Program : MAPMAN
Version : 990129
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 : manipulation and analysis of electron-density maps
Package : RAVE
Reference(s) for this program:
* 1 * T.A. Jones & S. Thirup (1986). Using known substructures in protein model building and crystallography. EMBO J 5, 819-822. [http://www.ncbi.nlm.nih.gov/htbin-post/Entrez/query?uid=3709525&form=6&db=m&Dopt=r]
* 2 * 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.
* 3 * 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.
* 4 * G.J. Kleywegt & T.A. Jones (1996). xdlMAPMAN and xdlDATAMAN - programs for reformatting, analysis and manipulation of biomacromolecular electron-density maps and reflection data sets. Acta Cryst D52, 826-828. [http://www.iucr.ac.uk/journals/acta/tocs/actad/1996/actad5204.html]
* 5 * G.J. Kleywegt (1996). Making the most of your search model. CCP4/ESF-EACBM Newsletter on Protein Crystallography 32, June 1996, pp. 32-36. [http://alpha2.bmc.uu.se/usf/factory_6.html]
* 6 * 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]
* 7 * G.J. Kleywegt & T.A. Jones (2037 ?). Convenient single and multiple crystal real-space averaging. To be published ???
* 8 * G.J. Kleywegt & T.A. Jones (1998 ?). Software for handling macromolecular envelopes. To be published.
* 9 * G.J. Kleywegt (1998 ?). Local density correlation and ... To be published.
* 10 * G.J. Kleywegt & T.A. Jones (1999 ?). Chapter 25.2.6. O and associated programs. Int. Tables for Crystallography, Volume F. To be published.
930409 - 0.5 - first production version; first manual
930410 - 0.6 - implemented HISTO, SCALE, ZERO
930413 - 0.7 - implemented UVW, SPACEGROUP
930416 - 0.8 - bug fix (reading XPLOR maps)
930420 - 0.9 - more formats supported
930510 - 1.0 - implemented EXTRACT
930513 - 1.1 - removed bugs in (NEW)EZD scale calculation
930602 - 1.3 - made smaller ESV version (only 3 maps of
approximately 3 MW each); print program
dimensioning with "?" option
930608 - 1.4 - implemented MOMENTS, $ and NORMALISE options
930615 - 2.0 - new production version; implemented ADD
930705 - 2.1 - new options MIN_MAX and CORRELATE
930803 - 2.2 - implemented PICK commands
930805 - 2.3 - implemented new READ format DSN6/BRICK,
so that you may RECONSTRUCT OLD BRICK files !
930806 - 2.4 - implemented CELL option to change cell
constants of a map (sometimes needed when
reconstructing an old BRICK file)
930825 - 2.5 - made NEW-EZD format compatible with O 5.9.1
930901 -2.5.1- removed bug from reading NEW-EZD files
930928 - 3.0 - implemented BONES and SWAPBYTES options
931001 - 3.1 - implemented BONES PRUNE (for iterative
skeletonisation)
931004 -3.1.1- sped up BONES PRUNE by a factor of ~200
931109 - 3.2 - implemented 3DMATRIX (from XPLOR) input
format to enable display of rotation and
translation functions with O and O2D
931117 - 3.3 - extended ODl command
931124 - - made paper manual; drastically shortened this one
940303 - - store spare bones randomly throughout skeleton
940323 - 3.4 - Steve Muchmore (Purdue) implemented TNT input format
940415 - 3.5 - improved O2D plot files
940525 - 3.6 - option DH produces Density Histogram
940806 - 3.7 - new output format ENVELOPE (for CCP4 masks)
950118 - 3.8 - sensitive to environment variable CCP4_OPEN
950207 -3.8.1- removed minor bug in LIst command
950216 -3.8.2- removed sign-reversal bug from NOrmalise command
(it used to *add* rather than subtract the average)
950512 - 3.9 - implemented BRix command; added PHASES and FSMASK
input formats for PHASES maps and masks, respectively
(both are *UN*tested !)
950630 -3.9.1- minor bug fixes; added 1D_projection and 2D_projection
950717 - 4.0 - implemented loads of "filters"
950719 -4.0.1- fixed bug in reading DSN6 files (should now work properly
on all machine types, little- and big-endian)
951020 - 4.1 - new command ERase, INtegrate, PAste and FRame
951102 - 4.2 - new PIck INtegrate command; fixed bug which made that
peak interpolation only worked the first time PI PE/IN
was used, but not thereafter
951113 - 4.3 - added WRite format X-PLOR (ASCII only); changed X-PLOR
reading routine to utilise X-PLOR version 4 addition of
average and sigma at end of map file
960124 -4.3.1- minor bug fix; print prod/plus and dynamic range
whenever any of them changes
960125 -4.3.2- new VAlue_at command to list density value at a certain
grid point (plus those of its neighbours)
960215 - 4.4 - try to restore lost changes (yet another disk crash ...);
recalculate & display Prod & Plus whenever the dynamic
range of the map changes; improve error message when
Prod out of bounds; new VAlue_at command (different
from the version before the disk crash); new CHange_value
command to set all map values within a certain range
to another value
960409 - 4.5 - macro mechanism (@ filename)
960411 -4.5.1- picked peaks can now be written as an AMORE rotation
function solution file
960415 -4.5.2- minor bug fixes
960517 - 4.6 - implemented simple symbol mechanism
960629 -4.6.1- changed mask output format to OMASK
960827 -4.6.2- map statistics now do get updated for the MI, CO and AD
commands
961121 - 4.7 - implemented PIck HIgh option (e.g., to pick high values
in a rotation function map, rather than just the peaks)
961125 - 5.0 - implemented dynamic memory allocation
970501 -5.0.1- MStats command to get statistics about map points
inside/outside a mask
970626 - 5.1 - support initialisation macro (setenv GKMAPMAN macrofile)
970628 - 5.2 - several minor changes; new PEek commands
970630 - 5.3 - removed "MAXREC=" from OPEN statements for DSN6 files
(this stemmed from the PDP11 days !); implemented
reading of BRIX maps; added map type "XPLOR" (easier
to type than "X-PLOR" ;-)
971120 -5.3.1- NEWEZD files shouldn't contain null characters any
longer (I hope; only happened on SGIs); the EZD format
has been renamed to OLDEZD. From now on, "the EZD" format
by default refers to the (NEW)EZD format. (NEW)EZD files
can be contoured directly in O using the fm_* commands
980113 - 5.4 - added new map output format "AMORE" which will write
*binary* maps for use with Jorge Navaza's version of
AMORE (*not* the CCP4 version as far as I know !). They
cannot be read back into MAPMAN at present, but if anyone
needs that, let me know.
980428 -5.4.1- fixed bug which caused a crash if all points in a
map have the same value
980715 -5.4.2- added option Mean to the "mode" parameter of the PEek
CUbe and PEek SPhere commands
980922 -5.4.3- removed bug so that BRIX files are now read correctly
on little-endian machines (DEC ALPHA) as well
980929 - 5.5 - new ZP_restart command to re-start the program with
different memory allocation
981008 -5.5.1- new QInvert command to do quick-and-dirty inversion of
a map (i.e., swap rho(1,1,1) and rho(NX,NY,NZ) etc.)
981021 -5.5.2- new ECho command to echo command-line input (useful
in scripts)
981022 - 5.6 - implemented command history (# command)
990129 -5.6.1- BOnes commands will print more information when allocated
storage space is exceeded
From version 5.1 on, MAPMAN can execute a macro at start-up (whether it is run interactively or in batch mode). This can be used to execute commands which you (almost) always want to have executed. To use this feature, set the environment variable GKMAPMAN to point to a MAPMAN macro file, e.g.:
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- setenv GKMAPMAN /home/gerard/mapman.init ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
From version 5.0 onward, MAPMAN allocates memory for maps dynamically. This means that you can increase the size and number of maps that the program can handle on the fly:
1 - through the environment variables MAPSIZE and NUMMAPS (must be in capital letters !), for example put the following in your .cshrc file:
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- setenv MAPSIZE 8000000 setenv NUMMAPS 3 ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
2 - by using command-line arguments MAPSIZE and NUMMAPS (need not be in capitals), for example:
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- run mapman mapsize 20000000 nummaps 1 ----- 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 which is bigger than that, you can use the command-line argument(s).
From version 5.5 on, you can also use ZP_restart from within the program itself to increase memory allocation. WARNING : all memory is reset, so any unsaved data will be lost !!!
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.
MAPMAN needs space for NUMMAPS + 1 maps.
MAPMAN is a program for manipulation of electron-density files. Its applications comprise:
1 - map exchange among different machines through intermediate
EZD files
2 - conversion of maps produced by different programs
3 - producing DSN6-files for "O"/FRODO (a la MAPPAGE or BRIX)
4 - simple mathematics on maps
5 - combination of different maps
6 - peak picking
7 - creating BONES skeletons
8 - swap bytes on VAX maps
MAPMAN allows you to work with several maps simultaneously ! The wild-card character "*" can be used for most single-map options if you want to carry out an operation for all maps in memory.
When you read a map, you give it a name by which you can refer to it later. All names are converted to uppercase, so "m1" and "M1" are the same maps ! MAPMAN checks that you don't use duplicate map names.
MAPMAN is command-driven; the first TWO letters of each command are unique (so you don't have to type the rest); the commands are automatically converted to uppercase, so no worries there either.
Parameters to commands may be supplied on the same line as the command itself. MAPMAN will prompt you for the values of any parameters that were not supplied in this way.
MAPMAN runs in interactive mode by default. This means that if
(a) a file can not be opened, MAPMAN will ask you what to do
(b) if you delete a map which has unsaved changes, MAPMAN will
ask you if you're absolutely sure
(c) if you quit and there are maps with unsaved changes, MAPMAN
will ask you if you really want to quit
You may run MAPMAN in batch mode by supplying the command line option -b (or -batch). In that case, MAPMAN will crash if she can't open a file and any unsaved changes (with QUIT or DELETE) are lost forever. You may want to use this mode if you run MAPMAN in batch (using an input script).
NOTE: all output files are opened as "UNKNOWN", which means that any existing files will be overwritten !
At present, the following map formats are supported:
- INPUT: PROTEIN FFT-Y TENEYCK2 CCP4 X-PLOR EZD MASK NEWEZD BINXPLOR BRICK DSN6 3DMATRIX TNT PHASES FSMASK
- OUTPUT: CCP4 EZD MASK NEWEZD ENVELOPE X-PLOR
NOTE: only binary XPLOR files produced by 32-bit versions of the program can be read !
NOTE: we are unable to test whether or not the following formats actually work: PROTEIN FFT-Y TENEYCK2 PHASES FSMASK
NOTE: if you write a map as a mask file (format MASK or ENVELOPE) you must provide a cut-off to decide between solvent and protein density; the output file will contain zeros and ones.
NOTE: format ENVELOPE does not work correctly yet !!!!!
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 print a warning message. To fix this, put the following line in your .login or .cshrc file: setenv CCP4_OPEN UNKNOWN
MAPMAN welcomes you with the current array dimensions and a list of supported formats for input and output files. It then gives you a list of all available commands:
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- *** MAPMAN *** MAPMAN *** MAPMAN *** MAPMAN *** MAPMAN *** MAPMAN ***Version - 981008/5.5.1 (C) 1992-98 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, E. Dodson, etc. etc.
Started - Sat Oct 17 00:41:07 1998 User - gerard Mode - interactive Host - sarek ProcID - 9077 Tty - /dev/ttyq17
*** MAPMAN *** MAPMAN *** MAPMAN *** MAPMAN *** MAPMAN *** MAPMAN ***
Reference(s) for this program:
* 1 * T.A. Jones & S. Thirup (1986). Using known substructures in protein model building and crystallography. EMBO J 5, 819-822. [http://www.ncbi.nlm.nih.gov/htbin-post/Entrez/query?uid=3709525&form=6&db=m&Dopt=r]
* 2 * 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.
* 3 * 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.
* 4 * G.J. Kleywegt & T.A. Jones (1996). xdlMAPMAN and xdlDATAMAN - programs for reformatting, analysis and manipulation of biomacromolecular electron-density maps and reflection data sets. Acta Cryst D52, 826-828. [http://www.iucr.ac.uk/journals/acta/tocs/actad/1996/actad5204.html]
* 5 * G.J. Kleywegt (1996). Making the most of your search model. CCP4/ESF-EACBM Newsletter on Protein Crystallography 32, June 1996, pp. 32-36. [http://alpha2.bmc.uu.se/usf/factory_6.html]
* 6 * 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]
* 7 * G.J. Kleywegt & T.A. Jones (1998 ?). Software for handling macromolecular envelopes. To be published.
* 8 * G.J. Kleywegt (1998 ?). Local density correlation and ... To be published.
* 9 * G.J. Kleywegt & T.A. Jones (2037 ?). Convenient single and multiple crystal real-space averaging. To be published ???
* 10 * G.J. Kleywegt & T.A. Jones (1999 ?). Chapter 25.2.6. O and associated programs. Int. Tables for Crystallography, Volume F. To be published.
==> For manuals and complete references, visit: ==> http://alpha2.bmc.uu.se/usf
*** MAPMAN *** MAPMAN *** MAPMAN *** MAPMAN *** MAPMAN *** MAPMAN ***
Allocate maps of size : ( 5000000) Max number of maps : ( 3) Max nr of maps in memory : 3 Max nr of points in map : 5000000 Max nr of picked peaks : 65536 Max size of density buffer : 1048576 Max nr of BONES points : 100000 Max nr of BONES branches : 100000 Max nr of BONES connections : 200000 Record length for DSN6/BRIX : 128
Input formats : ( PROTEIN FFT-Y TENEYCK2 CCP4 X-PLOR OLDEZD MASK NEWEZD BINXPLOR BRICK DSN6 3DMATRIX TNT PHASES FSMASK BRIX XPLOR CNS EZD)
Output formats : ( CCP4 OLDEZD MASK NEWEZD ENVELOPE X-PLOR DSN6 BRIX XPLOR CNS EZD AMORE)
MAPMAN's options :
? (list options) ! (comment) QUit $ shell_command & symbol value & ? (list symbols) @ macro_file ZP_restart mapsize nummaps
REad map file fmt WRite map file fmt [cutoff] DElete map LIst [map] HIsto map x1 x2 x3 [...] EXtract map file type plane MOments map DH map plot_file nr_bins 1D_proj map file type 2D_proj map file type first last
UVw map u v w SPacegroup map ispcgr LAbel map text CEll map a b c al be ga PRod_plus map prod plus RAnge map low high MUltiply map factor DIvide map factor PLus map value ODl map odl_file type mode SCale map low high ZEro map low high NOrmalise map ERase map e1 .. e6 INtegrate map e1 .. e6 FRame map type e1 e2 e3 VAlue_at map e1 .. e6 CHange_value map lo hi new
PEek VAlue map pdb_in pdb_out mode PEek CUbe map pdb_in pdb_out mode nr_points PEek SPhere map pdb_in pdb_out mode radius
SImilarity map1 map2 DUplicate map oldmap ADd map map_to_add MIn_max map1 map2 COrrelate map1 map2 PAste map1 e1 .. e6 map2 e1 e2 e3 MStats map mask_map cutoff QInvert map oldmap
BOnes SKel map base step nr_spares BOnes COnnect file id mc BOnes ? BOnes PRune file mc bfac
MAppage map file BRix map file SWapbytes brick_file
PIck PDb res atom first PIck LImits e1 .. e6 PIck LEvel threshold PIck ? PIck PEaks map file format PIck INtegrate map file format PIck HIgh map file format
FIlter ? FIlter EDge map a b FIlter MEdian map size FIlter AVerage map size FIlter MInimum map size FIlter MAximum map size FIlter SMooth map FIlter SIgnal/noise map size FIlter GRadient map FIlter LAplace map FIlter KHighest map size k FIlter KLowest map size k FIlter VAr_thr map size a b FIlter STat_diff map size a b c
Max nr of maps in memory : 3 Max nr of points in map : 5000000 Max nr of picked peaks : 65536 Max size of density buffer : 1048576 Max nr of BONES points : 100000 Max nr of BONES branches : 100000 Max nr of BONES connections : 200000 Record length for DSN6/BRIX : 128
MAPMAN > ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- MAPMAN > $ xterm & MAPMAN > $ ls -FartCos m1*E 3435 -r--r--r-- 1 gerard 1758288 Jun 2 23:54 m1_start.E 1634 -rw-r--r-- 1 gerard 836224 Jun 8 13:46 m1_startx.E ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
Example of a MAPMAN macro:
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- ! mappage10.mapmac ! ! read a map, set sigma level to 10.0, mappage for O ! ! enter map file name, then map type read m1 ! ! normalise map to get sigma level at 1.0 norm m1 ! ! multiply by 10 to get sigma level at 10.0 multiply m1 10 ! ! enter O map file name mappage m1 ! ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
When executed, this gives:
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- MAPMAN > @mappage10.mapmac ... Opened macro file : (mappage10.mapmac) ... On unit : ( 61) > (!) > (! enter map file name, then type) > (read m1) File name ? (not_defined) /nfs/scr_uu1/gerard/scratch/all4_amore.map Format ? (CCP4) Read header ... CPU total/user/sys : 3.3 1.9 1.4 > (!) > (! normalise map) > (norm m1) Normalise : (M1) Subtract average : ( 2.566E-07) Divide by sigma : ( 1.407E+00) ... CPU total/user/sys : 3.9 3.9 0.0 > (!) > (! multiply by 10 to get sigma level at 10.0) > (multiply m1 10) Multiply : (M1) ... CPU total/user/sys : 1.9 1.9 0.0 > (!) > (! enter O map file name) > (mappage m1) Brick file ? (10) /nfs/scr_uu1/gerard/scratch/q.E Opening DSN6 file : (/nfs/scr_uu1/gerard/scratch/q.E) Little-endian machine; will swap bytes Scale constant for cell : ( 80) Pages along X, Y and Z : ( 21 21 38) Nr of records written : ( 16759) CPU total/user/sys : 8.0 6.3 1.7 > (!) ... End of macro file ... Control returned to terminal ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
This command can be used to manipulate symbols. These are probably
only useful for advanced users who want to write fancier macros.
The command can be used in three ways:
(1) & ? -> lists currently defined symbols
(2) & symbol value -> sets "SYMBOL" to "value"
(3) & symbol -> prompts the user to supply a value for "SYMBOL"
(even if the program is executing a macro)
A few symbols are predefined:
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- MAPMAN > & ? Nr of defined symbols : ( 4) Symbol PROGRAM : (MAPMAN) Symbol VERSION : (960517/4.6) Symbol START_TIME : (Fri May 17 20:26:49 1996) Symbol USERNAME : (gerard) ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
The symbol mechanism is fairly simplistic and has some limitations:
- max length of a symbol name is 20 characters
- max length of a symbol value is 80 characters
- max number of symbols is 100
- symbols can not be deleted, but they can be redefined
- symbol values are accessed by supplying $SYMBOL_NAME as an
argument on the command line; the line that you type on the terminal
(or in a macro) is parsed once; if there are additional parameters
which the program prompts you for, you cannot use symbols for those
- only one substitution per argument (e.g., "$file1 $file2" will
lead to a substituion of the entire argument by the value of
symbol FILE1 only !)
- command names (first argument on any command line) cannot be
replaced by a symbol (e.g.: "$command $arg1 $arg2" is not valid)
- symbols may be equated to each other, e.g. "& file2 $file1" will
give FILE2 the same value as FILE1
- symbol substitution is not recursive (e.g., if you set the value
of FILE2 to be "$file1", any reference to $FILE2 will be replaced
by "$file1", not by the value of FILE1
- symbols on comment lines (starting with "!") are not expanded
- symbols on system command lines (starting with "$") are not expanded
NOTE: binary XPLOR maps can only be read if they were created by an XPLOR version which uses 32 bits for reals and integers !!!
NOTE: you may also read old mappaged files (BRICK or
DSN6 files) ! This enables you to convert ancient
VAX PROTEIN maps into UNIX CCP4 format:
- create or read from tape your old PROTEIN map
- run AMAPPAGE on your VAX
- FTP (binary) the DSN6 file to your UNIX box
- run MAPMAN and do: SWapbytes old.map
- REad M1 old.map dsn6
- WRite M1 new.E ccp4
NOTE: from version 5.3, BRIX maps can also be read back into MAPMAN
If you have saved the full range of electron density
values when you mappaged the file, you should be able
to get correlation coefficients of ~0.998 between the
original map and the new CCP4 map !
Note that the spacegroup is set to P1 by default.
Note that the program knows if it should do a swap-bytes
on the header record of the brick file, so you can read
BRICK files made on any type of machine into MAPMAN
running on any type of machine.
Sometimes the cell constants are slightly altered when
moving from VAX to UNIX (round-off error plus intermediate
conversion to integers); in such cases, use the CELL
command to get them right again.
From version 4.3 onwards, X-PLOR version 4 maps are recognised by the fact that they have the original average and sigma density stored at the end of the map. If these values are found, the map will be changed such that the original density values are restored (in e-/A3).
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
MAPMAN > re m1 x ?
Supported formats : ( PROTEIN FFT-Y TENEYCK2 CCP4 X-PLOR EZD MASK NEWEZD
BINXPLOR BRICK DSN6 3DMATRIX TNT)
MAPMAN > re m1 p21_start.E ccp4
Read header
Filename : (p21_start.E)
...
Fourier parameters as read from the data-set
Origin ................................ 0 0 0
Extent ................................ 70 48 88
Grid .................................. 70 48 88
uvw (fast, medium, slow) .............. Z X Y
Header done
Map read into memory
CPU total/user/sys : 2.2 1.6 0.5
MAPMAN > re m2 map.tnt tnt
Read header
Input map : (map.tnt)
Title : (*Density map produced by RFACTOR)
Title : (*Density map calculated by inverting coefficients.)
Title : (*Coefficients were of type 2FO-FC)
Title : ( Map file PUNCHed on 11-Mar-94 11:54:15.)
Fast, medium, slow axes ? ( 1 2 3)
Number of sections ? ( 10) 170
Unit cell constants ? ( 100.000 100.000 100.000 90.000 90.000
90.000) 109.900 138.800 79.900 90.000 116.500 90.000
Parameters as read from the map file
Origin ...................... -39 0 -62
Extent ...................... 232 167 170
Grid ........................ 160 200 120
Cell axes ................... 109.90 138.80 79.90
Cell angles ................. 90.00 116.50 90.00
UVW (fast, medium, slow) .... X Y Z
Header done
Not in core
Reading levels ...
Level number : ( 10)
Level number : ( 20)
...
Level number : ( 160)
Level number : ( 170)
Sum of density in map : ( 9.406E+05)
Map read into memory
Closing TNT map on unit : ( 1)
CPU total/user/sys : 32.0 29.4 2.6
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- MAPMAN > re m4 q.xplor x-plor Read header Input map : (q.xplor) Title : (REMARKS FILENAME="q.xplor") Title : (REMARKS Created by MAPMAN V. 951113/4.3 at Mon Nov 13 19:50:32 1995 for user ger) ... Header done Not in core Reading levels ... Level number : ( 10) Level number : ( 20) Level number : ( 30) Level number : ( 40) Level number : ( 50) Level number : ( 60) This is an X-PLOR version 4 map ! Average density : ( 1.411E-04) Sigma level : ( 6.193E+00) Restoring original density values (e-/A3) Sum of density in map : ( 1.689E+02) Map read into memory Closing XPLOR map on unit : ( 1) CPU total/user/sys : 2.3 2.2 0.1 ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- MAPMAN > wr m1 x ? Supported formats : ( CCP4 EZD MASK NEWEZD ENVELOPE X-PLOR) MAPMAN > wr m1 p21_start.ezd ezd Writing EZD map ... CPU total/user/sys : 12.5 11.4 1.1 MAPMAN > wr m1 p21_start.mask mask 0.1 Writing MASK ... Border between 0 and 1 : ( 0.100) Nr of mask points set : ( 135304) Writing mask (compressed format) Grid points : ( 295680) Stretches : ( 33321) Mask points : ( 135304) Mask write OK CPU total/user/sys : 12.4 11.4 0.9 MAPMAN > wr m1 qq.xplor x-plor Writing ASCII X-PLOR map ... CPU total/user/sys : 6.0 3.9 2.1 ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- MAPMAN > map m1 p21_start.map Opening DSN6 file : (p21_start.map) Big-endian machine; will NOT swap bytes Pages along X, Y and Z : ( 9 6 11) Nr of records written : ( 649) CPU total/user/sys : 3.8 3.3 0.4 ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- MAPMAN > br m1 m1_1.brix Opening DSN6 file : (m1_1.brix) Little-endian machine; will swap bytes Pages along X, Y and Z : ( 11 11 10) Nr of records written : ( 1211) ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- MAPMAN > fr Which map ? (M1) Input Indices/Fractional/Cartesian (I/F/C) ? (I) Value for X ? (0.0000000E+00) 20 Value for Y ? (0.0000000E+00) 40 Value for Z ? (0.0000000E+00) 77 Indices : ( 20 40 77) Fractional : ( 0.333 0.417 0.642) Cartesian : ( 3.017 31.292 57.333) Point lies inside the map ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- MAPMAN > fr m1 fr 0.333 0.417 0.642 Fractional : ( 0.333 0.417 0.642) Indices : ( 20 40 77) Cartesian : ( 2.994 31.317 57.363) Point lies inside the map ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- MAPMAN > fr m1 cart 3.017 31.292 57.333 Cartesian : ( 3.017 31.292 57.333) Fractional : ( 0.333 0.417 0.642) Indices : ( 20 40 77) Point lies inside the map ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- MAPMAN > in m1 10 50 20 60 30 70 Limits : ( 10 50 20 60 30 70) Integrate : (M1) Nr of points summed : ( 68921) Sum of density : ( 1.105E+02) Sum of | density | : ( 5.356E+04) Average zeroed density : ( 1.603E-03) Average | zeroed dens | : ( 7.771E-01) ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- MAPMAN > er m1 10 50 20 60 30 70 Limits : ( 10 50 20 60 30 70) Erase : (M1) Nr of points set to zero : ( 68921) Sum of zeroed density : ( 1.105E+02) Sum of | zeroed dens | : ( 5.356E+04) Average zeroed density : ( 1.603E-03) Average | zeroed dens | : ( 7.771E-01) ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- MAPMAN > va m1 -20 -20 -20 -20 -20 -20 Limits : ( 8 8 20 20 -15 -15) List values : (M1) Nr of map points to list : ( 1)X Y Z Density 8 20 -15 0.0000E+00
Nr of points listed : ( 1) Sum of density : ( 0.000E+00) Sum of | density | : ( 0.000E+00) Average density : ( 0.000E+00) Average | dens | : ( 0.000E+00) MAPMAN > va m1 40 42 70 72 40 42 Limits : ( 40 42 70 72 40 42) List values : (M1) Nr of map points to list : ( 27)
X Y Z Density 40 70 40 8.1301E+00 40 70 41 9.2141E+00 40 70 42 1.0705E+01 40 71 40 8.1301E+00 40 71 41 9.6206E+00 40 71 42 1.1789E+01 40 72 40 5.2846E+00 40 72 41 7.8591E+00 40 72 42 1.1111E+01
X Y Z Density 41 70 40 1.3008E+01 41 70 41 1.3008E+01 41 70 42 1.3686E+01 41 71 40 1.3008E+01 41 71 41 1.3008E+01 41 71 42 1.4092E+01 41 72 40 1.0705E+01 41 72 41 1.2195E+01 41 72 42 1.4092E+01
X Y Z Density 42 70 40 1.5176E+01 42 70 41 1.5447E+01 42 70 42 1.5176E+01 42 71 40 1.5176E+01 42 71 41 1.5447E+01 42 71 42 1.5176E+01 42 72 40 1.4905E+01 42 72 41 1.5447E+01 42 72 42 1.5176E+01
Nr of points listed : ( 27) Sum of density : ( 3.358E+02) Sum of | density | : ( 3.358E+02) Average density : ( 1.244E+01) Average | dens | : ( 1.244E+01) ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
With the PEek VAlue command, the density at the atomic centre will be
extracted; the "mode" parameter may be:
* N = Nearest - this will extract the value at the nearest grid point
* I = Interpolate - this will do linear interpolation of the 8 grid points
surrounding each atom
* S = Spline - this will do spline interpolation using a 4 * 4 * 4 cube
surrounding each atom
With the PEek CUbe command, density in the neighbourhood of atomic
positions will be extracted; the "mode" parameter may be:
* I = Integrate - simply add up the density values inside the cube
* M = Mean - calculate the average of the density values inside the cube
* A = Absolute integral - add up the absolute density values
* R = Rms - calculate the root-mean-square density
You need to supply the number of grid points around each atom that
will be included in the calculations (e.g., 1 or 2). Using a
margin of 1 grid point means that 27 grid points will be considered
(in general: (1+2*N)**3, where N is the number you supply).
Note that the affected bit of the map is cubic only for cubic cells;
in general it will be a parallellopiped.
The PEek SPhere command is very similar to the PEek CUbe command, except that a sphere of points around each atom is used. You must supply the mode (same options as for PEek CUbe), and the radius around each atom.
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- MAPMAN > peek value m1 m6a.pdb Output PDB file ? (out.pdb) value_spline.pdb Mode (Nearest|Interpolate|Spline) ? (Spline) s Grid spacing (A) : ( 0.501 0.499 0.489) Peeking ... New PDB file created MAPMAN > peek cube m1 m6a.pdb cube_rms2.pdb rms 2 Grid spacing (A) : ( 0.501 0.499 0.489) Peeking ... New PDB file created MAPMAN > peek sph m1 m6a.pdb sphere_rms2.pdb rms 2 Grid spacing (A) : ( 0.501 0.499 0.489) Peeking ... New PDB file created CPU total/user/sys : 13.0 13.0 0.0 MAPMAN > peek sph m1 m6a.pdb sphere_abs2.pdb abs 2 Grid spacing (A) : ( 0.501 0.499 0.489) Peeking ... New PDB file created CPU total/user/sys : 13.0 13.0 0.0 ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- MAPMAN > si m1 m2 Similarity Map : (M1) Similarity Map : (M2) ... Nr of points in common grid : ( 295680) Correlation coefficient : ( 1.000) R-factor w.r.t. map 1 : ( 35.424) R-factor w.r.t. map 2 : ( 0.973) RMS difference : ( 1.961E+02) Shape similariy index : ( 0.239) ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
The map and the "mask map" must have the same grid and cell.
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
MAPMAN > re m1 m11_2fofc.map dsn6
...
MAPMAN > re m2 m1.mask mask
...
MAPMAN > mstats m1 m2 0.5
Masked stats Map : (M1)
Mask : (M2)
Lower limits common volume : ( -56 -51 -46)
Upper limits common volume : ( 71 63 69)
Limits first map : ( 1 128 1 115 1
116)
Limits second map : ( 11 138 14 128 17
132)
Number of common map points : ( 1707520)
Density inside the mask :
Nr of points : ( 280522)
Average density : ( 2.528E-02)
St. deviation : ( 1.803E+01)
Minimum value : ( -5.488E+01)
Maximum value : ( 1.000E+02)
Sum of values : ( 7.091E+03)
Density outside the mask :
Nr of points : ( 2910308)
Average density : ( -3.621E-01)
St. deviation : ( 1.432E+01)
Minimum value : ( -5.488E+01)
Maximum value : ( 9.756E+01)
Sum of values : ( -1.054E+06)
CPU total/user/sys : 10.0 9.7 0.3
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- MAPMAN > pa m1 10 50 20 60 30 70 m3 10 20 30 Limits : ( 10 50 20 60 30 70) Nr of points copied : ( 68921) Sum of OLD density : ( 1.879E+02) Sum of NEW density : ( 1.105E+02) ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- MAPMAN > hi m1 -100 -50 -30 -20 -10 0 10 20 30 40 50 100 Histrogram limits : ( -1.000E+02 -5.000E+01 -3.000E+01 -2.000E+01 -1.000E+01 0.000E+00 1.000E+01 2.000E+01 3.000E+01 4.000E+01 5.000E+01 1.000E+02) Histogram : (M1)Nr of values < -100.00 : 0 ( 0.000 %) Nr of values >= -100.00 and < -50.00 : 780 ( 0.264 %) Nr of values >= -50.00 and < -30.00 : 15222 ( 5.148 %) Nr of values >= -30.00 and < -20.00 : 23328 ( 7.890 %) Nr of values >= -20.00 and < -10.00 : 42825 ( 14.484 %) Nr of values >= -10.00 and < 0.00 : 77377 ( 26.169 %) Nr of values >= 0.00 and < 10.00 : 66974 ( 22.651 %) Nr of values >= 10.00 and < 20.00 : 28849 ( 9.757 %) Nr of values >= 20.00 and < 30.00 : 16553 ( 5.598 %) Nr of values >= 30.00 and < 40.00 : 11028 ( 3.730 %) Nr of values >= 40.00 and < 50.00 : 6946 ( 2.349 %) Nr of values >= 50.00 and < 100.00 : 5797 ( 1.961 %) Nr of values >= 100.00 : 1 ( 0.000 %) ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- MAPMAN > li m1 ... File = crabp.difpat Grid = 40 40 200 Origin = 0 0 0 Extent = 40 21 200 Cell = 41.500 41.500 203.500 90.000 90.000 90.000 ... MAPMAN > ex m1 z25.o2d z 50 O2D file written MAPMAN > ex m1 z50.o2d z 100 O2D file written ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- MAPMAN > 1d Which map ? (m1) O2D plot file ? ( ) c.plt ONTO which axis (X/Y/Z) ? (Z) Nr of points in projection : 301 Average density : 3.9404E+01 Standard deviation : 2.3940E+03 Minimum density : -4.5252E+03 Maximum density : 4.9876E+03 O2D file written ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- MAPMAN > 2d Which map ? (M1) O2D plot file ? ( ) ab.plt ALONG which axis (X/Y/Z) ? (Z) Start plane ? (0) End plane ? (300) Nr of points in projection : 16641 Average density : 7.1369E-01 Standard deviation : 2.8884E+02 Minimum density : -8.0051E+02 Maximum density : 1.2097E+03 O2D file written CPU total/user/sys : 3.6 3.4 0.2 ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- ... Density min,max,ave = -7.2651E+01 1.0000E+02 1.5338E-08 Sigma, variance = 1.9707E+01 3.8836E+02 Mappage prod/plus = 1.4770E+00 107 Mappage dyn. range = -7.2446E+01 1.0021E+02 ... MAPMAN > sc m1 -1 1 Scale : (M1) MAPMAN > li Nr of maps in memory : ( 1)Map 1 = M1 ... Density min,max,ave = -1.0000E+00 1.0000E+00 -1.5841E-01 Sigma, variance = 2.2829E-01 5.2117E-02 Mappage prod/plus = 1.2750E+02 127 Mappage dyn. range = -9.9608E-01 1.0039E+00 ... ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- ... Density min,max,ave = -7.2651E+01 1.0000E+02 1.5338E-08 Sigma, variance = 1.9707E+01 3.8836E+02 Mappage prod/plus = 1.4770E+00 107 Mappage dyn. range = -7.2446E+01 1.0021E+02 ... MAPMAN > zero m1 0 40 Zero : (M1) Less than lower bound : ( 159532) Greater than upper bound : ( 12744) MAPMAN > li m1 Nr of maps in memory : ( 1)Map 1 = M1 ... Density min,max,ave = 0.0000E+00 3.9999E+01 5.0790E+00 Sigma, variance = 8.9967E+00 8.0940E+01 Mappage prod/plus = 6.3751E+00 0 Mappage dyn. range = 0.0000E+00 3.9999E+01 ... ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- MAPMAN > ch Which map ? (m1) Lower bound ? ( -1.0000E+04) -0.001 Upper bound ? ( 9.9900E-01) 0.001 New value ? ( 0.0) -100 Change : (M1) Nr of points changed : ( 61484) Requested dynamic range : -1.0000E+02 1.6125E+01 Value of Prod and Plus : 2.1959E+00 220 Actual dynamic range : -1.0019E+02 1.5939E+01 ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- MAPMAN > mom m1 Moments : (M1)Extensive map statistics Number of data points ................... 439296 Average electron density ................ -1.18879E-07 RMS density ("sigma") ................... 1.24695E+01 Mean Absolute Deviation from the mean ... 8.93063E+00 Variance ................................ 1.55488E+02 Standard deviation ...................... 1.24695E+01 Skewness (third moment) ................. 7.29890E-01 Sigma(skewness) estimate ................ 3.69570E-03 Skewness / Sigma(skewness) .............. 1.97497E+02 Asymmetric tail extending towards positive density Kurtosis (fourth moment) ................ 2.47488E+00 Sigma(kurtosis) estimate ................ 7.39140E-03 Kurtosis / Sigma(kurtosis) .............. 3.34832E+02 Leptokurtic (sharp) distribution ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- MAPMAN > list m1 ... Nr of points = 208800 Density min,max,ave = -4.5111E+01 1.0000E+02 -5.0106E-03 Sigma, variance = 4.3394E+00 1.8831E+01 Mappage prod/plus = 1.7573E+00 79 Mappage dyn. range = -4.4956E+01 1.0016E+02 ... MAPMAN > no m1 Normalise : (M1) Subtract average : ( -5.011E-03) Divide by sigma : ( 4.339E+00) CPU total/user/sys : 1.5 1.4 0.0 MAPMAN > li m1 ... Nr of points = 208800 Density min,max,ave = -1.0397E+01 2.3043E+01 -2.3120E-03 Sigma, variance = 1.0000E+00 1.0000E+00 Mappage prod/plus = 7.6256E+00 79 Mappage dyn. range = -1.0360E+01 2.3080E+01 ... ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- MAPMAN > sw q2.map Origin 0 0 0 Extent 85 66 157 Grid 84 128 156 Cell 49.10 75.80 92.90 89.99 103.20 89.99 Prod/Plus 1.00 0 Scale1/2 100 100 Bricks in x,y,z 11 9 20 Nr of records 1981 Total number of records written = 1981 CPU total/user/sys : 7.0 1.7 5.3 ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- MAPMAN > dh m1 m1bins.plt 500 Calculating histogram ... O2D file written CPU total/user/sys : 2.7 2.5 0.1 ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- % 420 gerard rigel 00:51:31 dirs/p2 > o2dps m1bins.plt hi... o2dps ... convert O2D plot files to PostScript ...
Will convert m1bins.plt to m1bins.ps with option hi ...
Running O2D ...
Lowest X-value : ( -6.610E+01) Highest X-value : ( 8.682E+01) Lowest Y-value : ( 0.000E+00) Highest Y-value : ( 3.158E+05) ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- MAPMAN > pi ?Peak residue & atom names : |HOH| O1 | First peak residue number : 1001 Peak threshold level : 6.0000E+00 Pick limits : 0 0 0 0 0 0 ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- MAPMAN > pick pdb H2O " O " 501 MAPMAN > pi ?Peak residue & atom names : |H2O| O | First peak residue number : 501 Peak threshold level : 6.0000E+00 Pick limits : 0 0 0 0 0 0 ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- MAPMAN > pi lim 0 0 10 -10 5 Upper bound for Z ? (0) 95 MAPMAN > pi ?Peak residue & atom names : |H2O| O | First peak residue number : 501 Peak threshold level : 6.0000E+00 Pick limits : 0 0 10 -10 5 95 ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- MAPMAN > pi lev 5.5 ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- MAPMAN > pi pea m1 peaks.pdb pdb Pick level : ( 5.500E+00) Pick limits : ( 1 64) Pick limits : ( 1 87) Pick limits : ( 5 64) Nr of points in pick volume : ( 334080) Nr of points >= pick level : ( 820) ... Nr of peaks found : ( 52) MAPMAN > $ cat peaks.pdb REMARK Created by MAPMAN V. 930803/2.2 at Tue Aug 3 17:14:32 1993 for user gerard REMARK 52 peaks picked above level 5.500000 REMARK Map file ../../scratch/am/crabp21.difpat REMARK Map name M1 REMARK Map text Read from ../../scratch/am/crabp21.difpat REMARK CRYST1 37.127 106.501 40.495 90.00 110.05 90.00 REMARK Peak # 1 @ 3.220 16.397 46.593 $ 5.985534E+00 ATOM 1 O H2O 501 -7.990 9.922 26.855 1.00 20.00 ... REMARK Peak # 52 @ 65.191 73.900 33.332 $ 5.892479E+00 ATOM 52 O H2O 552 29.660 44.718 19.212 1.00 20.00 END ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- MAPMAN > pi pea m1 multi_roting.log amore Pick level : ( 1.000E+00) Pick limits : ( 1 46) Pick limits : ( 1 71) Pick limits : ( 1 142) Nr of points in pick volume : ( 463772) Nr of points >= pick level : ( 174271) Picking ... Interpolate intensity Nr of peaks found : ( 340) CPU total/user/sys : 1.0 1.0 0.1 MAPMAN > $ cat multi_roting.log REMARK Created by MAPMAN V. 960411/4.5.1 at Thu Apr 11 20:49:51 1996 for user gerard REMARK 340 peaks picked above level 1.000000 REMARK Map file multi_rot.map REMARK Map name M1 REMARK Map text Read from multi_rot.map SOLUTIONRC 1 2.19 40.87 190.94 0.00000 0.00000 0.00000 3.0 0.0 SOLUTIONRC 1 1.43 56.65 354.18 0.00000 0.00000 0.00000 2.9 0.0 SOLUTIONRC 1 2.78 71.59 156.24 0.00000 0.00000 0.00000 3.7 0.0 SOLUTIONRC 1 1.25 85.11 105.13 0.00000 0.00000 0.00000 3.3 0.0 ... SOLUTIONRC 1 113.66 140.50 322.90 0.00000 0.00000 0.00000 3.7 0.0 SOLUTIONRC 1 114.53 156.38 25.65 0.00000 0.00000 0.00000 4.0 0.0 ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- MAPMAN > pick int m1 integrate.pdb pdb Pick level : ( 4.850E+01) Pick limits : ( 9 176) Pick limits : ( 27 233) Pick limits : ( 26 257) Nr of points in pick volume : ( 8068032) Nr of points >= pick level : ( 3903) Picking ... Integrate intensity Nr of peaks found : ( 436) CPU total/user/sys : 17.7 17.6 0.1 MAPMAN > $ head -10 integrate.pdb REMARK Created by MAPMAN V. 951102/4.2 at Thu Nov 2 21:55:50 1995 for user gerard REMARK 436 peaks picked above level 48.50000 REMARK Map file /nfs/scr_uu1/gerard/scratch/m2_fofc.xE REMARK Map name M1 REMARK Map text Read from /nfs/scr_uu1/gerard/scratch/m2_fofc.xE REMARK CRYST1 49.100 75.800 92.900 90.00 103.20 90.00 REMARK Peak # 1 @ 9.346 134.124 169.783 $ 9.681636E+02 ATOM 1 O1 HOH 1001 -14.274 66.886 80.822 1.00 20.00 REMARK Peak # 2 @ 11.919 161.172 115.088 $ 1.303484E+03 ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- MAPMAN > re m1 all1_amore.map ccp4 MAPMAN > his m1 30 32 34 36 38 39 40 MAPMAN > pick lev 39 MAPMAN > pick high m1 Output file ? (peaks.pdb) Format (Pdb|Amore) ? (PDB) amo Pick level : ( 3.900E+01) Pick limits : ( 1 82) Pick limits : ( 1 119) Pick limits : ( 1 250) Nr of points in pick volume : ( 2439500) Nr of points >= pick level : ( 156) Picking ... High-density values Nr of peaks found : ( 156) CPU total/user/sys : 8.7 8.5 0.2 ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- MAPMAN > bo ?Current BONES parameters and defaults : Current BONES map : M1 From file : test.E Skeletonised with base level 5.000 and step 2.000 And including 100 spare points Yielding 2373 points and 2555 connections BONES file : sgi.bones BONES ID for O : SKL Minimum length for main-chain fragments = 4 ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- MAPMAN > bo sk m1 5 2 100 Constructing envelope with base level 5.000 Level increment ..................... 2.000 Number of levels (max. 10) .......... 10 Nr of points (level > 0) in input map 12802 Ditto, in skeletonised map .......... 2273Nr of points in the bones : 2373 (includes spare points !) Nr of spare points : 100 Nr of connections : 2555 Nr of branch-points : 741
Nr of fragments Size less than or equal to 1 = 18 Size less than or equal to 2 = 30 Size less than or equal to 3 = 9 ... Size less than or equal to 100 = 0 Size greater than 100 = 1 Maximum fragment size = 919
CPU total/user/sys : 80.2 78.8 1.4 ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- MAPMAN > bo co sgi.bones skl Min length main-chain fragments ? ( 5) 4 Min length for main-chain fragments : 4 Nr of main-chain connections : 1879 Nr of side-chain connections : 675 eq 1 1 2273 Histogram of bones types 1,2,3.... Bone type : 1 481 1791 100 0 0 0 0 0 0 Type 2 = side-chain; 3 = main-chain Type 1 = left-overs; 4 = spare parts ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- MAPMAN > bo pr bones.pdb 6 5.0 Min length for main-chain fragments : 6 Nr of main-chain connections : 5074 Nr of side-chain connections : 5912 Nr of BONES with 0 neighbours = 372 Nr of BONES with 1 neighbours = 3713 Nr of BONES with 2 neighbours = 5396 Nr of BONES with 3 neighbours = 715 Nr of BONES with 4 neighbours = 22 Nr of BONES with 5 neighbours = 0 Nr of BONES with 6 neighbours = 0 Pruning BONES ... Nr of BONES written to PDB file : ( 6424) Nr of BONES with code 1,2,... written: Nr : (0 1479 4945 0 0 0 0 0 0 0) Nr of BONES with code 1,2,... NOT written: Nr : (1 3793 0 0 0 0 0 0 0 0) CPU total/user/sys : 5.3 5.0 0.3 ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
Some (early) observations:
- MEdian, AVerage, SMooth and VAr_thr reduce noise somewhat
- MAximum and KHighest smear out the density
- SIgnal/noise may bring out density for surface side chains
- LAplace shows the edges of the molecule (sometimes)
- EDge and STat_diff are rather neutral operations
- KLowest, GRadient and MInimum are rather useless
These filters are intended to clean up your density a bit, or to
enhance real features.
An as yet unexplored application lies in the use of these techniques
in density modification.
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- MAPMAN > filter ?Filter options: --------------- MEdian - replace point by median value in local cube MInimum - replace point by minimum value in local cube MAximum - replace point by maximum value in local cube AVerage - replace point by average value in local cube i.e., convolution with 1 1 1 1 1 1 1 1 1 (1/27) * 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 SMooth - convolution with 1 2 1 2 3 2 1 2 1 (1/55) * 2 3 2 3 5 3 2 3 2 1 2 1 2 3 2 1 2 1 EDge - convolution with A A A A A A A A A (1/B) * A A A A B-26A A A A A (A<0, B>0) A A A A A A A A A SIgnal/noise - replace point by average/sigma in local cube GRadient - convolution with (-1 0 +1) in 3 directions LAplace - convolution with (-1 2 -1) in 3 directions KLowest - replace point by average of K lowest nbrs KHighest - replace point by average of K highest nbrs VAr_thr - variable threshold (A, B in <0,1]): NEW = old - (A*sigma + B*ave) STat_diff - statistical differencing (A, B, C in <0,1]): NEW = (1-A)*old + (old-ave)*B*C/(C+B*sigma)
Parameters: Size = one-sided size of small, local cube (usually, 1) A,B,C = parameters that determine the convolution matrix (the program suggests sensible defaults) K = number of neigbours to use in averaging
Further reading : Wayne Niblack, "An Introduction to Digital Image Processing", Prentice-Hall International, London, 1986. ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
MAPMAN > fil smo m1
SMooth - working ...
Filter : ( 1.000 2.000 1.000 2.000 3.000 2.000 1.000
2.000 1.000 2.000 3.000 2.000 3.000 5.000 3.000
2.000 3.000 2.000 1.000 2.000 1.000 2.000 3.000
2.000 1.000 2.000 1.000)
Sum : ( 55.000)
CPU total/user/sys : 3.9 3.9 0.0
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
Some of the input and output formats don't work properly (yet).
Created at Sat Jan 30 02:51:11 1999
by MAN2HTML version 971024/1.6