Uppsala Software Factory

Uppsala Software Factory - AVE Manual


Program : AVE
Version : 080625
Author : Gerard J. Kleywegt & T. Alwyn Jones, Dept. of Cell and Molecular Biology, Uppsala University, Biomedical Centre, Box 596, SE-751 24 Uppsala, SWEDEN
E-mail : gerard@xray.bmc.uu.se
Purpose : single- or multiple-domain, single-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. [http://xray.bmc.uu.se/gerard/papers/halloween.html]

* 3 * G.J. Kleywegt & R.J. Read (1997). Not your average density. Structure 5, 1557-1569. [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Retrieve&list_uids=9438862&dopt=Citation]

* 4 * R.J. Read & G.J. Kleywegt (2001). Density modification: theory and practice. In: "Methods in Macromolecular Crystallography" (D Turk & L Johnson, Eds.), IOS Press, Amsterdam, pp. 123-135.

* 5 * Kleywegt, G.J., Zou, J.Y., Kjeldgaard, M. & Jones, T.A. (2001). Around O. In: "International Tables for Crystallography, Vol. F. Crystallography of Biological Macromolecules" (Rossmann, M.G. & Arnold, E., Editors). Chapter 17.1, pp. 353-356, 366-367. Dordrecht: Kluwer Academic Publishers, The Netherlands.


930331 - 0.0 - empty manual
930505 - 1.1 - basic manual
930602 - 1.2 - new version; decouple average and expand steps for proper symmetry buffs; calculate and print the correlation coefficient for each of the operators
930603 - 1.3 - check that map and mask have same cell and grid
930615 - 2.0 - new production version
931216 - 3.0 - implemented positivity and multiple-domain averaging
940113 -3.0.2- minor changes
950118 - 3.1 - sensitive to environment variable CCP4_OPEN
951022 - 3.2 - made sensitive to OSYM
951030 - 3.3 - enable reading of one OR MANY NCS operators from each file
951121 - 3.4 - included mask-less averaging
960412 - 3.5 - echo all input to help debug scripts
961122 - 4.0 - dynamic memory allocation at last; bug fix (wrong interpolation routine was called ;-()
970523 -4.0.1- print solvent fraction in expansion step (when calculating solvent density)
010122 - 5.0 - use C routines to do dynamic memory allocation and port to Linux
040701 -5.0.1- changed checks of dynamic memory allocation to allow for pointers with negative values as returned by some recent Linux versions
080625 -5.0.2- suppress error messages if more than 10 of them


From version 4.0 onward, AVE 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 ave -b mapsize 10000000 masksize 5000000 < ave.inp >& ave.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.

AVE needs space for 2 maps and 1 mask.


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

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 3.3 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 mixtur of this.


NOTE: from version 1.2 onwards the input has changed since you can now run average and expand separately. THIS MEANS YOU HAVE TO CHANGE OLD COMMAND FILES !!!

You may use this program to:
- average density onto a mask
- expand density into an asymmetric unit or unit cell
- do both in one go (usual m.o.)

These two steps need to be separated if yoy want to employ proper symmetry. For example, you have a tetramer with proper 222 symmetry; in that case proceed as follows:
- make a mask around the whole tetramer
- average with this mask and the four NCS operators
- expand with ONLY the unit NCS operator


Input items:

task = both
unaveraged map
mask file
output averaged & expanded map
spacegroup symmetry operators
NCS operators

task = average
unaveraged map
mask file
output averaged map
spacegroup symmetry operators
NCS operators

task = expand
example map (comprising one ASU or unit cell)
mask file
averaged map (on the same grid as the mask)
output expanded map (same grid as example map)
spacegroup symmetry operators
NCS operators

- all maps are in CCP4 binary format
- masks may come in any format supported by MAMA
- spacegroup symmetry and NCS operators should be provided as "O" datablock files
- the NCS operators would normally explicitly include the UNIT OPERATOR !
- signal the end of the NCS input by an empty line


- if you get "severe FRCSYM errors" during the averaging step, your map probably does not encompass N asymmetric units PLUS ONE POINT ON ALL SIDES

- if you get "interpolation errors" during the expansion step, your mask probably extends too close to the border(s) of its grid (use MAMA to test and remedy this)


8.1 Version 3.0

You are now presented with the following options on startup:

 ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
 Which task ?
  A = Average (normal)
  E = Expand (normal)
  B = Both average and expand (normal)
  Q = Quit right now
  T = Test interpolation
  P = Average; enforce positivity
  R = Average and expand; enforce positivity
  X = Expand; keep zero background
  Y = Average and expand; keep zero background
  Z = Average and expand; zero back; positivity
 ----- 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 AVE to do multiple domain NCS averaging. For example, if you have a hetero-dimer in which each monomer has its own mask and NCS operators, you could proceed as follows:

* calculate a map
* for each domain, average and expand, BUT keep the background density at zero (e.g. with option Y or Z)
* combine the individual expanded map with COMDEM (NOT with COMAP); this will add all contributions together and afterwards calculate the average background density to which all the points which were still at zero will be set
* calculate structure factors, scale them against Fobs and calculate a new map
* average and expand each domain separately again, etc.

8.2 Version 3.4

A new option has been implemented, namely mask-less averaging. This can be used when the boundaries of your molecule are not clear yet (i.e., the extent of the cell where the local (NCS) symmetery operators apply). Probably the way to use it is:
- provide a map around your N-mer (e.g., tetramer)
- run one cycle of mask-less averaging (without expansion !)
- check where in the map density survives and where it doesn't

With improper NCS, only density for one molecule should remain; with proper NCS the boundaries of the whole N-mer should become visible. In the latter case, you can then either use a mask which covers the entire N-mer, or a mask which covers an *arbitrary* 1/N-th of the complete N-mer. However, beware that "proper" symmetry can sometimes be a trifle improper (e.g., a 222 tetramer with small translational components); in such a case, the assumptions break down. In general, it is therefore safest to assume improper symmetry in all cases (my humble opinion).

With mask-less averaging, the major loop is not over mask points, but over points in your asymmetric unit or unit cell. For each point, all NCS operators are applied, and the density is averaged. This means that there are no separate averaging and expansion steps !
The input to the program is the same as usual, except that you don't need to supply a mask file (obviously).


None, at present.

Uppsala Software Factory Created at Thu Jun 26 11:57:37 2008 by MAN2HTML version 070111/2.0.8 . This manual describes AVE, a program of the Uppsala Software Factory (USF), written and maintained by Gerard Kleywegt. © 1992-2007.