-structures with a variety of atom types, it may be
   necessary to increase <cutd>. However for structures where the atom
   types are all more or less the same, the default value is appropriate.

   Example: Set the upper cut off factor to 5.0.
  CUTD 5.0

  CCFINISH <ccfinish>

   (optional) - Default: <ccfinish> = value determined by the ACORN.

   If CC is greater than <ccfinish> at the end of refinement pass, ACORN
   will output the refined phases and weights for all the reflections,
   then stop.

   Example: ACORN will stop at CC greater than 0.25.
  CCFIN 0.25

  PSFINISH <psfinish>

   (optional) - Default: <psfinish> = 0.5 degrees

   If the phase shift between two consecutive cycles of DDM is less than
   <psfinish> the DDM try will finish and ACORN-PHASE will go to the next
   step if any.

   Example: Set the phase shift between two cycles to 0.8 degrees.
  PSFIN 0.8

  MAXSET <maxset>

   (optional) - Default: <maxset> = 100

   The number of sets of initial phases for ACORN-PHASE to refine. The
   maximum number is 1000.

   Example: Refine 500 sets of initial phases.
  MAXSET 500

  NTRY <ntry>

   (optional) - Default: <ntry> = 10

   The number of tries to cycle through DDM, ENHS and SER phase
refinement
   for each set of initial phases. The maximum number is 500. In each try
   ACORN-PHASE will combine the procedures DDMK and SER for the number of
   cycles specified in NCDDM and NCSER or one cycle of enhancement ENHS.

   If the average phase shift between two cycles is less than <psfinish>
   (see PSFINISH) or if the CC is not increasing after 5 cycles the try
   will be terminated, and the procedure will go on to the next try.
ACORN
   will stop if the CC is greater than <ccfinish> (see CCFINISH).

   Example 1: Use 8 tries with default values for ENHS, NCSER and NCDDM.
  NTRY 8

   which is the same as
  NTRY 8
  ENHS    0   0   0   0   1   1   1   1
  NCSER   0   2   2   2   0   0   0   0
  NCDDM 500 500 500 500 500 500 500 500

   Example 2: If user wants to do 2 cycles of SER and 200 cycles of DDM
   for the first try and one cycle of SER and 300 cycles of DDM for the
   other 9 tries. When SER is used in a try then ENHS will be set to 0
for
   this try. Then
  NTRY 10
  NCSER   2   1   1   1   1   1   1   1   1   1
  NCDDM 200 300 300 300 300 300 300 300 300 300

  NCSER <nc01> [<nc02>] ... [<nc500>]

   (optional) - Default: <nc01> <nc02> ... <nc500> = 0 2 2 2 0 0 ... 0 if
   the number of atoms in the fragment less then 50. Otherwise Sayre
   Equation Refinement will not be used.

   The maximum number of cycles in each try for Sayre Equation
Refinement.

   <nc01> <nc02> ... <nc500>
          number of cycles.

   Example: Use 2 cycles of SER in first try and one cycle of SER for the
   second and third try.
  NTRY 3
  NCSER 2 1 1

  NCDDM <nc01> [<nc02>] ... [<nc500>]

   (optional) - Default: <nc01> <nc02> ... <nc500> = 500 500 ... 500

   The maximum number of cycles in each try for Dynamic Density
   Modification.

   <nc01> <nc02> ... <nc500>
          number of cycles.

   Example: Use 50 cycles of DDM for the first three tries and 500 cycles
   of DDM for the fourth try.
  NTRY 4
  NCDDM 50 50 50 500
     SUPP <nsup>

     (optional) - Default: ACORN determines if the Patterson superposition
     function is used or not.

     Use the Patterson superposition function to improve the initial phases
     before phase refinement by SER and DDM.

     User can set <nsup> = 0 not to use SER or <nsup> = 1 to use SER.

      Example: Use the Patterson superposition function.
     SUPP 1

     DDMK <nc01> [<nc02>] ... [<nc500>]

     (optional) - Default: ACORN will use DDM0 first in each try. When CC
is
     greater than <ccddm1> DDM1 will be used. When CC is greater than
     <ccddm2> DDM2 will be used. See CCDDM.

     There are three kinds of map coefficients used in DDM procedure:

       <nc01>=0 --- DDM0: Wt*Eo for the observed reflections and Wt*Ex for
     the extended reflections.

       <nc01>=1 --- DDM1: Wt*(2*Eo-Ec) for the observed reflections and
     Wt*(2*Ex-Ec) for the extended reflections.

     <nc01>=2 --- DDM2: 2*M*Eo-SigmaA*Ec for the observed reflections and
   2*M*Ex-SigmaA*Ec for the extended reflections. where Eo - the observed
   normalized structure factors. Ex - the extended normalized structure
   factors (Ex=1.0). Ec - the calculated normalized structure factors
from
   a fragment or a modified map. M - a figure of merit from SigmaA.

      Example: Use DDM0 for the first 5 tries and DDM1 for try 6 to 9. DDM2
      for try 10.
     NTRY 10
     DDMK 0 0 0 0 0 1 1 1 1 2

     CCDDM <ccddm1> <ccddm2>

     (optional) - Default: <ccddm1> = 0.12, <ccddm2> = 0.20.

     If CC is greater than <ccddm1> ACORN will use DDM1 automatically with
     default DDMK. If CC is greater than <ccddm2> ACORN will use DDM2
     automatically with default DDMK.

      Example: ACORN will use DDM1 at CC greater than 0.10 and DDM2 at CC
      greater than 0.15 with default DDMK.
     CCDD 0.10 0.15

     ENHS <nc01> [<nc02>] ... [<nc500>]
   (optional) - Default: <nc01> <nc02> ... <nc500> = 0 1 ... 1

   <nc01>=1 means using weak density enhancement in cycle 1 for each try.
   The enhancement will not be used if the Sayre Equation Refinement is
   used.

   Example: Use two cycles of SER for try 2 to 5 and ENHS for next 5
   tries.
  NTRY 10
  ENHS 0 0 0 0 0 1 1 1 1 1
  NCSER 0 2 2 2 2 0 0 0 0 0

  RADIUS <radius>

   (optional) - Default: <radius> = 4.0 Å

   The radius value used to calculate envelop.

   Example: ACORN will use 5.0 Å of radius to calculate envelope.
  RADI 5.0

  SOLVENT <solvent>

   (optional) - Default: <solvent> = 0.5

   The ratio of solvent region.

   Example: ACORN will set 45% as solvent region to calculate envelope.
  SOLV 0.45

INPUT AND OUTPUT FILES

   The input files are the keyword file, a standard MTZ reflection data
   file and a PDB file containing a fragment if needed.

   Input:

   HKLIN
             input data file(MTZ).
   XYZIN
             input fragment file(PDB)

   Output:

   HKLOUT
             output data file(MTZ).

   Here are the definitions for the labels:

   Name Item
   H, K, L Miller indices.

   E E-values (normalized structure factors).
   FP Observed structure factors. SIGFP Sigma of FP. PHIN Known phases.
   WTIN Weights of known phases. FCIN Calculated magnitudes with the
known
   phases.

   EOEXT E values for observed and extended reflections. PHIOUT New
phases
   from last cycle of the best set. WTOUT Weights from last cycle of the
   best set. PHIOUT Map coefficients from last cycle of DDM0, DDM1 or
   DDM2.

PRINTER OUTPUT

     The printed output starts with details from the input keyword data
     lines. Then information from the input MTZ file follows. An error
     message will be printed out if any illegal input in the keyword data
     lines has been found and the program will stop.

EXAMPLES

      * Example 1: Use a constellation of correctly placed atoms as the
        starting point.
      * Example 2: Use a constellation of correctly placed atoms as the
        starting point.
      * Example 3: Use a fragment already positioned by some other MR
        procedure (e.g. AMoRe).
      * Example 4: Test for the best result from 10 possible heavy atoms.
      * Example 5: Use a randomly placed single atom as a starting point
        for a complete structure solution.
      * Example 6: Determine the position of heavy atoms in a protein
        structure from the anomalous and isomorphous differences.
      * Example 7: Use a randomly placed single atom as a starting point
to
       determine the position of the sub-structure from both the
anomalous
       differences.
     * Example 8: Solve a small molecular structure.
     * Example 9: Use standard alpha helices as search models for a
       complete molecular replacment (MR) search.
     * Example 10: Use standard alpha helices as search models for random
       MR search.
     * Example 11: Use a fragment from a similar structure for MR search.
     * Example 12: Use externally determined phases and weights as a
       starting point.
     * Example 13: Restart using results from previous run of ACORN.
     * Example 14: Use the results from AMoRe given as Euler angles and
       translation components to position the model atoms correctly.
     * Example 15: Use all extended reflections in the file and start
from
       a heavy atom.
     * Example 16: Use the extended reflections within 50.0 to 1.0 Å and
       start from molecular replacement model.
     * Example 17: Use the extended reflections within 50.0 to 1.0 Å and
       start from experimental phases.
  Example 1:

   This example uses the two known Zn atom positions which are in the
file
   $HOME/test-zn.pdb to calculate the starting phases then refines them
by
   500 cycles of DDM (default for ACORN-PHASE): Since the Zn atoms are
   much heavier than the protein atoms, the density CUToff is set higher
   than the default.
#!/bin/csh -f
#
acorn \
hklin $HOME/test.mtz \
hklout $SCRATCH/test-acorn.mtz \
xyzin $HOME/test-zn.pdb \
<< eof

!General keywords:
TITLE   Start from input ZN position(s).
LABI E=EO FP=FP SIGFP=SIGFP

!Keywords for ACORN-MR:
POSI 1
CUTD 5.0

END
eof

  Example 2:

   This example uses the two known S atom positions which are in the file
   $HOME/sulphurs.pdb to calculate the starting phases then refines them
   by 500 cycles of DDM (default for ACORN-PHASE):
#!/bin/csh -f
#
acorn \
hklin $HOME/test.mtz \
hklout $SCRATCH/test-acorn.mtz \
xyzin $HOME/sulphurs.pdb \
<< eof

!General keywords:
TITLE   Start from input ZN position(s).
LABI E=EO FP=FP SIGFP=SIGFP

!Keywords for ACORN-MR:
POSI 1

END
eof

  Example 3:
   This example uses a fragment in the correct orientation and position
   found by AMoRe to calculate a set of initial phases. The phases are
   refined, first with Patterson superposition then with 3 tries each
with
   2 cycles of SER and 200 cycles of DDM:
#!/bin/csh -f
#
acorn \
hklin $HOME/test.mtz \
hklout $SCRATCH/test-acorn.mtz \
xyzin $HOME/solution-amore-pdbset.pdb \
<< eof

!General keywords:
TITLE   Start from a fragment positioned by AMoRe.
LABI E=EO FP=FP SIGFP=SIGFP

!Keywords for ACORN-MR:
POSI 1
!NAFRAG ALL

!Keywords for ACORN-PHASE:
SUPP 1
NTRY 3
NCSER 2 2 2
NCDDM 200 200 200

END
eof

  Example 4:

   This example calculates the CC of each atom from 10 possible Selenium
   atoms and refines the best set of the phases, ie that with the largest
   CC, using only DDM (default for ACORN-PHASE):
#!/bin/csh -f
#
acorn \
hklin $HOME/test.mtz \
hklout $SCRATCH/test-acorn.mtz \
xyzin $HOME/test-10Se.pdb \
<< eof

!General keywords:
TITLE   Start from the best Selenium atom from 10 positions.
LABI E=EO FP=FP SIGFP=SIGFP

!Keywords for ACORN-MR:
NAFRAG 1
POSI 10

!Keywords for ACORN-PHASE:
MAXSET 1
END
eof

  Example 5:

   This example can be used to place a sub structure, or solve a
   macro-molecular structure which contains calculates the CC for 5000
   randomly positioned "single atom fragments" for 20% of reflections
(the
   default) and sorts them on CC. The top 1000 sets are selected to
   re-calculate the full CC for all reflections which are again sorted.
   Then the best MAXSET (default 100) phase sets are refined.
#!/bin/csh -f
#
acorn \
hklin $HOME/test.mtz \
hklout $SCRATCH/test-acorn.mtz \
<< eof

TITLE   ACORN willl use 5000 sets of one random atom.
LABI E=EO FP=FP SIGFP=SIGFP

RATM 5000

END
eof

  Example 6:

   This example is to find the Selenium atoms using the estimate of the
   sub-structure amplitude generated from the MAD measurements by REVISE.
   The keyword CONTENT indicates that there are 80 Selenium atoms in the
   unit cell and the resolution is cut to use only reflections from 10.0
   to 3.5 Å. The keywords NSTR and NWEA are used to select 800 strong and
   400 weak reflections. THE CC for 10000 sets of single randomly placed
   atom fragments are checked with 20% of the reflections and the initial
   phases for the top 100 sets are refined. There are 20 tries with the
   default NCSER and NCDDM:
#!/bin/csh -f
# Use REVISE to generate FM
#
acorn \
HKLIN $HOME/test-mad-revise.mtz \
hklout $SCRATCH/test-acorn.mtz \
<< eof

!General keywords:
TITLE    to determine Selenium atoms.
LABI E=EM_RE FP=FM_RE SIGFP=SFM_RE
cont SE 80
reso 10.0 3.5
nstr 800
nwea 400
ratm 10000

! After the Random atom search ACORN will refine the phases for the
best 100 s
olutions
! the default value for MAXSET is 100.
end
eof

  Example 7:

   This example is to find the Selenium atoms using the estimate of the
   sub-structure amplitude taken from the Peak anomalous difference. The
   keyword CONTENT indicates that there are 80 Selenium atoms in the unit
   cell and the resolution is cut to use only reflections from 10.0 to
3.5
   Å. Anomalous differences greater than 30 ( These are on an arbitrary
   scale and the cutoff value ischosen by looking at the loggraph
analyses
   from SCALEIT) and weak F+ and F- are excluded. The keywords NSTR and
   NWEA are used to select 800 strong and 400 weak reflections. THE CC
for
   10000 sets of single randomly placed atom fragments are checked with
   20% of the reflections and the initial phases for the top 100 sets are
   refined. There are 20 tries with the default NCSER and NCDDM:
#!/bin/csh -f
#
ecalc \
HKLIN $HOME/test-sad-data.mtz \
HKLOUT $HOME/test-sad-E.mtz \
<< eof
LABI FPH=F_peak(+) SIGFPH=SIGF_peak(+) FP=F_peak(-) SIGFP=SIGF_peak(-)
LABO E=Esad
EXCL SIGPH 3.0 SIGP 3 DIFF 30
END
eof
#
acorn \
HKLIN $HOME/test-sad-E.mtz \
hklout $SCRATCH/test-acornsadE.mtz \
<< eof

!General keywords:
TITLE    to determine Selenium atoms.
LABI E=Esad FP=F_peak SIGFP=SIGF_peak
cont SE 80
reso 10.0 3.5
nstr 800
nwea 400

!Keywords for ACORN-MR:
ratm 10000

!Keywords for ACORN-PHASE:
! The Random atom search will refine the phases for the best 100
solutions
! the default value for MAXSET is 100.
CCFIN 0.1 ! The final correlation coefficient will be lower for SAD
terms.
end
eof

  Example 8:

   This example solves a small molecular structure. The keywords RESO and
   GRID are needed for small molecule determination. The CC for 2000 sets
   of single randomly placed atom fragments are checked with all the data
   and the top 100 sets of the initial phases refined by 2 cycles of SER
   and 300 cycles of DDM:
#!/bin/csh -f
#
acorn \
HKLIN $HOME/test.mtz \
hklout $SCRATCH/test-acorn.mtz \
<< eof

!General keywords:
TITLE    to solve a small molecular structure.
LABI E=EO FP=FP SIGFP=SIGFP
RESO 50.0 0.8
GRID 0.3

!Keywords for ACORN-MR:
RATM 2000 100.0

!Keywords for ACORN-PHASE:
NCSER 2
NCDDM 300

end
eof

  Example 9:

   This example uses 50 atoms (10 residues) from the library idealised
   alpha helix for a MR search with the default parameters. ACORN-PHASE
   will refine the phases from the top 100 sets of positioned alpha
   helices by DDM only:
#!/bin/csh -f
#
acorn \
hklin $HOME/test.mtz \
hklout $SCRATCH/test-acorn.mtz \
xyzin $CLIBD/fraglib/theor-helix-70.pdb \
<< eof

!General keywords:
TITLE   Start from standard alpha helices.
LABI E=EO FP=FP SIGFP=SIGFP

!Keywords for ACORN-MR:
NAFRAG 50
ROTF
TRAN

END
eof

     Example 10:

   This example is the same as example 9, but uses random rotation and
   random translation starting values to select the 100 most likely
   positions for the alpha helix.
#!/bin/csh -f
#
acorn \
hklin $HOME/test.mtz \
hklout $SCRATCH/test-acorn.mtz \
xyzin $CLIBD/fraglib/theor-helix-70.pdb \
<< eof

!General keywords:
TITLE   Start from standard alpha helices.
LABI E=EO FP=FP SIGFP=SIGFP

!Keywords for ACORN-MR:
NAFRAG 50
RROT
RTRA

END
eof

     Example 11:

     This example uses a suitable fragment for a MR search. The rotation
     function is first calculated with a step size of 3.0 degrees for 20%
of
   the reflections to 2.0 Å resolution. The best orientation is selected,
   and 50000 trials of random translational shifts are evaluated, again
   for 20% of the reflections to 1.0 Å resolution. ACORN-PHASE will
refine
   the top 100 solutions for the translation search by DDM(default for
   ACORN-PHASE):
#!/bin/csh -f
#
acorn \
hklin $HOME/test.mtz \
hklout $SCRATCH/test-acorn.mtz \
xyzin $HOME/test-other-similar.pdb \
<< eof
!General keywords:
TITLE   Start from other similar fragment.
LABI E=EO FP=FP SIGFP=SIGFP

!Keywords for ACORN-MR:
ROTF 3 20.0 2.0
RTRA 50000 20.0 1

END
eof

  Example 12:

   This example uses known phases with input magnitudes and assign new
   labels for the final output phases and weights. ACORN-PHASE will use
   500 cycles of DDM for the first try then one cycles of ENH and 500
   cycles of DDM for the second try (default ENHS and NCDDM):
#!/bin/csh -f
#
acorn \
hklin $HOME/test.mtz \
hklout $SCRATCH/test-acorn.mtz \
<< eof

!General keywords:
TITLE   Start from input known phases and magnitudes.
LABI E=EO FP=FP SIGFP=SIGFP PHIN=AC FCIN=FCcal
LABO PHIOUT=NEWPHASE WTOUT=NEWT

!Keywords for ACORN-PHASE:
NTRY 2
ENHS 0 1
NCDDM 500 500
END
eof

  Example 13:

   This example takes 9 solutions from a previous run of ACORN-MR for
   positoning standard alpha helices. The input rotation angles and
   translational shifts are applied to the first 50 atoms of
   $CLIBD/fraglib/theor-helix-70.pdb the phases generated from these
   fragments are refined by DDM, the default:
#!/bin/csh -f
#
acorn \
hklin $HOME/test.mtz \
hklout $SCRATCH/test-acorn.mtz \
xyzin $CLIBD/fraglib/theor-helix-70.pdb \
<< eof

!General keywords:
TITLE   Use results from previous run of ACORN.
LABI E=EO FP=FP SIGFP=SIGFP
!Keywords for ACORN-MR:
NAFRAG 50
 INITIAL TRAN   117.07      48.00    141.00    0.04537   0.00000   0.19480
 INITIAL TRAN   117.07      48.00    141.00    0.04331   0.00000   0.19480
 INITIAL TRAN   117.07      48.00    141.00    0.04537   0.00000   0.19784
 INITIAL TRAN   117.07      48.00    141.00    0.04331   0.00000   0.19784
 INITIAL TRAN   117.07      48.00    141.00    0.11136   0.00000   0.09740
 INITIAL TRAN   117.07      48.00    141.00    0.10311   0.00000   0.05174
 INITIAL TRAN   117.07      48.00    141.00    0.15467   0.00000   0.40177
 INITIAL TRAN   117.07      48.00    141.00    0.23716   0.00000   0.31959
 INITIAL TRAN   117.07      48.00    141.00    0.08043   0.00000   0.49308

END
eof

  Example 14:

   This example tests 7 solutions from AMoRe. AMoRe has been used with
   input Es, and the TABLE structure factors have also been normalised
   (see AMoRe documentation). The input rotation angles and translational
   shifts are applied to the XYZOUT PDB file generated in the TABFUN
stage
   by AMoRe and the resultant phases refined by DDM, the default:
#!/bin/csh -f
#
acorn \
hklin $HOME/test.mtz \
hklout $SCRATCH/test-acorn.mtz \
xyzin $HOME/amore-TABFUN-trial.pdb \
<< eof

!General keywords:
TITLE   Use the solutions from AMoRe.
LABI E=EO FP=FP SIGFP=SIGFP

!Keywords for ACORN-MR:
SOLUTIONTF1_4   1 272.09     90.00     35.82   0.0312    0.0000    0.0268
SOLUTIONTF1_5   1 269.00     90.00    214.85   0.4688    0.0000    0.4732
SOLUTIONTF1_2   1 271.38     74.93     28.08   0.4125    0.0000    0.4911
SOLUTIONTF1_18 1 346.95      45.50    205.48   0.2000    0.0000    0.4464
SOLUTIONTF1_1   1   57.94    82.77    157.51   0.2250    0.0000    0.4464
SOLUTIONTF1_19 1 241.70      39.54     77.96   0.1125    0.0000    0.0446
SOLUTIONTF1_14 1    60.65    12.39    109.53   0.4000    0.0000    0.4286

END
eof

  Example 15:

   This example uses the observed reflections within 9.0 to 1.55 Å plus
   all the extended reflections in the file $HOME/test.mtz and the one
   known Zn atom position which is in the file $HOME/test-zn.pdb to
   calculate the starting phases then refines them by one cycle of SUPP
   and 10 tries with SER from try 2 to 4 and ENHS for rest of tries. DDM1
   will be used for try 5 to 9 and DDM2 will be used for final try. Since
   the Zn atoms are much heavier than the protein atoms, the density
   CUToff is set higher than the default.
#!/bin/csh -f
#
acorn \
hklin $HOME/test.mtz \
hklout $SCRATCH/test-acorn.mtz \
xyzin $HOME/test-zn.pdb \
<< eof

!General keywords:
TITLE   Start from input ZN position(s).
LABI E=EO FP=FP SIGFP=SIGFP

!Keywords for select reflections:
RESO 9.0 1.55

!Keywords for ACORN-MR:
POSI 1

!Keywords for ACORN-PHASE:
CUTD 5.0
SUPP 1
NTRY 10
NCSER 0 2 2 2
DDMK 0 0 0 0 1 1 1 1 1 2

END
eof

  Example 16:

   This example uses the observed strong E>0.8 within 20.0 to 1.65 Å plus
   the extended reflections wihtin 50.0 to 1.0 Å in the file
   $HOME/test.mtz and the MR model from MOLREP which is in the file
   $HOME/test-molrep.pdb to calculate the starting phases then refines
   them by 150 tries with default ENHS and DDMK values. Set 45% of the
   solvent region by SOLV 0.45.
#!/bin/csh -f
#
acorn \
hklin $HOME/test.mtz \
hklout $SCRATCH/test-acorn.mtz \
xyzin $HOME/test-molrep.pdb \
<< eof

!General keywords:
TITLE   Start from input MOLREP model.
LABI E=EO FP=FP SIGFP=SIGFP

!Keywords for select reflections:
RESO 20.0 1.65
EXTEND 50.0 1.0
ESTRO 0.8

!Keywords for ACORN-MR:
POSI 1

!Keywords for ACORN-PHASE:
SOLV 0.45
NTRY 150

END
eof

  Example 17:

   This example uses the observed strong E>0.8 within 10.0 to 1.50 Å plus
   the extended reflections wihtin 50.0 to 1.0 Å and the experimental
   phases from SAD data in the file $HOME/test.mtz and then refines them
   by default values. Set 45% of the solvent region by SOLV 0.45.
#!/bin/csh -f
#
acorn \
hklin $HOME/test.mtz \
hklout $SCRATCH/test-acorn.mtz \
<< eof

!General keywords:
TITLE   Start from input experiment phases with weights.
LABI E=EO FP=FP SIGFP=SIGFP PHIN=PHI_Se16 WTIN=WT_Se16

!Keywords for select reflections:
RESO 10.0 1.50
EXTEND 50.0 1.0
ESTRO 0.8

!Keywords for ACORN-PHASE:
SOLV 0.45

END
eof

AUTHOR

   Yao Jia-xing
   Email: yao@ysbl.york.ac.uk

REFERENCES

      1. Foadi,J., Woolfson,M.M., Dodson,E.J., Wilson,K.S., Yao Jia-xing
and
         Zheng Chao-de (2000) Acta. Cryst. D56, 1137-1147.
      2. Yao Jia-xing (2002) Acta. Cryst. D58, 1941-1947.
      3. Yao Jia-xing, Woolfson,M.M., Wilson,K.S. and Dodson,E.J. (2002) Z.
         Kristallogr. 217, 636-643.
    4. Yao Jia-xing, Woolfson,M.M., Wilson,K.S. and Dodson,E.J. (2005)
       Acta. Cryst. D61, 1465-1475.

SEE ALSO

     AMoRe DM PDBSET UNIQUE

				
DOCUMENT INFO
Shared By:
Categories:
Tags: acorn
Stats:
views:25
posted:10/28/2012
language:English
pages:32