AMoRe
- Jorge Navaza's state-of-the-art molecular replacement package, updated February 1999.
The SORTFUN and TABFUN output are NOT compatible with the old version.
New keyword CRYSTAL for TABFUN.
[Keyworded input]
AMoRe includes routines to run a complete molecular replacement.
As well as carrying out ROTATION and TRANSLATION searches against various targets, and doing RIGID BODY REFINEMENT, there are routines to reformat the observed data from the new crystal form, and to generate and tabulate structure factors from the model in a large P1 cell. See reference [1].
The steps are usually carried out in the following order:
AMoRe requires a LOT of memory and this may cause problems on some machines. However this new release is considerably less demanding than the older one (see Memory allocation).
The procedure is:
Expected Error in R factor with SCALE = 4 - 3 % Expected Error in R factor with SCALE = 3 - 9 % Expected Error in R factor with SCALE = 2 - 17 %You may need to generate tables for several models, e.g. for different domains. Up to four different table<i> files can be assigned during the translation search, and for rigid body refinement.
Runs the rotation function. Does the following four stages (they can be run separately but I can't think why..).
Keyword: GENERATE - calculates structure factors for model in a suitable cell, and packs them in the same format as the output of SORTFUN.
Keyword: CLMN - calculates spherical harmonics for crystal and models.
Keyword: ROTATE - calculates rotation function and finds many possible solutions by Patterson overlap.
Keyword: SHIFT - converts the Eulerian angle solutions determined for the model stored in XYZOUT<i> to give solutions to be applied to original MODEL.
This can be replaced by PDBSET; see example [1j].
Calculates the translation function using various target options.
Performs rigid-body refinement for any specified solution of the rotation or translation search, see reference [5].
Check that the CCs and RF_F have improved.
This works out the appropriate rotation and translation parameters to apply to the initial model (can also be done while running ROTFUN or FITFUN).
Some common errors:
The various data control lines are identified by keywords. Only the first 4 characters of a keyword are significant. Records may be continued across line breaks using & or - as the last character on the line to be continued. The available keywords are listed below grouped according to their function:
These call the appropriate procedures.
May be used for the given functions.
| Keyword | Used in |
|---|---|
| LABIN | SORTFUN |
| CRYSTAL | TABFUN, TRAFUN, FITFUN |
| MODEL | TABFUN |
| SAMPLE | TABFUN |
| GENERATE | ROTFUN |
| CLMN | ROTFUN |
| ROTATE | ROTFUN |
| SHIFT | ROTFUN, FITFUN, REORIENTATE |
| SOLUTION | TRAFUN, FITFUN |
| SYMMETRY | TRAFUN, FITFUN |
| REFSOLUTION | FITFUN |
| END |
These modify the following primary keywords. Most use sensible defaults.
| Keyword | Subsidiary Keywords |
|---|---|
| SORTFUN | RESOLUTION, MODEL |
| LABIN | FP=?? SIGFP=?? PHI=?? FOM=?? FC=?? PHIC=?? |
| TABFUN | NOROTATE, NOTRANSLATE, NOTAB, HKLOUT, SFOUT |
| MODEL | BTARGET, BREPLACE, BADD, NORMALISE |
| CRYSTAL | ORTH |
| SAMPLE | RESOLUTION, SCALE, SHANNON |
| ROTFUN | |
| GENERATE | RESOLUTION, CELL_MODEL |
| CLMN | CRYSTAL, MODEL, ORTH, FLIM, SHARP | BADD, RESOLUTION, SPHERE |
| ROTATE | CROSS | SELF, MODEL, BESLIM, STEP, PKLIM, NPIC, BMAX, LOCK |
| SHIFT | COM, EULER |
| TRAFUN | CB, CO, PT or PTF, HL, CC, NMOL, NCSTRANS, RESOLUTION, PKLIM, NPIC |
| SYMMETRY | |
| CRYSTAL | FLIM, ORTH, SHARP | BADD, RESOLUTION |
| SOLUTION | FIX |
| FITFUN | NMOL, RESOLUTION, ITER, CONV |
| CRYSTAL | FLIM, ORTH, SHARP | BADD, RESOLUTION |
| SYMMETRY | |
| REFSOLUTION | BF AL BE GA X Y Z |
| SOLUTION | |
| SHIFT | COM, EULER |
| REORIENTATE | |
| SHIFT | COM, EULER |
| SOLUTION |
This signals the beginning of Step_1 SORTFUN.
[Compulsory]
A line giving the names of the input data items to be selected followed by <program_label>=<file_label> assignments. Acceptable labels are:
FP SIGFP PHI [W] FC PHIC
FC PHIC must be assigned for structure factors input.
FP must be assigned for creating the list of observations.
If PHI and optionally W is assigned, W*FP and PHI are stored and can be used for phased translation searches.
Example:
LABIN FP=F [ SIGFP=SIGF or PHI=PHIexptl W=FOM]
LABIN FC=FC_domainA PHIC=PHIC_domainA
This signals the beginning of Step_2 TABFUN.
<i> is the model number and is followed by all information needed to work with the model. At least one model must be specified to get any output.
PLEASE NOTE that if all the B-factors are zero in your model, then <badd> MUST be set to a sensible positive value.
The coordinates written to XYZOUT will have the same B-factors as the input coordinates, but the table will be generated using the modified B-factors.
Examples:
MODEL 1 BTARGET 23.5 MODEL 1 BREPLACE 0 BADD -10
Optional.
Cell dimensions for observed data used to generate PDB style header for XYZOUT. The default is to use the TABFUN cell to generate the CRYST1 and SCALEi records.
Example:
CRYSTAL 112.32 112.32 85.14 90 90 120 ORTH 1
<i> is the model number and is followed by the sampling control parameters.
Example:
SAMPLE 1 RESO 3 SHANN 2.5 SCALE 4.0
This signals the beginning of Step_3 ROTFUN with subsequent keywords as follows.
<i> is the model number.
This routine calculates the model `structure factors' in a suitable P1
cell, and writes them in the same format as the SORTFUN output for the
crystal amplitudes. The file is assigned to HKLPCK1.
"This model cell needs to be chosen carefully. Ideally you need to use dimensions of Twice maximal distance from Centre of Mass + SPHERE_<Irmax> + a small safety term."She says always use a cubic cell because elongated cells can cause trouble.
{smallest box containing model} + {integration radius (<Irmax>)} + resolution(not necessarily cubic)
Example:
GENERATE RESO 20 3.2 CELL_MODEL 89 89 89
Calculates spherical harmonics for crystal and models.
Examples:
CLMN CRYSTAL RESO 20.0 4.0 SPHERE 30 -
ORTH 1 SHARP -10.0 FLIM 0.E0 1.E8
CLMN MODEL 1 RESO 20.0 4.0 SPHERE 30
This routine calculates the rotation function.
DC1(axis1)*DC1(axis2) + DC2(axis1)*DC2(axis2) + DC3(axis1)*DC3(axis2) = 0.0
Example
ROTA CROSS MODEL 1 [ BESLIMI 6 120 STEP 2.5 PKLIM 0.5 NPIC 100 LOCK 1 POLAR 54 45 180]
Reorientate stage. Moves Eulerian angle solutions determined for shifted model stored in XYZOUT<Model_number> to give solutions to be applied to original model. Needed if you want your solutions converted back to ones to apply to original coordinates.
Example
SHIFT 1 COM 17.3 -10.5 28.7 EULER 301.2 35.7 185.2
There are various translation function targets. Each takes each orientation solution in turn and searches for the NPIC "best" translational Xi Yi Zi for this orientation. Good solutions should give high correlation coefficients between FP and FC, and low Rfactors. Only one target can be specified for each run.
Each function tests each orientation solution in turn and searches for the best translational Xi Yi Zi for this orientation. Good solutions should give high correlation coefficients between FP and FC, and low Rfactors. For the first molecule all <Xi> <Yi> <Zi> belonging to the Cheshire cell are searched (see reference [7]). The Cheshire cell is the minimum volume which will allow a unique solution. For the first molecule it will be the cell which covers a volume from one possible origin to the next - you can usually see it by inspection of International Tables, e.g.: For P212121, the Cheshire cell is 0-0.5,0-0.5,0-0.5. For P21 the Cheshire cell is 0-0.5,any y,0-0.5. If you are searching for the NMOLth molecule of a set, the Cheshire cell will now be the whole primitive volume. You have assigned the origin by choosing the position of the first molecule, and the other molecules will have to be positioned relative to that choice.
A map of the Cheshire cell for each search is written to the file assigned to MAPOUT. N.B. the same file is used for all solutions - only the final one will be saved. If you wish to plot your best solution you will have to recalculate it.
Translation functions use a great deal of memory. The whole FFT transform is held in memory at once, and the calculation is done over a set of reciprocal lattice coefficients which can be twice the size of Hmax, Kmax, Lmax.
Example
TRAFUN CO NMOL 1 RESO 8 4 PKLIM 0.5 NPIC 10 NCStran 0.03 0.0 0.5
(Optional)
Spacegroup name or spacegroup number. It will default to that of the CRYSTAL data, picked up at the SORTFUN step. You may need to change it to test other possibilities; e.g. enantiomorphic spacegroups - P65 instead of P61. If you are not sure of your spacegroup, the translation function is a good way to distinguish the true spacegroup; e.g. you may need to test all possible orthorhombic possibilities; P222; P2 2 21; P2 21 2; P2 21 21; P21 2 2; P 21 2 21; P21 21 2; P 21 21 21; See example [1d], [1e].
(Optional)
Information used to modify the CRYSTAL amplitudes. See descriptions above for CLMN.
Example:
CRYSTAL ORTH 1 FLIMI 0.E0 1.E8 SHARP 0.0
SOLUTIONTF1 FIX 1 <alpha1> <beta1> <gamma1> <X1> <Y1> <Z1>followed by the set of possible rotation function solutions. Each rotation orientation is tested in turn with the previous input FIXed solution. If you want to test several translation solutions, you can repeat the FIX information, and again follow it with the set of possible rotation function solutions.
SOLUTIONTF1 FIX 1 <alpha1> <beta1> <gamma1> <X1> <Y1> <Z1> SOLUTIONTF2 FIX 1 <alpha2> <beta2> <gamma2> <X2> <Y2> <Z2>There is a limit of 99 (calculated as NMOL* Number_of_solutionrc) on the number of orientation solutions which can be included in one run. However there is no extra overhead in submitting several runs. This list should come last and is terminated by end-of-file or the keyword END.
Examples
SOLUTIONTF FIX 1 27.8 100.7 350.1 0.146 0.566 0.00 17.4 52.5 SOLUTIONRC 1 25.211 105.573 339.440
To extract the rotation information, `grep' (Unix) for `SOLUTIONRC' in the ROTFUN output. Edit the resulting list to include only those solutions you want to run the translation search on, and include them in the input data e.g. with `@<file>'.
If you are searching for the <nmol>th molecule of a set, you must FIX <nmol>-1 solutions and search for the <nmol>th one. You will probably have several sets of the fixed solutions to test, plus many possible orientation solutions.
FIXed solutions will be extracted from your previous TRAFUN log. They will be followed by the list of solutions to the Rotation function output by Step_3. Structure factors calculated from the FIXed solutions are added to those generated for search molecules.
To extract the information for FIXed, grep for `SOLUTIONTF'. You will need to sort these to find those with the highest correlation coefficients, and lowest Rfactors.
sort -r +8 -9 tra.list > tra_cc.list # sort on correlation coefficient. sort +9 -10 tra.list > tra_rf.list # sort on Rfactor
(Be careful to keep sets of solutions together!)
See the Unix plumbing in the example scripts, e.g., `auto-amore'.
This signals the beginning of Step_5 FITFUN which performs Rigid-body refinement. It minimises the sum over all hkl of ({Fo*exp(-Bs**2)}**2 - {k*Fc**2})**2 with respect to scale, B-factor and rotation and translation parameters.
Subsidiary words after FITFUN (many same as TRAFUN):
Example
FITFUN NMOL 3 RESO 20 4.5 ITER 10 CONV 1.E-3
(Optional)
Information used to modify the CRYSTAL amplitudes. See descriptions above for CLMN.
(Optional)
Spacegroup name or spacegroup number. It will default to that of the CRYSTAL data, picked up at the SORTFUN step. You may need to change it to test other possibilities; e.g. enantiomorphic spacegroups - P65 instead of P61.
Refinement to be done for any of temperature factor, alpha, beta, gamma, x, y, z. Remember - in polar spacegroups you cannot refine either y or z parameter for one solution. This defaults to sensible values for different space groups.
Optional: program chooses sensible defaults.
Example
REFSOL AL BE GA X Y Z BF
Examples
SOLUTIONTF 1 25.1 105.6 339.5 0.1139 0.5691 0.0000 SOLUTIONTF 1 27.6 100.6 350.3 0.1461 0.5716 0.6476 48 51 SOLUTIONTF 1 27.7 115.9 353.5 0.1439 0.6027 0.3584 49 54
This list is terminated by end-of-file or the keyword END.
This list of Eulerian angles and translations can be extracted from the log file and edited in here. To extract the information from the previous log file, grep for `SOLUTIONTF'. You will need to sort these to find those with the highest correlation coefficients, and lowest Rfactors as described in step_4a, and edit to include only those solutions you want to run the rigid body refinement on to include them in the input data.
Reorientate stage. Moves Eulerian angle solutions determined for shifted model stored in XYZOUT<i> to give solutions to be applied to original MODEL. Needed if you want your solutions converted back to ones to apply to original coordinates.
Example
SHIFT 1 COM 17.3 -10.5 28.7 EULER 301.2 35.7 185.2
This signals the beginning of Step_6 - reorientate stage. This step can be run as a standalone step or as part of ROTFUN or FITFUN. It moves Eulerian angle solutions determined for shifted model stored in XYZOUT<i> to give solutions to be applied to original MODEL. Needed if you want your solutions converted back to ones to apply to original coordinates.
Example
SHIFT 1 COM 17.3 -10.5 28.7 EULER 301.2 35.7 185.2
There may be up to 99 solutions given. This list is terminated by end-of-file or the keyword END.
Examples
SOLUTIONTF 1 25.1 105.6 339.5 0.1139 0.5691 0.0000 SOLUTIONTF 1 27.6 100.6 350.3 0.1461 0.5716 0.6476 43.5 46.5 SOLUTIONTF 1 27.7 115.9 353.5 0.1439 0.6027 0.3584 41.3 47.3
Must be last keyword. Used as termination for list of solutions.
The program has been made more memory-efficient, but still uses a lot, at several points a whole Fourier transform is held in memory. The defaults are estimated to allow the observed and tabulated structure factors to be stored. However if the estimate is too low it is able to use dynamic memory allocation; the amount to be allocated at runtime is parameterised by assigning values to logical names. There may be some trial and error involved in setting appropriate values.
If the allocation for an array isn't large enough, the program stops with a message which should indicate at least which parameter needs to be increased and, in most cases, to what value. If the message doesn't make it clear what needs to be increased, please report the fact. Using the keyword VERBOSE may give more indication. The current values are printed in the output (look for `Memory allocation'). They may be changed by giving the appropriate logical names an integer value (which represents the size of an array) in any of possible ways:
The last option may be most appropriate on a system with lots of memory to provide large defaults and the distributed default.def contains commented-out values for a `big' version used at York and Cambridge.
The convention is that the orthogonalised coordinates of "crystal 2" (usually the model) are rotated to overlap the orthogonalised coordinates of crystal 1.
i.e. [XO1] = [ROT] [XO2]
[YO1] [YO2]
[ZO1] [ZO2]
This means that axis permutations introduced by using NCODE = 2, 3 or 4 will result in apparently different solutions, although the effect on the fractional coordinates is the same.
In Polar angles:
If l m n are the direction cosines of the axis about which the rotation k = kappa takes place, and:
( l ) ( sin omega cos phi ) ( m ) = ( sin omega sin phi ) ( n ) ( cos omega )where omega is the angle the rotation axis makes to the ZO direction, and phi is the angle the projection of the rotation axis onto the XO-YO plane makes to the XO axis.
[ROT] = ( l**2+(m**2+n**2)cos k lm(1-cos k)-nsin k nl(1-cos k)+msin k ) ( lm(1-cos k)+nsin k m**2+(l**2+n**2)cos k mn(1-cos k)-lsin k ) ( nl(1-cos k)-msin k mn(1-cos k)+lsin k n*2+(l**2+m**2)cos k )Note that if omega = 0 or 180, then phi is indeterminate and is flagged as 999 in the SOLUTIONs output by AMoRe.
In Eulerian angles:
If a (alpha) represents a rotation about the initial ZO axis,
b (beta) represents a rotation about the new position of the YO axis, and
g (gamma) represents a rotation about the final ZO axis:[ROT] = ( cosa cosb cosg - sina sing -cosa cosb sing - sina cosg cosa sinb ) ( sina cosb cosg + cosa sing -sina cosb sing + cosa cosg sina sinb ) ( -sinb cosg sinb sing cosb )
orthogonalisation code NCODE = 1, orthogonal x y z along a,c*xa,c* (Brookhaven, default) = 2 b,a*xb,a* = 3 c,b*xc,b* = 4 a+b,c*x(a+b),c* = 5 a*,cxa*,c (Rollett)
The automated procedure to find 3 molecules for spmi. Usually this would be run from the interface but the command scripts are these. The space group is either P61 or P65.
Tabling run to generate structure factors from model;
Sorting run to reformat observed reflections;
Rotation Patterson search;
Translation search for one molecule in space group P61;
Translation search for one molecule in space group P65
(The rotation solutions are the same for either P61 or P65)The correlation coefficient are higher for the P65 spacegroup.
To make absolutely sure search for the 2nd molecule in both P61
and P65, but as expected P65 is much the better result.# #############
# tabling run:
# #############
#
# The B factor for the crystal obtained from the Wilson plot is 23.5
#
# TABFUN first rotates and shifts the model coordinates to the origin
# then produces a table of structure factors in a large unit cell:
#
# xyzout contains the rotated and shifted coordinates.
#
amore xyzin1 search.pdb
xyzout1 searchrot.pdb \
table1 search-sfs.tab << eof
TITLE : Produce table for MODEL FRAGMENT
VERBOSE
TABFUN
CRYSTAL 112.32 112.32 85.14 90 90 120 ORTH 1
MODEL 1 BTARGET 23.5
SAMPLE 1 RESO 2.5 SHANN 2.5 SCALE 4.0
eof
# ############
# sorting run:
# #############
# MTZ file contains cell and symmetry.
#
amore hklin spmi_trun.mtz
hklpck0 spmipch.hkl << eof
TITLE ** spmi packing h k l F for crystal**
SORTFUN RESOL 100. 2.5
LABI FP=F SIGFP=SIGF
eof
# ############
# roting run:
# ############
#
# straightforward rotation function.
#
amore table1 search-sfs.tab \
HKLPCK1 $CCP4_SCR/search.hkl \
hklpck0 spmipch.hkl \
clmn1 $CCP4_SCR/search.clmn \
clmn0 $CCP4_SCR/spmipch.clmn \
MAPOUT $CCP4_SCR/amore_cross.map << eof
ROTFUN
VERB
TITLE : Generate HKLPCK1 from MODEL FRAGMENT 1
GENE 1 RESO 100.0 3.0 CELL_MODEL 80 75 65
CLMN CRYSTAL ORTH 1 RESO 20.0 4.0 SPHERE 30
CLMN MODEL 1 RESO 20.0 4.0 SPHERE 30
ROTA CROSS MODEL 1 PKLIM 0.5 NPIC 100
eof
# #############################
# traing run: NMOL = 1 - P61
# #############################
#
amore table1 search-sfs.tab \
HKLPCK0 spmipch.hkl \
MAPOUT $CCP4_SCR/amore_transjunk1.map << eof
TRAFUN CB NMOL 1 RESO 8 4 PKLIM 0.5 NPIC 10
SYMM P61
VERB
TITLE : Translation function P61 - one molecule
SOLUTIONRC 1 25.211 105.573 339.440
SOLUTIONRC 1 27.757 100.743 350.082
SOLUTIONRC 1 27.939 115.792 353.601
SOLUTIONRC 1 27.596 60.308 43.149
SOLUTIONRC 1 38.604 77.537 160.999
SOLUTIONRC 1 16.079 130.379 261.311
SOLUTIONRC 1 7.264 66.987 88.523
SOLUTIONRC 1 4.345 82.989 95.253
SOLUTIONRC 1 26.903 76.829 37.613
SOLUTIONRC 1 1.477 33.145 73.636
SOLUTIONRC 1 42.057 104.775 163.088
SOLUTIONRC 1 0.492 90.289 275.552
SOLUTIONRC 1 53.344 135.528 269.211
SOLUTIONRC 1 34.118 74.264 244.711
SOLUTIONRC 1 42.237 147.472 263.153
SOLUTIONRC 1 33.968 5.665 291.432
eof
# #############################
# traing run: SYMMETRY P65 - same rotation solns
# #############################
#
amore table1 search-sfs.tab \
HKLPCK0 spmipch.hkl \
MAPOUT $CCP4_SCR/amore_transjunk5.map << eof
TRAFUN CB NMOL 1 RESO 8 4 PKLIM 0.5 NPIC 10
SYMM P65
VERB
TITLE : Translation function P65 - one molecule
SOLUTIONRC 1 25.211 105.573 339.440
SOLUTIONRC 1 27.757 100.743 350.082
SOLUTIONRC 1 27.939 115.792 353.601
SOLUTIONRC 1 27.596 60.308 43.149
SOLUTIONRC 1 38.604 77.537 160.999
SOLUTIONRC 1 16.079 130.379 261.311
SOLUTIONRC 1 7.264 66.987 88.523
SOLUTIONRC 1 4.345 82.989 95.253
SOLUTIONRC 1 26.903 76.829 37.613
SOLUTIONRC 1 1.477 33.145 73.636
SOLUTIONRC 1 42.057 104.775 163.088
SOLUTIONRC 1 0.492 90.289 275.552
SOLUTIONRC 1 53.344 135.528 269.211
SOLUTIONRC 1 34.118 74.264 244.711
SOLUTIONRC 1 42.237 147.472 263.153
SOLUTIONRC 1 33.968 5.665 291.432
eof
# #############################
# traing run: SEarch for 2nd molecule P61
# #############################
#
amore table1 search-sfs.tab \
HKLPCK0 spmipch.hkl << eof
TRAFUN PTF NMOL 2 RESO 8 4 PKLIM 0.5 NPIC 10
SYMM P61
VERB
TITLE : Translation function P61 - 2 mols together.
SOLUTIONTF FIX 1 27.76 100.74 350.08 0.145 0.566 0.000 17.4 52.5
SOLUTIONRC 1 27.94 115.80 353.60
SOLUTIONRC 1 25.21 105.57 339.45
SOLUTIONRC 1 27.94 115.80 353.60
SOLUTIONRC 1 27.76 100.74 350.08
eof
# #############################
# traing run: 2nd Molecule - P65
# #############################
#
amore table1 search-sfs.tab \
HKLPCK0 spmipch.hkl << eof
TRAFUN PTF NMOL 2 RESO 8 4 PKLIM 0.5 NPIC 10
SYMM P65
VERB
TITLE : Translation function P65 - 2 mols together.
SOLUTIONTF FIX 1 27.76 100.74 350.08 0.116 0.437 0.000 19.4 51.7
SOLUTIONRC 1 27.94 115.80 353.60
SOLUTIONRC 1 25.21 105.57 339.45
SOLUTIONRC 1 27.94 115.80 353.60
SOLUTIONRC 1 27.76 100.74 350.08
eof
# ###########################
# traing run: Search for 3rd molecule - P65
# ###########################
#
# (no point in testing P61 now - P65 gives higher correlations and lower Rfactor)
#
amore table1 search-sfs.tab \
HKLPCK0 spmipch.hkl \
TRAFUN trafun.9 << eof
TRAFUN PTF NMOL 3 RESO 8 4 PKLIM 0.5 NPIC 10
SYMM P65
VERB
TITLE : Translation function P65 - 2 mols together.
SOLUTIONTF FIX 1 25.21 105.57 339.45 0.113 0.567 0.000 38.0 46.7
SOLUTIONTF FIX 1 27.76 100.74 350.08 0.146 0.571 0.652 38.0 46.7
SOLUTIONRC 1 27.94 115.80 353.60
SOLUTIONTF FIX 1 25.21 105.57 339.45 0.111 0.567 0.000 35.8 47.0
SOLUTIONTF FIX 1 27.94 115.80 353.60 0.144 0.603 0.358 35.8 47.0
SOLUTIONRC 1 27.76 100.74 350.08
SOLUTIONTF FIX 1 27.76 100.74 350.08 0.145 0.566 0.000 31.3 48.8
SOLUTIONTF FIX 1 27.94 115.80 353.60 0.144 0.603 0.705 31.3 48.8
SOLUTIONRC 1 25.21 105.57 339.45
eof
# ############
# fiting run: 3 molecules Symm P65
# ############
#
amore table1 search-sfs.tab \
HKLPCK0 spmipch.hkl <<eof
FITFUN NMOL 3 RESO 20 4.5
TITLE *** spmi structure ***
SYMM P65
VERBOSE
REFSOL AL BE GA X Y Z BF
SOLUTIONTF 1 25.02 105.58 339.46 0.113 0.569 0.000 27.5 51.7
SOLUTIONTF 1 27.60 100.60 350.29 0.146 0.571 0.649 43.5 46.5
SOLUTIONTF 1 27.72 115.95 353.54 0.143 0.602 0.351 41.3 47.3
eof
# # Build the solution file with with PDBSET. # Assume the following three solutions from AMoRe: # SOLUTIONF 1 56.35 74.98 145.14 0.3883 -0.0061 0.2757 55.7 45.2 57.1 28 # SOLUTIONF 1 295.44 70.84 148.61 0.8273 0.9301 0.2737 55.7 45.2 57.1 29 # SOLUTIONF 1 164.23 69.22 147.81 0.0896 0.8444 0.2876 55.7 45.2 57.1 30 Then: pdbset \ xyzin /y/ccp4/work/model-rot.pdb \ xyzout /y/ccp4/work/model-rot-sol1.pdb \ <<eof CELL 78.700 40.400 56.000 90.00 117.10 90.00 SYMM C2 rotat euler 56.35 74.98 145.14 shift frac 0.3883 -0.0061 0.2757 55.7 45.2 57.1 28 chain A end eof # pdbset \ xyzin /y/ccp4/work/model-rot.pdb \ xyzout /y/ccp4/work/model-rot-sol2.pdb \ <<eof # Use -0.5,-0.5,0 = other C2 solution CELL 78.700 40.400 56.000 90.00 117.10 90.00 SYMM C2 rotat euler 295.44 70.84 148.61 shift frac 0.3273 0.4301 0.2737 55.7 45.2 57.1 29 chain B end eof # pdbset \ xyzin /y/ccp4/work/model-rot.pdb \ xyzout /y/ccp4/work/model-rot-sol3.pdb \ <<eof # Subtract 1 from y CELL 78.700 40.400 56.000 90.00 117.10 90.00 SYMM C2 rotat euler 164.23 69.22 147.81 shift frac 0.0896 -0.1556 0.2876 55.7 45.2 57.1 30 chain C end eof # cat the three solution coordinates into one pdb file - model-rot-sol123.pdb. Check if there are bad symmetry clashes. distang \ xyzin /y/ccp4/work/model-rot-sol123.pdb \ <<eof SYMM C2 RADI CA 2 eof
# # Tabulating structure factors generated from a blob of electron density # The blob has been placed in a large "P1 unit cell" to give a finely sampled reciprocal lattice. # #!/bin/csh -f ########################################################### # # There are lots of alternative ways of getting a masked block of density. # You first need a mask. This does not need to cover the whole molecule. # The simplest technique I have used is to place a large sphere # at the centre of mass of a likely region. # This can be done by placing an "atom" at the centre of mass of a likely region # and specified a large atomic radius for it. # # Another way is to edit bones generated from a map to include only those # which are likely to belong to one molecule, then use bones_to_pdb to write out a # cordinate file, and use ncsmask with that set, and the default atom radius. # ( 3A I think..) # #################################################################### # Make a spherical mask centred at the centroid of the chosen block of # density. ########################################################### # P65_block_com.pdb # REMARK Centre of Mass: X ~35/102, Y~ 42/102, Z~75/96 = (0.343 0.412 0.781) # REMARK COM in As: 0.343 * 208.4 = 71.510 ; 0.412 *208.4 =85.812 0.781=75.156 # P65_block_com.pdb CRYSTL 208.400 208.400 96.200 90.00 90.00 120.00 P65 ATOM 1 N COM C 3 71.510 85.812 75.156 1.00 41.63 N # # Set atomic radius; i.e. radius of sphere to 18Å ncsmask xyzin ./P65_block_com.pdb \ mskout $SCRATCH/P65_block_com.msk <<eof # I have taken a 1A grid. GRID 204 204 96 AXIS Y X Z RADIUS 18 END eof # ########################################################### # extend the DM map to the same limits as the msk; # you will have to look at the log of Step 1. # ( You can get the mask extent by typing # prmap mapin $CCP4_SCR/P65_block_com.msk ) ########################################################### mapmask mapin /y/work2/suresh//nat3_au5_hg2_dm.map \ mapout $CCP4_SCR//nat3_au5_hg2_dm.ext << eof GRID 204 204 96 XYZLIM 57 93 62 101 56 91 END eof # # ########################################################### # Now the clever bit - put the "masked" density in the big P1 cell: # maprot \ wrkin $CCP4_SCR//nat3_au5_hg2_dm.ext \ mskin $CCP4_SCR/P65_block_com.msk \ mapout $CCP4_SCR/nat3_au5_hg2_dm_cent_bigdummycell.map \ <<eof # "MODE TO" moves the WRKIN map ( after masking with MSKIN) to the given cell and grid. MODE TO # No averaging; this is the identity.. GRID XTAL 300 300 300 ! Fine grid for structure factors CELL XTAL 240.000 240.000 240.000 90.00 90.00 90.00 SYMM P1 AVERAGE 1 ROTATE EULER 0 0 0 TRANS 0 0 0 END eof # ########################################################### # # Generate structure factors from this density ready for Amore # Then delete the *bigdummy*maps - they are HUGE.. sfall \ mapin $CCP4_SCR/nat3_au5_hg2_dm_cent_bigdummycell.map \ hklout $CCP4_SCR/nat3_au5_hg2_dm_cent_bigdummycell.mtz \ <<eof MODE SFCALC MAPIN SYMM P1 RESO 37 2.5 LABO FC=FC1 PHIC=PHIC1 END eof # # Now read these SFS from the mtz file into Amore and generate the table # Then the molecular replacement can continue as above. # amore \ hklin $CCP4_SCR/nat3_au5_hg2_dm_cent_bigdummycell.mtz \ table1 $CCP4_SCR/nat3_au5_hg2_dm_cent_bigdummycell.tab \ <<eof VERBOSE TITLE ** packing h k l For the "model" structure factors. SORTFUN MODEL 100 2.5 LABI FC=FC1 PHIC=PHIC1 eof # eof
# # Using the locked rotation function # amore HKLPCK0 bgltp2peak+resolve.hkl CLMN0 $CCP4_SCR/bgltp2peak+resolve_0.clmn MAPOUT $CCP4_SCR/insmon_304_rot.map table1 newbuiltA_MR_trial.tab CLMN1 $CCP4_SCR/newbuiltA_MR_trial.clmn HKLPCK1 $CCP4_SCR/insmon_304_3_hkl.tmp <<eof title Run bglt _ locked rotn_ polar 42.87 0 180 rotfun generate 1 resolution 15.0 3.0 cell_model 81.366 81.096 84.366 clmn crystal orth 1 resolution 15.0 3.0 clmn model 1 resolution 15.0 3.0 sphere 24.936 rotate CROSS model 1 npic 20 pklim 0.5 lock 1 polar 43 0 180 # or #rotate CROSS model 1 npic 20 pklim 0.5 lock 1 euler 0 86 180 end eof
#
# Using a non-crystallographic translation
#vector to find pairs of solutions in the same orientation.
#
amore
HKLPCK0 /y/work/ccp4/dm-av-noav-sharp+dm-jtfree.hkl
MAPOUT /tmp/ccp4/hpce_225_tran.map
table1 xv11Aa_MR_trial.tab
<<eof
title Hpce P212121 _ test NCS vector
trafun PTF NMOL 1 -
resolution 91.287 3.0 -
npic 20 -
pklim 0.5 NCST 0.028 0 0.5
crystal orth 1
symmetry P212121
SOLUTION 1 359.78 360.00 0.00 0.0000 0.0000 0.0000 20.7 55.9 28.5 25.3 1
SOLUTION 1 179.92 0.00 0.00 0.0000 0.0000 0.0000 20.7 55.9 28.5 25.3 3
SOLUTION 1 2.12 0.00 0.00 0.0000 0.0000 0.0000 18.3 56.6 25.5 22.0 6
SOLUTION 1 29.44 64.50 28.89 0.0000 0.0000 0.0000 16.1 57.3 22.3 15.7 11
SOLUTION 1 94.46 79.60 349.04 0.0000 0.0000 0.0000 14.3 57.7 18.7 16.8 16
SOLUTION 1 359.92 85.64 181.65 0.0000 0.0000 0.0000 14.2 57.9 18.3 9.9 17
SOLUTION 1 25.17 67.80 29.14 0.0000 0.0000 0.0000 14.2 57.7 18.7 16.5 18
SOLUTION 1 41.98 49.77 203.98 0.0000 0.0000 0.0000 14.1 57.8 19.3 14.0 19
eof
amore
HKLPCK0 /y/work/ccp4/dm-av-noav-sharp+dm-jtfree.hkl
MAPOUT /tmp/ccp4/hpce_227_tran.map
table1 xv11Aa_MR_trial.tab
<<eof
title Hpce P212121 _ test NCS vector
trafun PTF NMOL 3 -
resolution 91.287 3.0 -
npic 20 -
pklim 0.5 NCST 0.028 0 0.5
crystal orth 1
symmetry P212121
SOLUTION fix 1 359.78 0.00 0.00 -0.0025 0.4977 0.4797 40.6 56.5 40.2 1 81.2
SOLUTION fix 1 359.78 0.00 0.00 0.0255 0.4977 -0.0203 40.6 56.5 40.2 1 76.9
SOLUTION 1 359.78 360.00 0.00 0.0000 0.0000 0.0000 20.7 55.9 28.5 25.3 1
SOLUTION fix 1 359.78 0.00 0.00 -0.0025 0.4977 0.4797 40.6 56.5 40.2 1 81.2
SOLUTION fix 1 359.78 0.00 0.00 0.0255 0.4977 -0.0203 40.6 56.5 40.2 1 76.9
SOLUTION 1 29.44 64.50 28.89 0.0000 0.0000 0.0000 16.1 57.3 22.3 15.7 11
SOLUTION fix 1 29.44 64.50 28.89 0.2282 0.2346 0.3130 31.4 59.8 29.1 1 74.2
SOLUTION fix 1 29.44 64.50 28.89 0.2562 0.2346 -0.1870 31.4 59.8 29.1 1 74.2
SOLUTION 1 359.78 360.00 0.00 0.0000 0.0000 0.0000 20.7 55.9 28.5 25.3 1
SOLUTION fix 1 29.44 64.50 28.89 0.2282 0.2346 0.3130 31.4 59.8 29.1 1 74.2
SOLUTION fix 1 29.44 64.50 28.89 0.2562 0.2346 -0.1870 31.4 59.8 29.1 1 74.2
SOLUTION 1 29.44 64.50 28.89 0.0000 0.0000 0.0000 16.1 57.3 22.3 15.7 11
eof
Jorge Navaza. Adapted for CCP4 by Eleanor Dodson.