Program : MAVE
Version : 961122
Author : Gerard J. Kleywegt & T. Alwyn Jones,
Dept. of Cell and Molecular Biology,
Uppsala University, Biomedical Centre, Box 590,
SE-751 24 Uppsala, SWEDEN
E-mail : gerard@xray.bmc.uu.se
Purpose : multiple-crystal averaging of electron-density maps
Package : RAVE
Reference(s) for this program:
* 1 * T.A. Jones (1992). A, yaap, asap, @#*? A set of averaging programs. In "Molecular Replacement", edited by E.J. Dodson, S. Gover and W. Wolf. SERC Daresbury Laboratory, Warrington, pp. 91-105.
* 2 * G.J. Kleywegt & T.A. Jones (1994). Halloween ... Masks and Bones. In "From First Map to Final Model", edited by S. Bailey, R. Hubbard and D. Waller. SERC Daresbury Laboratory, Warrington, pp. 59-66.
* 3 * G.J. Kleywegt & R.J. Read (1997). Not your average density. Structure 5, 1557-1569. [http://www4.ncbi.nlm.nih.gov/htbin-post/Entrez/query?uid=9438862&form=6&db=m&Dopt=r]
* 4 * G.J. Kleywegt & T.A. Jones (2037 ?). Convenient single and multiple crystal real-space averaging. To be published ???
* 5 * G.J. Kleywegt & T.A. Jones (1999 ?). Chapter 25.2.6. O and associated programs. Int. Tables for Crystallography, Volume F. To be published.
930331 - 0.5 - first production version; started manual
930602 - 0.6 - print corr coeffs for each NCS operator
930615 - 1.0 - new production version
930726 - 1.1 - bug hunt
931216 - 2.0 - implemented domain averaging and positivity
940113 -2.0.2- minor changes
950118 - 2.1 - sensitive to environment variable CCP4_OPEN
951022 - 2.2 - made sensitive to OSYM
951030 - 2.3 - enable reading of one OR MANY NCS operators
from each file
951106 - 2.4 - implemented EZ skewing
960315 - 2.5 - changed minimum allowed cell axis length from 10.0
to 1.0 A so the program can be used with small
molecules; removed nasty bug when using a mask
whose origin and extent were not the same as that
of the input map for skewing; wrote a jiffy script
OMAC/plane_extract.csh to plot density (2D projection)
for *any* plane defined by three atoms (e.g., to get
a 2D plot for the density of a Trp ring !)
960322 -2.5.1- more changes needed for small-molecule applications
(minor ones having to do with deciding what are
reasonable values to expect for grid spacing etc.)
960412 - 2.6 - echo all input to help debug scripts
961122 - 3.0 - dynamic memory allocation
From version 3.0 onward, MAVE allocates memory for maps and masks dynamically. This means that you can increase the size of maps and masks that the program can handle on the fly:
1 - through the environment variables MAPSIZE and MASKSIZE (must be in capital letters !), for example put the following in your .cshrc file or your RAVE script:
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- setenv MAPSIZE 8000000 setenv MASKSIZE 3000000 ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
2 - by using command-line arguments MAPSIZE and MASKSIZE (need not be in capitals), for example in your RAVE script:
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- run mave -b mapsize 10000000 masksize 5000000 < mave.inp >& mave.out ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
Note that command-line arguments take precedence over environment variables. So you can set the environment variables in your .cshrc file to "typical" values, and if you have to deal with a map and/or mask which is bigger than that, you can use the command-line argument(s).
If sufficient memory cannot be allocated, the program will print a message and quit. In that case, increase the amount of virtual memory (this will not help, of course, if you try to allocate more memory than can be addressed by your machine (for 32-bit machines, something 2**32-1 bytes, I think), or reduce the size requirements.
MAVE needs space for 2 maps and 1 mask.
NOTE: this program is sensitive to the environment variable CCP4_OPEN. If this variable has *not* been set, you will not be able to create any CCP4 maps. If this happens, the program will abort execution on startup. To fix this, put the following line in your .login or .cshrc file: setenv CCP4_OPEN UNKNOWN
NOTE: this program is sensitive to the environment variable OSYM.
It should point to your local copy of $ODAT/symm, the directory
which contains the spacegroup symmetry operators in O format.
When asked for a file with spacegroup operators in O format,
you may either provide a filename, or the name of a sapcegroup
(including blanks if you like, case doesn't matter). The program
will try to open the following files, assuming that STRING is the
what you input:
(1) open a file called STRING
(2) if this fails, check if OSYM is defined and open $OSYM/STRING
(3) if this fails, open $OSYM/string.sym
(4) if this fails, open $OSYM/string.o
Hint: if you make soft links in the OSYM directory, you can also type
spacegroup numbers (e.g.: \ln -s p212121.sym 19.sym).
NOTE: from version 2.3 onwards, you may choose to enter NCS operators either one by one (as it used to be), or all in one go (by putting them all in one file), or a mixture of this.
NOTE: from 960410 onwards, there is a little jiffy program called CRAVE which can be used to auto-generate C-shell scripts for multiple crystal averaging using MAVE (up to 25 crystal forms; only for single domains at present). See the CRAVE manual for details !!!
MAVE is a program for multiple-crystal form averaging. It may be used to carry out the following tasks:
(1) NCS-averaging density within one unit cell and projecting it onto a mask in the REFERENCE crystal
(2) projection of density from a map around a mask in the REFERENCE crystal into a different unit cell and expansion according to NCS-operators
(3) improvement of approximate RT-operators which relate a reference molecule (mask) in the reference crystal and in any other crystal
(4) easy skewing of maps (transforming them from one cell/grid to another)
When you start the program, you will see the following:
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----*** MAVE *** MAVE *** MAVE *** MAVE *** MAVE *** MAVE *** MAVE *** MAVE ***
Version - 931216/2.0 (C) 1993 - Gerard J. Kleywegt & T. Alwyn Jones, BMC, Uppsala (S) User I/O - routines courtesy of Rolf Boelens, Univ. of Utrecht (NL) Others - T.A. Jones, G. Bricogne, Rams, W.A. Hendrickson Others - W. Kabsch, CCP4, PROTEIN, etc. etc.
Started - Fri Dec 17 17:01:06 1993 User - gerard Mode - interactive Host - rigel ProcID - 2183 Tty - /dev/ttyq16
*** MAVE *** MAVE *** MAVE *** MAVE *** MAVE *** MAVE *** MAVE *** MAVE ***
Max size of maps and masks : ( 4194304) Max nr of spacegroup symm ops : ( 64) Max nr of NCS symm ops : ( 64)
Which task ? A = Average map on mask in reference crystal P = average & enforce positivity E = Expand map from mask in reference crystal F = expand & keep zero background I = Improve RT-operator from reference to target Q = Quit right now Task ? (A) ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
Since the input and output are different depending on the option that you select, we shall discuss each of them separately.
Use this option to do NCS-averaging and to project the density onto a map which is on the same grid and in the same cell and position as the mask.
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- Task ? (A) aver Task : (A)IMPORTANT NOTE ... The REFERENCE and TARGET crystals may be identical !
Map to be averaged of TARGET crystal ? () p212121_start.E Read header. ... Header done. Map read OK. Cell axes (A) : ( 62.100 46.700 92.100) Cell angles (d) : ( 90.000 90.000 90.000) Grid axes (pts) : ( 60 48 90) Origin (pts) : ( 0 0 0) Extent (pts) : ( 32 26 90) ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- Mask in REFERENCE crystal ? () p21_start.mask Reading mask (old format) Mask read OK Number of points in mask : ( 66214) Cell axes (A) : ( 67.000 50.500 86.700) Cell angles (d) : ( 90.000 100.100 90.000) Grid axes (pts) : ( 70 48 88) Origin (pts) : ( -22 -27 -3) Extent (pts) : ( 76 78 77) ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- File with RT FROM reference TO target crystal ? () p21_to_p212121.o Opening O datablock : (p21_to_p212121.o) Datablock : (.space_group_operators) Data type : (R) Number : (12) Format : ((3f15.6)) ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- File with symmetry operators for TARGET crystal ? () p212121.sym Opening O datablock : (p212121.sym) Datablock : (.space_group_operators) Data type : (r) Number : (48) Format : ((3F10.5)) Nr of symmetry operators : ( 4) ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- File with NCS operator for TARGET crystal ? () rt_unit.o Opening O datablock : (rt_unit.o) Datablock : (unit_operator) Data type : (R) Number : (12) Format : ((3f15.7)) File with NCS operator for TARGET crystal ? () ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- I need parameters from the averaged map around the mask in the REFERENCE crystal Averaged map in REFERENCE crystal ? () /nfs/scratch/gerard/p21_0x.E Reading header ... Header done Cell axes (A) : ( 67.000 50.500 86.700) Cell angles (d) : ( 90.000 100.100 90.000) Grid axes (pts) : ( 70 48 88) Origin (pts) : ( -22 -27 -3) Extent (pts) : ( 76 78 77) Thanks ! ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- Averaged map on mask in REFERENCE crystal ? () /nfs/scratch/gerard/eikel.E CPU total/user/sys : 11.3 8.2 3.1 Start averaging ... ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
Afterwards, you will get the following output:
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- Calls to BLDBIT : ( 1688) CPU total/user/sys : 58.6 57.9 0.7 (Q)QOPEN allocated stream 3 ... Minimum density in map = -86.12376 Maximum density = 101.20619 Mean density = -0.02977 Rms deviation from mean = 8.75672Map written out. Map written
*** MAVE *** MAVE *** MAVE *** MAVE *** MAVE *** MAVE *** MAVE *** MAVE ***
Version - 930331/0.5 Started - Wed Mar 31 20:12:40 1993 Stopped - Wed Mar 31 20:22:15 1993
CPU-time taken : User - 74.2 Sys - 4.4 Total - 78.6
*** MAVE *** MAVE *** MAVE *** MAVE *** MAVE *** MAVE *** MAVE *** MAVE ***
STOP ... All done ... statement executed 74.1u 4.4s 9:35 13% ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
Use this option to project the density (after averaging with COMAP) back into the cells of ALL crystal forms.
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- ... Which task ? A = Average map on mask in reference crystal E = Expand map from mask in reference crystal I = Improve RT-operator from reference to target Task ? (A) expand Task : (E)IMPORTANT NOTE ... The REFERENCE and TARGET crystals may be identical !
Averaged map in mask of REFERENCE crystal ? () /nfs/scratch/gerard/comap_0x.E Read header. ... Map read OK. Cell axes (A) : ( 67.000 50.500 86.700) Cell angles (d) : ( 90.000 100.100 90.000) Grid axes (pts) : ( 70 48 88) Origin (pts) : ( -22 -27 -3) Extent (pts) : ( 76 78 77) Mask in REFERENCE crystal ? () p21_start.mask Reading mask (old format) Mask read OK Number of points in mask : ( 66214) Cell axes (A) : ( 67.000 50.500 86.700) Cell angles (d) : ( 90.000 100.100 90.000) Grid axes (pts) : ( 70 48 88) Origin (pts) : ( -22 -27 -3) Extent (pts) : ( 76 78 77) File with RT FROM reference TO target crystal ? () p21_to_p212121.o Opening O datablock : (p21_to_p212121.o) Datablock : (.space_group_operators) Data type : (R) Number : (12) Format : ((3f15.6)) File with symmetry operators for REFERENCE crystal ? () p21.sym Opening O datablock : (p21.sym) Datablock : (.space_group_operators) Data type : (r) Number : (24) Format : ((3F10.5)) Nr of symmetry operators : ( 2) File with symmetry operators for TARGET crystal ? () p212121.sym Opening O datablock : (p212121.sym) Datablock : (.space_group_operators) Data type : (r) Number : (48) Format : ((3F10.5)) Nr of symmetry operators : ( 4) File with NCS operator for TARGET crystal ? () rt_unit.o Opening O datablock : (rt_unit.o) Datablock : (unit_operator) Data type : (R) Number : (12) Format : ((3f15.7)) File with NCS operator for TARGET crystal ? () I need parameters from a map in the asymmetric unit of the TARGET crystal Asymmetric unit map of TARGET crystal ? () p212121_start.E Reading header ... Header done Cell axes (A) : ( 62.100 46.700 92.100) Cell angles (d) : ( 90.000 90.000 90.000) Grid axes (pts) : ( 60 48 90) Origin (pts) : ( 0 0 0) Extent (pts) : ( 32 26 90) Thanks ! Expanded map in TARGET crystal ? () /nfs/scratch/gerard/zeikerd.E CPU total/user/sys : 11.3 8.4 2.9 Start expanding ... ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
The program goes to work. Again "severe FRCSYM" errors should NOT
occur.
The output may look as follows:
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- Nr of asymm units in map : ( 1.156) Nr of asymm units in map : ( 1) ... Calls to BLDBIT : ( 0) Points in mask : ( 66214) Set in asymm unit : ( 58567) Total points set : ( 58567) Average density inside masks : ( -6.058E-02) Average density in solvent : ( 4.505E-01) Average density overall : ( -1.474E-06) ... Map written ... ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
Use this option to improve the Cartesian RT-operator FROM the reference molecule in the reference crystal TO the reference molecule in the target crystal.
This option has the same input parameters as IMP, the program that improves NCS-operators, except that you have to supply two map files instead of only one. See the IMP manual for more details.
A typical session may go as follows (NOTE: in real life, a sample density of 10 is too coarse; use 5 for an automatic search and then finetune the rotation and translation operators with a sample density of 1; this takes quite some CPU-time, but it's worth it):
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- ... Which task ? A = Average map on mask in reference crystal E = Expand map from mask in reference crystal I = Improve RT-operator from reference to target Task ? (A) imp Task : (I)Map of TARGET crystal ? () p212121_start.E Read header. ... Map read OK. Cell axes (A) : ( 62.100 46.700 92.100) Cell angles (d) : ( 90.000 90.000 90.000) Grid axes (pts) : ( 60 48 90) Origin (pts) : ( 0 0 0) Extent (pts) : ( 32 26 90) Mask in REFERENCE crystal ? () p21_start.mask Reading mask (old format) Mask read OK Number of points in mask : ( 66214) Cell axes (A) : ( 67.000 50.500 86.700) Cell angles (d) : ( 90.000 100.100 90.000) Grid axes (pts) : ( 70 48 88) Origin (pts) : ( -22 -27 -3) Extent (pts) : ( 76 78 77) File with RT FROM reference TO target crystal ? () bad_or2or.o Opening O datablock : (bad_or2or.o) Datablock : (.p21_to_p212121_bad) Data type : (R) Number : (12) Format : ((3f15.6)) File with symmetry operators for REFERENCE crystal ? () p21.sym Opening O datablock : (p21.sym) Datablock : (.space_group_operators) Data type : (r) Number : (24) Format : ((3F10.5)) Nr of symmetry operators : ( 2) File with symmetry operators for TARGET crystal ? () p212121.sym Opening O datablock : (p212121.sym) Datablock : (.space_group_operators) Data type : (r) Number : (48) Format : ((3F10.5)) Nr of symmetry operators : ( 4) Map in REFERENCE crystal ? () p21_start.E Read header. ... Map read OK. Cell axes (A) : ( 67.000 50.500 86.700) Cell angles (d) : ( 90.000 100.100 90.000) Grid axes (pts) : ( 70 48 88) Origin (pts) : ( 0 0 0) Extent (pts) : ( 70 48 88) CPU total/user/sys : 9.9 7.9 2.0
Select one of the options Q(uit), T(ranslation), R(otation) or A(uto) Search type ? (A) t Step size ? ( 0.500) 1 Enter the sample density; 1 means: use all points, 3 means: use every third point etc. Higher value -> faster (but less accurate) Sample density ? ( 4) 10
Cell A : ( 62.100 46.700 92.100 90.000 90.000 90.000) Origin A : ( 0 0 0) Extent A : ( 32 26 90) Grid A : ( 60 48 90) Spacing A : ( 1.035 0.973 1.023) AFORGN : ( 0.000 0.000 0.000) AFEXT : ( 0.517 0.521 0.989) AGEXT : ( 0.500 0.500 0.978) Cell B : ( 67.000 50.500 86.700 90.000 100.100 90.000) Origin B : ( 0 0 0) Extent B : ( 70 48 88) Grid B : ( 70 48 88) Spacing B : ( 0.957 1.052 0.985) BFORGN : ( 0.000 0.000 0.000) BFEXT : ( 0.986 0.979 0.989) BGEXT : ( 0.971 0.958 0.977)
Start Rotation Matrix -0.106810 0.673974 0.730998 -0.422524 0.634750 -0.646978 -0.900048 -0.377965 0.216976 Start Translation 25.850410 19.666836 7.992209 Rotation origin at -16.336 3.610 28.965 Centre of mask in REFERENCE : ( 8.922 14.729 35.888) Centre of mask in TARGET : ( -13.627 21.464 12.771) Nr of points in mask : ( 66214) Shift= -1.000000 -1.000000 -1.000000 | Corr coeff= 0.017661 Shift= -1.000000 -1.000000 0.000000 | Corr coeff= 0.096346 Shift= -1.000000 -1.000000 1.000000 | Corr coeff= 0.076221 ... Shift= 1.000000 1.000000 -1.000000 | Corr coeff= -0.022900 Shift= 1.000000 1.000000 0.000000 | Corr coeff= 0.044593 Shift= 1.000000 1.000000 1.000000 | Corr coeff= 0.046751 Nr of mask points checked : 6621 CPU total/user/sys : 199.6 198.1 1.6 Best Rotation Matrix -0.106810 0.673974 0.730998 -0.422524 0.634750 -0.646978 -0.900048 -0.377965 0.216976 Best Translation 26.850410 18.666836 7.992209 Correlation Coefficient = 0.406828 ... Select one of the options Q(uit), T(ranslation), R(otation) or A(uto) Search type ? (T) r Step size ? ( 0.300) 0.2 Enter the sample density; 1 means: use all points, 3 means: use every third point etc. Higher value -> faster (but less accurate) Sample density ? ( 10) Start Rotation Matrix -0.111713 0.673555 0.730651 -0.422476 0.633309 -0.648420 -0.899475 -0.381117 0.213815 Start Translation 26.824198 18.712788 8.502277 Rotation origin at -15.820 4.995 29.441 Centre of mask in REFERENCE : ( 8.922 14.729 35.888) Centre of mask in TARGET : ( -12.676 20.372 13.144) Nr of points in mask : ( 66214) Shift= -0.200000 -0.200000 -0.200000 | Corr coeff= 0.428738 Shift= -0.200000 -0.200000 0.000000 | Corr coeff= 0.429371 ... Shift= 0.200000 0.200000 0.000000 | Corr coeff= 0.429088 Shift= 0.200000 0.200000 0.200000 | Corr coeff= 0.428719 Nr of mask points checked : 6621 CPU total/user/sys : 197.5 196.0 1.5 Best Rotation Matrix -0.116613 0.673152 0.730257 -0.422418 0.631838 -0.649891 -0.898880 -0.384257 0.210674 Best Translation 26.845713 18.850735 8.640188 Correlation Coefficient = 0.430368
Select one of the options Q(uit), T(ranslation), R(otation) or A(uto) Search type ? (R) q File for new operator ? () rt_better.o
*** MAVE *** MAVE *** MAVE *** MAVE *** MAVE *** MAVE *** MAVE *** MAVE ***
Version - 930331/0.5 Started - Wed Mar 31 20:39:26 1993 Stopped - Wed Mar 31 21:05:05 1993
CPU-time taken : User - 1192.9 Sys - 11.9 Total - 1204.8
*** MAVE *** MAVE *** MAVE *** MAVE *** MAVE *** MAVE *** MAVE *** MAVE ***
STOP ... All done ... statement executed 1192.9u 11.9s 25:39 78% ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
MAVE could previously be used for mask skewing, but many people found the operation too complicated. Therefore, from version 2.4, there is a dedicated, simple skewing option ("ez skewing").
What is skewing ? Transforming a map in one unit cell/grid (the so-called REFERENCE crystal) to another cell and/or grid (the TARGET crystal).
Why do you want to do it ? If you *only* want to do it for display
purposes, i.e. to see how well your monoclinic model fits your
tetragonal map, DO NOT USE MAVE !!! There's a command in O called
Rot_Tran_Obj with which you can apply an arbitrary operation to
a graphics object. Simply contour the map around your monoclinic
model and use Rot_Tran_Obj to rotate and/or translate the map
object on top of your tetragonal model.
If you want to actually *use* the skewed map (e.g., to calculate
structure factors for Molecular Replacement exercises), then you
can use MAVE to do just that.
How is it done ? Skewing as implemented in this special-purpose
MAVE option, is simply a special case of the Extend operation
of the program. It is easier to set up and use, and has some
extra bells and whistles to make it easier and more transparent.
Compared to the Extend command, there are a couple of things which
you do not have to provide:
- NCS operators for the TARGET crystal; only the unit operator
is used
- symmetry operators of the TARGET crystal; only the identity
operator is used
- an example map to get some map parameters for the TARGET crystal;
the origin and extent are figured out automagically by the program;
the order of the axes is set to X-Y-Z (if you or your program don't
like that, "reslice" the map with MAPMAN using the UVw command);
you are prompted for the spacegroup *NUMBER* (1-230)
- a mask in the REFERENCE crystal; if you *DO* supply it, it will be
used and only density inside the mask will be moved to the TARGET
map; if you don't supply it, a dummy mask encompassing the *ENTIRE*
REFERENCE map is generated automatically
Let's go through an example to show how it works (in this case, skewing a P1 map into a P21 cell):
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- *** MAVE *** MAVE *** MAVE *** MAVE *** MAVE *** MAVE *** MAVE *** MAVE ***Max size of maps and masks : ( 5242880) Max nr of spacegroup symm ops : ( 96) Max nr of NCS symm ops : ( 96)
Which task ? A = Average map on mask in reference crystal P = average & enforce positivity E = Expand map from mask in reference crystal F = expand & keep zero background I = Improve RT-operator from reference to target S = ez Skewing Q = Quit right now
Task ? (A) ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
Select task "S", for EZ skewing.
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- Input map of REFERENCE crystal ? ( ) p1.E Read header Input map : (p1.E) ... Map read OK Closing BINARY CCP4 map on unit : ( 1) Cell axes (A) : ( 49.600 67.500 53.800) Cell angles (d) : ( 76.300 75.200 78.400) Grid axes (pts) : ( 84 112 90) Origin (pts) : ( -66 -64 -62) Extent (pts) : ( 138 128 132)Mask is *OPTIONAL* for skewing ! If you do not provide a mask name the entire map will be skewed. Mask in REFERENCE crystal ? ( ) p1.mask Input mask : (p1.mask) Reading mask (compressed format) Grid points : ( 2331648) Stretches : ( 7064) Mask points : ( 280522) Number of points in mask : ( 280522) Cell axes (A) : ( 49.600 67.500 53.800) Cell angles (d) : ( 76.300 75.200 78.400) Grid axes (pts) : ( 84 112 90) Origin (pts) : ( -66 -64 -62) Extent (pts) : ( 138 128 132) ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
Supply the name of the existing (REFERENCE) map, and -optionally- a mask file (which must have the same grid and cell as the input map).
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- File with RT FROM reference TO target crystal ? ( ) p1_to_p21.o Opening O datablock : (p1_to_p21.o) Datablock : (.LSQ_RT_P1_TO_P21) Data type : (R) Number : (12) Format : ((3F15.8)) ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
Provide a file with the O-style operator FROM reference TO target (NOTE the FROM and TO !!!). If you don't care, use the unit operator. If you want the map centred on (0,0,0), use the identity rotation and -1.0 * (centre-of-gravity vector) of your REFERENCE model as the translation vector.
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- File with symmetry operators for REFERENCE crystal ? ( ) p1 ... Nr of symmetry operators : ( 1)Nr of spacegroup symmetry operators : 1
SYMOP 1 = 1.0000 0.0000 0.0000 0.000 0.0000 1.0000 0.0000 0.000 0.0000 0.0000 1.0000 0.000 Determinant of rotation matrix = 1.000000 Rotation angle = 0.000000 ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
Supply the O-style symmetry operators for the input REFERENCE map.
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- Output map in TARGET crystal ? ( ) p21.E Output map : (p21.E) Cell parameters of TARGET crystal ? ( 100.000 100.000 100.000 90.000 90.000 90.000) 49.1 75.8 92.9 90 103.2 90 Spacegroup NUMBER ? ( 1) 4 Grid of TARGET crystal ? ( 83 126 155) 84 126 156 ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
Answer some questions w.r.t. the output nap in the TARGET cell. Enter the name of the map file, the TARGET cell constants, and the *NUMBER* of the spacegroup. The program will suggest a grid which has a similar spacing as the input map. Note that some programs have special requirements w.r.t. the grid for their FFTs. For CCP4 maps, the maximum prime factor should be less than or equal to 19. Therefore, in this case, "84" was used instead of "83", and "156" instead of "155". Of course you don't have to enter a grid with similar spacing, but I don't think it's wise to use a much finer spacing than in the REFERENCE map.
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- Min mask indices in new map : ( 10 26 28) Max mask indices in new map : ( 106 106 130) Origin of new map : ( 0 16 18) Extent of new map : ( 117 101 123) ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
The program checks all mask points to find the minimum and maximum fractional coordinates in the new TARGET map. From that it calculates the origin and extent needed for the new TARGET map (plus 10 safety points on all sides).
Now the program goes to work:
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- REF -> TARGET : ( -0.996 0.078 0.047 0.026 0.743 -0.669 - 0.087 -0.665 -0.742 23.261 40.250 43.040) TARGET -> REF : ( -0.996 0.026 -0.087 0.078 0.743 -0.665 0.047 -0.669 -0.742 18.002 -1.742 60.717) Nr of asymm units in map : ( 0.880) Nr of asymm units in map : ( 1) ERROR --- Less than one asymmetric unit Skewing - create only one copy of the map Points in mask : ( 280522) Progress (% mask) : ( 10.000) Progress (% mask) : ( 20.000) Progress (% mask) : ( 29.999) Progress (% mask) : ( 39.999) Progress (% mask) : ( 49.999) Progress (% mask) : ( 59.999) Progress (% mask) : ( 69.999) Progress (% mask) : ( 79.999) Progress (% mask) : ( 89.999) Progress (% mask) : ( 99.999) Calls to BLDBIT : ( 0) Points in mask : ( 280522) Set in asymm unit : ( 291239) Total points set : ( 291239) FRCTRN errors : ( 0) FRCSYM errors : ( 0) Interpolation errors : ( 0) FRCVAL errors : ( 0) Points outside mask : ( 10529) Points set > 1 * : ( 0) Keeping background at zero CPU total/user/sys : 45.0 30.6 14.4 Stamp : (Created by MAVE V. 951106/2.4 at Tue Nov 7 01:19:24 1995 for user gerard) (Q)QOPEN allocated # 1 User: gerard Logical Name: p21.E Status: UNKNOWN Filename: p21.EFile name for output map file on unit 4 : p21.E logical name p21.E
Minimum density in map = -54.86745 Maximum density = 97.98074 Mean density = 0.00024 Rms deviation from mean = 7.71887
Map written out Map written
*** MAVE *** MAVE *** MAVE *** MAVE *** MAVE *** MAVE *** MAVE *** MAVE ***
Version - 951106/2.4 Started - Tue Nov 7 01:14:51 1995 Stopped - Tue Nov 7 01:19:25 1995
CPU-time taken : User - 31.1 Sys - 14.7 Total - 45.8
*** MAVE *** MAVE *** MAVE *** MAVE *** MAVE *** MAVE *** MAVE *** MAVE *** ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
Note that (due to the fact that P1 symmetry without NCS is used for the TARGET crystal) you will get a map with *exactly one copy* of the density that existed inside the (mask in the) REFERENCE map. If this is not what you want, use the Extend option instead.
If you contour the skewed map, ignore its sigma; use the same level as for the original REFERENCE map.
Well, was this EZ or was it EZ ???
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- Which task ? A = Average map on mask in reference crystal P = average & enforce positivity E = Expand map from mask in reference crystal F = expand & keep zero background I = Improve RT-operator from reference to target Q = Quit right now Task ? (A) ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
If you want, you may enforce positivity of the density inside the mask. In this case, all mask points which receive an average density <= zero will be set to an arbitrary small positive value instead.
In addition, you can now use MAVE to do multiple crystal, multiple domain NCS averaging. In that case, keep the background at zero after expansion, and combine the various domain maps with COMDEM.
None, at present.
Created at Fri Dec 18 19:42:17 1998
by MAN2HTML version 971024/1.6