COMAP - GENERAL INFORMATION Program : COMAP Version ...

yakconspiracyΛογισμικό & κατασκευή λογ/κού

14 Δεκ 2013 (πριν από 3 χρόνια και 10 μήνες)

91 εμφανίσεις



** COMAP
-

GENERAL INFORMATION



Program : COMAP


Version : 040701


Author : Gerard J. Kleywegt & T. Alwyn Jones,


Dept. of Cell and Molecular Biology,


Uppsala University, Biomedical Centre, Box 596,


SE
-
751 24 Uppsala, SW
EDEN


E
-
mail : gerard@xray.bmc.uu.se


Purpose : combine maps for multiple
-
crystal averaging of


electron
-
density maps


Package : RAVE



** REFERENCES



Reference(s) for this program:



* 1 * T.A. Jones (1992). A, yaap, asap, @#*? A set of aver
aging


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 a
verage density.


Structure 5, 1557
-
1569.


[http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Retrieve&lis
t_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 Crystallogr
aphy, 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.



** VERSION HISTORY



930316
-

0.1
-

in
itial version from map_add.f


930615
-

1.0
-

new production version


931217
-

1.1
-

minor changes


940113
-
1.1.1
-

check that at least two maps entered


950118
-

1.2
-

sensitive to environment variable CCP4_OPEN


960412
-

1.3
-

echo all input to help debug
scripts


961122
-

2.0
-

dynamic memory allocation


010122
-

3.0
-

use C routines to do dynamic memory allocation


and port to Linux


040701
-
3.0.1
-

changed checks of dynamic memory allocation to allow


for pointers with negat
ive values as returned by


some recent Linux versions



** MAP SIZE



From version 2.0 onward, COMAP allocates memory for its maps


dynamically. This means that you can increase the size


that the program can handle on the fly:



1
-

th
rough 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
--
---


ru
n comap 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 maps


which are 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.



COMAP needs space for 3 maps.



** NOTES



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



** DESCRIPTION



With COMAP you can combine and scale various maps to


produce a weighted, averaged map. COMAP is a more


general version of Alwyn's map_a
dd program.



COMAP allows you to combine ANY number of maps,


provided all have the same grid, origin, extent and


unit cells (within 0.01 A or degree). The final


map contains the following density:



-----

EXAMPLE
-----

EXAMPLE
-----

EXAMPLE
----
-

EXAMPLE
-----

EXAMPLE
--
---


Ecombi (x,y,z) = W * SUM (weight(i)*scale(i)*map(i)(x,y,z))


i=1,


NMAP



-

weight (i) = weight for map nr I, defined by the user



/ 1.0, if I = 1


-

scale (i)

=


\

VAR(1)/VAR(I), if I > 1 (VAR = variance of the map)



-

W = 1.0 / (SUM (weight(i)*scale(i)))


-----

EXAMPLE
-----

EXAMPLE
-----

EXAMPLE
-----

EXAMPLE
-----

EXAMPLE
--
---



Note that by clever choices of the weights, COMAP can be


used

to add or subtract maps. The scale factors are


computed by the program and will ensure that (if the Fobs


used to produce the maps have been scaled appropriately)


the individual maps are scaled together properly.



** EXAMPLE



The following exam
ple shows how to add two maps


with weights 1.0 and 2.0:



Start the program and provide the name of the first map


and its weight:



-----

EXAMPLE
-----

EXAMPLE
-----

EXAMPLE
-----

EXAMPLE
-----

EXAMPLE
--
---

...


Reference map : av_0.E

...


Map nr
1 Size 352000


ED min, max, total
-
6.2134E+01 9.3133E+01 2.6856E+00


ED ave, var, stdev 7.6294E
-
06 1.9540E+02 1.3978E+01



Scale : ( 1.000)


Weight ? ( 1.000) 1


-----

EXAMPLE
-----

EXAMPLE
-----

EXAMPLE
-----

EXAMPLE
-----

EXAMPLE
--
-
--



Now give the name of the second file and its weight:



-----

EXAMPLE
-----

EXAMPLE
-----

EXAMPLE
-----

EXAMPLE
-----

EXAMPLE
--
---


Map nr : ( 2)


Map b: scr.E


Read header.

...


Map nr 2 Size 352000


ED min, max, total
-
3.6909E+02

5.0000E+02 2.4826E
-
02


ED ave, var, stdev 7.0529E
-
08 6.0782E+03 7.7963E+01



Scale : ( 0.032)


Weight ? ( 1.000) 2.0


Multiplier : ( 6.429E
-
02)


RMSD map A / B : ( 6.676E+01)


Shape similarity A / B : ( 0.834)


Busy ...


-----

EXAMPLE
-----

EXAMPLE
-----

EXAMPLE
-----

EXAMPLE
-----

EXAMPLE
--
---



Note that several statistics are printed: minimum, maximum


and integrated electron density, the average density, the


variance (used for scaling) and the standard deviation (the


square root

of the variance).



In addition, the RMS difference between this map and the


first one is printed, as is the "shape similarity index"


(values from
-
1 to +1; +1 means that the two maps have


identical shapes, irrespective of the scales they are on)
.



If you want to combine more masks, just keep supplying file


names to the program. Hit [RETURN] to indicate that there


are no more maps to be added.



Note that COMAP actually checks if the maps are on the same


grid etc. as the first one:



--
---

EXAMPLE
-----

EXAMPLE
-----

EXAMPLE
-----

EXAMPLE
-----

EXAMPLE
--
---


Map nr : ( 3)


Map b: av_2x.E


Read header.

...


Map read OK.


Grid : ( 100 110 64)


Origin : ( 31 45 8)


Extent : (

48 53 61)


Cell : ( 91.800 99.500 56.500 90.000 90.000 90.000)


ERROR
---

Different origin, extent, grid, cell


ERROR
---

This map will NOT be added



Map nr : ( 3)


Map b:


-----

EXAMPLE
-----

EXAMPLE
-----

EXAM
PLE
-----

EXAMPLE
-----

EXAMPLE
--
---



After all maps have been added, statistics for the combined


map are printed and you are asked to supply the name of the


output file:



-----

EXAMPLE
-----

EXAMPLE
-----

EXAMPLE
-----

EXAMPLE
-----

EXAMPLE
--
---


Map nr : ( 3)


Map b:


No more maps to add



Sum of weights and scales : ( 1.064E+00)


Map nr 0 Size 352000


ED min, max, total
-
7.7514E+01 1.1771E+02 9.8195E
-
01


ED ave, var, stdev 2.7896E
-
06 2.9797E+02 1.7262E+01



New summed C
CP4 map: sum.E

...


Map written out.

...


-----

EXAMPLE
-----

EXAMPLE
-----

EXAMPLE
-----

EXAMPLE
-----

EXAMPLE
--
---



** KNOWN BUGS



None, at present.