Program : MAPFIX
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 : fix CCP4 maps from RAVE
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.
From version 2.0 onward, MAPFIX allocates memory for its map dynamically. This means that you can increase the size that the program can handle on the fly:
1 - through the environment variable MAPSIZE (must be in capital letters !), for example put the following in your .cshrc file or your script:
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- setenv MAPSIZE 8000000 ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
2 - by using command-line argument MAPSIZE (need not be in capitals), for example in your script:
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- run mapfix mapsize 10000000 ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
Note that command-line argument takes precedence over the environment variable. So you can set the environment variable in your .cshrc file to a "typical" value, and if you have to deal with a map which is bigger than that, you can use the command-line argument.
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.
MAPFIX needs space for 1 map.
This is an unsupported jiffy program.
NOTE: this program is now 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
Quick-and-dirty program to fix the following in CCP4 maps:
- add a title
- alter the write-order of the axes
- add (or change) the spacegroup's symmetry operators
960116 - fixed bug which limited max size of map sections; check
for environment variable CLIBD to deduce the name of the
local CCP4 symm-op file
960412 - echo all input to help debug scripts
961122 - dynamic memory allocation
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- < % 119 gerard rigel 20:57:10 gerard/scratch> MAPFIX*** MAPFIX *** MAPFIX *** MAPFIX *** MAPFIX *** MAPFIX *** MAPFIX ***
Version - 930615/1.0 (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 - CCP4, PROTEIN, etc. etc.
Started - Tue Jun 15 21:03:55 1993 User - gerard Mode - interactive Host - rigel ProcID - 5991 Tty - /dev/ttyq0
*** MAPFIX *** MAPFIX *** MAPFIX *** MAPFIX *** MAPFIX *** MAPFIX ***
Max size of map : ( 4194304) Input map ? ( ) a2u/m5_4.E Read header Input map : (a2u/m5_4.E) ... Titles : new 2Fo-Fc map Created by AVE V. 930603/1.4 at Thu Jun 10 22:29:12 1993 for user A. Nonymous
Parameters as read from the map file Origin ...................... 0 0 0 Extent ...................... 140 80 144 Grid ........................ 140 80 144 Cell axes ................... 106.82 62.34 114.19 Cell angles ................. 90.00 90.00 90.00 UVW (fast, medium, slow) .... Z X Y
Header done Map read OK Cell axes (A) : ( 106.820 62.340 114.190) Cell angles (d) : ( 90.000 90.000 90.000) Grid axes (pts) : ( 140 80 144) Origin (pts) : ( 0 0 0) Extent (pts) : ( 140 80 144)
Output map ? (out.E) test.E
Title ? (RAVE/CCP4 map) test MAPFIX
UVW (write-order axes) ? ( 3 1 2) 2 3 1
Spacegroup ? ( 19) 5 Library file with symm-ops ? (/nfs/public/packages/ccp4/lib/data/symop.lib) ... Calculating min, max etc.
Minimum density in map = -53.37548 Maximum density = 93.61629 Mean density = 0.00001 Rms deviation from mean = 11.75688
Map written out
*** MAPFIX *** MAPFIX *** MAPFIX *** MAPFIX *** MAPFIX *** MAPFIX ***
Version - 930615/1.0 Started - Tue Jun 15 21:03:55 1993 Stopped - Tue Jun 15 21:06:28 1993
CPU-time taken : User - 39.0 Sys - 4.4 Total - 43.4
*** MAPFIX *** MAPFIX *** MAPFIX *** MAPFIX *** MAPFIX *** MAPFIX ***
>>> This program is (C) 1993, GJ Kleywegt & TA Jones <<< E-mail: "gerard@xray.bmc.uu.se" or "alwyn@xray.bmc.uu.se"
*** MAPFIX *** MAPFIX *** MAPFIX *** MAPFIX *** MAPFIX *** MAPFIX ***
STOP ... Toodle pip ... statement executed 39.0u 4.4s 2:33 28% ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
To show that it works, run EXTEND:
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- < % 123 gerard rigel 20:57:10 gerard/scratch> extend mapin test.E1### CCP PROGRAM SUITE: EXTEND VERSION 2.1.3: 28/08/92### User: gerard Run date: 6/15/93 Run time:21:11:43
xyzlim -10 10 -10 10 -10 10 end ... Number of columns, rows, sections ............... 80 144 140 Map mode ........................................ 2 Start and stop points on columns, rows, sections 0 79 0 143 0 139 Grid sampling on x, y, z ........................ 140 80 144 Cell dimensions ................................. 106.82000 62.34000 114.18999 90.00000 90.00000 90.00000 Fast, medium, slow axes ......................... Y Z X Minimum density ................................. -53.37548 Maximum density ................................. 93.61629 Mean density .................................... 0.00001 Rms deviation from mean density ................. 11.75688 Space-group ..................................... 5 Number of titles ................................ 3
Titles : new 2Fo-Fc map Created by AVE V. 930603/1.4 at Thu Jun 10 22:29:12 1993 for user A. Nonymous test MAPFIX ... Fractional limits of output map are -0.0714 0.0714-0.1250 0.1250-0.0694 0.0694 ... Symmetry operations : X,Y,Z * -X,Y,-Z
Symmetry operations : 1/2+X,1/2+Y,Z * 1/2-X,1/2+Y,-Z
Minimum density in map = -40.17652 Maximum density = 71.92261 Mean density = 0.16396 Rms deviation from mean = 17.06237 ... Number of columns, rows, sections ............... 21 21 21 Map mode ........................................ 2 Start and stop points on columns, rows, sections -10 10 -10 10 -10 10 Grid sampling on x, y, z ........................ 140 80 144 Cell dimensions ................................. 106.82000 62.34000 114.18999 90.00000 90.00000 90.00000 Fast, medium, slow axes ......................... Y Z X Minimum density ................................. -40.17652 Maximum density ................................. 71.92261 Mean density .................................... 0.16396 Rms deviation from mean density ................. 17.06237 Space-group ..................................... 5 Number of titles ................................ 1
Titles : new 2Fo-Fc map
Normal termination User: 0.50s System: 0.45s Elapsed: 00:11.00s ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
Now use MAPMAN to calculate the correlation coefficient between the new, small map and the original map (should be 1.000):
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- < % 125 gerard rigel 20:57:10 gerard/scratch> MAPMAN*** MAPMAN *** MAPMAN *** MAPMAN *** MAPMAN *** MAPMAN *** MAPMAN *** ... MAPMAN > re m1 MAPOUT ccp4 Read header Input map : (MAPOUT) ... Parameters as read from the map file Origin ...................... -10 -10 -10 Extent ...................... 21 21 21 Grid ........................ 140 80 144 Cell axes ................... 106.82 62.34 114.19 Cell angles ................. 90.00 90.00 90.00 UVW (fast, medium, slow) .... Y Z X
Header done Sum of density in map : ( 1.518E+03) Map read into memory MAPMAN > re m2 a2u/m5_4.E ccp4 Read header Input map : (a2u/m5_4.E) ... Parameters as read from the map file Origin ...................... 0 0 0 Extent ...................... 140 80 144 Grid ........................ 140 80 144 Cell axes ................... 106.82 62.34 114.19 Cell angles ................. 90.00 90.00 90.00 UVW (fast, medium, slow) .... Z X Y
Header done Sum of density in map : ( 9.694E+00) Map read into memory CPU total/user/sys : 14.2 12.0 2.2 MAPMAN > si m1 m2 Similarity Map : (M1) Similarity Map : (M2) Lower limits common volume : ( 0 0 0) Upper limits common volume : ( 10 10 10) Limits first map : ( 11 21 11 21 11 21) Limits second map : ( 1 11 1 11 1 11) Number of common map points : ( 1331) Nr of points in common grid : ( 1331) Correlation coefficient : ( 1.000) R-factor w.r.t. map 1 : ( 0.000) R-factor w.r.t. map 2 : ( 0.000) RMS difference : ( 0.000E+00) Shape similarity index : ( 1.000) MAPMAN > quit ... STOP ... Toodle pip ... statement executed 12.2u 2.6s 0:54 27% ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
None, at present.
Created at Fri Dec 18 19:42:15 1998
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