XDLMAPMAN (CCP4: Supported Program)
NAME
xdlmapman - X-windows tool; manipulation, analysis and reformatting of electron density maps.SYNOPSIS
xdlmapman [-font1 | font2 | font3 | font4 | font5][menu-driven command selection; interactive parameter input]
DESCRIPTION
xdlmapman can be used to read, write, analyse and manipulate electron-density maps from most biomacromolecular refinement packages, as well as from/for CCP4, PHASES and O.The program runs in interactive mode only. It uses the XDL_VIEW toolkit of J.W. Campbell to provide an easy-to-use interface. Commands are selected by clicking on the desired menu option. Map formats are selected with pop-up menus; all other parameters are set in pop-up dialogue boxes (cut-and-paste is supported). In most cases, default values are given in [square brackets]. To accept these defaults, hit the RETURN key. If multiple numbers are to be input (e.g., cell constants), and if only the first one needs to be changed, for instance, typing the new value for this first number followed by the RETURN key will preserve the values for the other five numbers.
There is a command line option (-font?) which will determine the size of the menu font. These fonts refer to the xdl fonts which are defined from 1 to 5. This can be useful if the window size is too large for the screen. The default font size is 2. The font definitions can be changed in the .Xdefaults file or xrdb, however all xdl programs will be then be effected.
Output from the program is written to a separate area of the main window. Output can be scrolled and cut and pasted into other documents.
For lengthy operations a progress bar shows how much of the operation has been completed.
HISTORY
xdlmapman is a CCP4 special version of MAPMAN (part of the Uppsala RAVE averaging package). This version is entirely interactive and has a user-friendly interface. However, this version can only handle one map at a time, and some of the functionality of the parent program is absent.MAPMAN was originally written as a simple format-exchange program, to convert X-PLOR maps to CCP4 format etc. It has grown quite a bit to handle many types of map, to include MAPPAGE functionality (previously provided as a stand-alone program from Uppsala), and to perform skeletonisation (also previously provided as a stand-alone program from Uppsala) and peak-picking.
Many (parts of) routines were written by other people including Soren Thirup, Morten Kjeldgaard, Wolfgang Steigemann and Phil Evans.
MENU OPTIONS
Commands are issued by moving the pointer over the desired menu option and clicking with the left mouse button.READ A NEW MAPFILE
Provide the name of the file and then select the appropriate file type from the pop-up menu. See FORMATS.LIST MAP STATISTICS
This prints some information and statistics pertaining to the map that is currently in memory.MOMENTS OF THE MAP
This calculates and lists statistical moments of the map (average, standard deviation, skewness and curtosis).MULTIPLY MAP BY A FACTOR
All density values will be multiplied by the number provided (if this number is not equal to zero or one).DIVIDE MAP BY A FACTOR
All density values will be divided by the number provided (if this number is not equal to zero or one).PLUS SOME VALUE
The number provided (if unequal zero) will be added to all density values.SCALE THE MAP TO A RANGE
The map is scaled such that all electron density values lie inside the range of numbers provided (e.g., -100 to +100).ZERO PARTS OF THE MAP
All density values which lie outside the range provided are set to zero.NORMALISE THE MAP
The map will be scaled such that the average density is zero and the standard deviation ("sigma") is one.UVW
The axis-order in which the map is written is changed according to the input by the user. For example, to write out XY sections with Y varying fastest, then X and then Z, use UVW = 2 1 3.SPACEGROUP OF THE MAP
The spacegroup *number* will be set to the number provided. For example, to change the spacegroup to P212121, the number 19 would be entered.CELL CONSTANTS
The cell constants can be edited. This is normally not a good idea. The only exception is when a map is read with a format that does not precisely enough reproduce the cell constants (e.g., integer*2 DSN6 maps). In such cases, angles of 90.0 degrees are sometimes converted to 89.9998.BONES SKELETONISE
This is the Thirup & Jones implementation of Greer's electron density skeletonisation algorithm. A base level (e.g., 1.5 * sigma) and a step size (e.g., sigma) need to be provided. This command would normally be followed by BONES WRITE (quod vide). the reason to separate the two is to enable (1) experimentation with different skeletonisation parameters without having to write out the BONES file, and (2) experimentation with parameters of the BONES WRITE command without a need to redo the skeletonisation.BONES WRITE
Transform the skeletonised density into a set of BONES suitable for use in O. Provide the filename, skeleton name and a cut-off length to partition bones into main-chain and side-chain fragments.PROD_PLUS FOR MAPPAGE/BRIX
With this command the value of Prod and Plus for MAPPAGE and BRIX can be changed. These values are normally set such that the entire range of density can be captured by the integer*2 format of DSN6 maps.RANGE FOR MAPPAGE/BRIX
Instead of supplying Prod and Plus for MAPPAGE and BRIX, the desired range of density values which should be covered in a DSN6 map can be supplied. The program will use this range to calculate appropriate values for Prod and Plus.MAPPAGE FILE
This produces a DSN6 map ("mini-map") suitable for use with O. The map is in binary DSN6 format, using one byte per density value.BRIX FILE
This produces a BRIX map ("mini-map") suitable for use with O. The map is in binary character format, which means that it can head inspected (using Unix commands such as cat, head, or more). In particular, the header record can be inspected in this fashion.SWAPBYTES
This command takes an existing DSN6 map file which was created on a VAX, swaps the bytes, and then writes the new records back to the *same* file.WRITE MAP
Provide the name of the file and then select the appropriate file type from the pop-up menu. See FORMATS.PICK PEAKS
With this command, peaks above a certain level and in a user-defined part of the map can be picked. They are written out as a PDB file containing dummy water molecules (in fact, water oxygen atoms). The algorithm is the same as that used to pick peaks in 2D and 3D NMR spectra (see REFERENCES).DELETE CURRENT MAP
Remove the current map from memory.HELP
This prints some brief information. Subsequently, click on *any* menu command to get a brief explanation of what that command does.QUIT
Stop working with the program.FORMATS
Supported input formats : PROTEIN FFT-Y TENEYCK2 CCP4 X-PLOR EZD MASK NEWEZD BINXPLOR BRICK DSN6 3DMATRIX TNT PHASES FSMASKSupported output formats : CCP4 EZD MASK NEWEZD ENVELOPE
Notes on formats :
- CCP4 - seems to work okay (not masks ?)
- PROTEIN/FFT-Y/TENEYCK2 - untested
- X-PLOR - ASCII maps; works okay
- BINXPLOR - binary maps; may work on 32-bit machines
- BRICK/DSN6 - O-type map files (not BRIX !)
- EZD/NEWEZD - O-type ASCII maps
- MASK - any of the Uppsala mask formats (output: COM only)
- 3DMATRIX - ASCII files from X-PLOR Rot Fun etc.
- TNT - untested
- PHASES - Furey maps; works except for scale
- FSMASK - Furey masks; not implemented yet
- ENVELOPE - CCP4-type masks; does not work ?
- PROTEIN/FFT-Y/TENEYCK2 - untested
REFERENCES
- XDLMAPMAN:
G.J. Kleywegt & T.A. Jones (1996), Acta Cryst. D52, 826-828. - XDL_VIEW:
J.W. Campbell (1995). "XDL_VIEW, an X-windows-based toolkit for crystallographic and other applications", J. Appl. Cryst. 28, 236-242. - RAVE:
G.J. Kleywegt & T.A. Jones (1994). "Halloween ... Masks and Bones", in "From First Map to Final Model" (S. Bailey, R. Hubbard & D. Waller, Eds.), SERC Daresbury Laboratory, pp. 59-66. - MINI-MAPS:
T.A. Jones (1978). "A graphics model building and refinement system for macromolecules", J. Appl. Cryst. 11, 268-272. - O/BONES:
T.A. Jones, J.Y. Zou, S.W. Cowan, & M. Kjeldgaard (1991). "Improved methods for building protein models in electron density maps and the location of errors in these models", Acta Cryst. A47, 110-119. - SKELETONISATION:
J. Greer (1974). "Three-dimensional pattern recognition: an approach to automated interpretation of electron density maps of proteins", J. Mol. Biol. 82, 279-301. - PEAK-PICKING:
G.J. Kleywegt, G.W. Vuister, A. Padilla, R.M.A. Knegtel, R. Boelens, & R. Kaptein (1993). "Computer-assisted assignment of homonuclear 3D NMR spectra of proteins. Application to pike parvalbumin III", J. Magn. Reson. B102, 166-176. - CCP4:
Collaborative Computational Project Number 4 (1994). "The CCP4 suite: programs for protein crystallography", Acta Cryst. D50, 760-763.
KNOWN BUGS
Some of the map formats are untested.If you improve the program, please notify GJK of your changes so that they can be implemented in future versions and the entire community may benefit from them (E-mail a brief description and the relevant pieces of code to "gerard@xray.bmc.uu.se").