[phenixbb] phenix.simple_ncs_from_pdb output... OMAT?

[Thomas C. Terwilliger]

Hi Francis,
No, I don't think it is the same as OMAT format.Here is the format from
phenix.simple_ncs_from_pdb (identical to the format from resolve):

(Mapping molecule j onto molecule 1)
(As input)
Operator # 1
New X-prime= 1.0000 X + 0.0000 Y + 0.0000 Z + 0.0000
New Y-prime= 0.0000 X + 1.0000 Y + 0.0000 Z + 0.0000
New Z-prime= 0.0000 X + 0.0000 Y + 1.0000 Z + 0.0000
Approximate center_of_mass of this object (from center_of_mass of
object 1 and NC symmetry) is -28.39 18.81 -16.36

Operator # 2
New X-prime= -1.0000 X + -0.0035 Y + -0.0040 Z + -4.1335
New Y-prime= 0.0043 X + -0.1070 Y + -0.9943 Z +-21.6192
New Z-prime= 0.0031 X + -0.9943 Y + 0.1070 Z +-19.2559
Approximate center_of_mass of this object (from center_of_mass of
object 1 and NC symmetry) is 24.44 -7.12 -39.79

would be represnted as:

rota_matrix 1.0000 0.0000 0.0000
rota_matrix 0.0000 1.0000 0.0000
rota_matrix 0.0000 0.0000 1.0000
tran_orth 0.0000 0.0000 0.0000
center_orth -28.3915 18.8125 -16.3621

rota_matrix -1.0000 -0.0035 -0.0040
rota_matrix 0.0043 -0.1070 -0.9943
rota_matrix 0.0031 -0.9943 0.1070
tran_orth -4.1335 -21.6192 -19.2559
center_orth 24.4419 -7.1171 -39.7930


This is in contrast to OMAT:

O/RAVE Format
OMAT
r11   r21   r31    (note that the rotation matrix is
r12   r22   r32    transposed with respect to CCP4
r13   r23   r33    or conventional matrix format)
t1     t2      t3
where
x' = r11 x + r12 y + r13 z + t1
y' = r21 x + r22 y + r23 z + t2
z' = r31 x + r32 y + r33 z + t3

I hope that helps!
-Tom T


>> Is the output rota_matrix (x3), and tran_orth(x1) in OMAT format?
>>
>> Thanks
>>
>> F
>>
>> ---------------------------------------------
>> Francis Reyes M.Sc.
>> 215 UCB
>> University of Colorado at Boulder
>>
>> gpg --keyserver pgp.mit.edu --recv-keys 67BA8D5D
>>
>> 8AE2 F2F4 90F7 9640 28BC  686F 78FD 6669 67BA 8D5D
>>
>>
>>
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