Hi, I trying to rotate a map so that I can section it perpendicular to a particular axis, to prepare a figure for publication. C2221, 88 x 94 x 96 A. Maprot isn't working for me.
The Details:
1. The molecular axis, call it "z1", that I want to align along X is [0.606,0.524,-0.599]. I'll then section perpendicular to X (YZ planes).
2. I created a rotation matrix to get my axis along X, namely MTX = [0.606,0.524,-0.599], [0.599,0.000,0.606], [0.317,-0.726,-0.314] (row1, row2, row3):
3. I checked that MTX rotates z1 onto X. It does, within a tiny fraction of a degree.
4. Matrix has Eulerian angles (ALMN convention) of alpha=134.7, beta=108.3, gamma=246.4 (at least that's what I calculate; am I screwing up here?).
5. Map that I want to plot has density where I think it should, i.e. at fractional coords [0.22,0.03,0.70]. Call this "z2". I checked this in O.
6. Ran Maprot, with above map, Eulerian angles, and told maprot to output a map centered on the **rotated** position of my density of interest, i.e. MTX * z2 = [-0.27,0.55,-0.17].
7. My density is not there. If I extend the output map limits, I can find my density (it's a difference map, and what I'm looking for is the highest point in the map), but my axis z1 is **not** aligned along X. (In O, the density I'm looking at and the atoms from which I calculated z1 are aligned nicely.)
8. Even if somehow I am screwing up the map output limits, should not my axis z1 be aligned (say, if I'm looking at some symmetry mate)? It is 222 symmetry, after all.
What am I doing wrong here? Here's my command script:
mapmask MAPIN test_DELFWT.map MAPOUT 105_1_map.tmp
XYZLIM CELL
#
maprot MAPIN 105_1_map.tmp WRKOUT test_DELFWT_B300X.map
MODE FROM
SYMMETRY WORK 1
XYZLIM -68.0 -28.0 92.0 132.0 -55.0 -15.0
GRID WORK 180 204 204
CELL WORK 87.67120 93.86360 95.78190 90.00000 90.00000 90.00000
AVERAGE
ROTATE EULER 134.7 108.3 246.4
TRANS 0.0 0.0 0.0
#
Input map info:
Overall maximum rho = 0.9436 on section Y = 7 at X = 39 Z = 142
Overall minimum rho = -0.4170 on section Y = 28 at X = 32 Z = 199
Number of columns, rows, sections ............... 204 91 52
Map mode ........................................ 2
Start and stop points on columns, rows, sections 0 203 0 90 0 51
Grid sampling on x, y, z ........................ 180 204 204
Cell dimensions ................................. 87.67120 93.86360 95.78190 90.00000 90.00000 90.00000
Fast, medium, slow axes ......................... Z X Y
Minimum density ................................. -0.41703
Maximum density ................................. 0.94364
Mean density .................................... -0.00002
Rms deviation from mean density ................. 0.06260
Space-group ..................................... 20
Number of titles ................................ 1
Thanks, Dave
~~~~~~~~~~~~~~~~~~~~~~~~
David W. Borhani, Ph.D.
Structural Biology Group Leader
Chemistry Department
Abbott Bioresearch Center
Vox: 508-688-3944
Fax: 508-754-7784
Email: [EMAIL PROTECTED]
Smail: Abbott Bioresearch Center, Inc.
100 Research Drive
Worcester, MA 01605 U.S.A.
http://abbott.com/abbottbioresearch/
~~~~~~~~~~~~~~~~~~~~~~~~
