On Thursday, 8 November, 2018, 3:56:39 PM GMT, Pavel Afonine
<[email protected]> wrote:
Perhaps
phenix.pdbtools model.pdb rotate=... translate=...
which should work with any PDB or mmCIF file.
I couldn't figure out what angles goes as input for "rotate=" and "translate="
option of the phenix.pdbtools.
I have the following transformation output from the superposition program
Gesamt.
===============================================================================
SUPERPOSITION
~~~~~~~~~~~~~
Q-score : 0.507
RMSD : 2.183
Aligned residues : 103
Sequence Id: : 0.553
Transformation matrix for FIXED structure is identity.
Transformation matrix for MOVING structure:
Rx Ry Rz T
-0.98464 -0.16942 0.04209 15.21830
-0.11460 0.44540 -0.88797 -6.73479
0.13169 -0.87915 -0.45798 -22.57825
Direction cosines of the rotation axis: 0.08359 -0.85001 0.52010
Rotation angle : 176.97882
in fractional coordinates of FIXED structure:
Rx Ry Rz T
-0.97659 -0.11038 0.02448 0.15823
-0.23171 0.44540 -0.59082 -0.15572
0.39704 -1.31089 -0.46603 -0.77840
-------------------------------------------------------------------------------
CENTROIDS
~~~~~~~~~ Orthogonal Fractional
X Y Z XF YF ZF
FIXED 12.62916 16.12512 -0.96160 0.14374 0.37284 -0.03315
MOVING 2.98457 -8.64561 -29.02767 -.-- -.-- -.--
Distance between centroids : 38.65633
Direction cosines of vector between centroids: -0.24950 -0.64079 -0.72604
Angle between rotation axis and vector between centroids: 81.59270
-------------------------------------------------------------------------------
CCP4 format rotation-translation operator
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Polar angles (omega,phi,kappa) : 58.66110 -84.38344 176.97882
Euler angles (alpha,beta,gamma) : -87.28605 117.25684 -98.51918
Orthogonal translation (Angstrom): 15.21830 -6.73479 -22.57825
===============================================================================
Thanks in advance,Kaushik
Pavel
On Thu, Nov 8, 2018 at 11:36 PM Tim Gruene <[email protected]> wrote:
Dear Kaushik,
you could try moleman2 from the Uppsala Software Factory,
http://xray.bmc.uu.se/usf/moleman2_man.html - maybe it keeps those cards
in the PDB file.
Best,
Tim
On 11/8/18 4:23 PM, KAUSHIK H.S. wrote:
> Hello,
>
> I want to transform (rotate+translate) structures determined by NMR. I
> tried using pdbset from the commandline. The program seems to remove
> "MODEL" and "TER" lines from the coordinate file. Is there a way to
> make pdbset retain these lines? or am I missing something obvious?
>
> I could split the ensemble into individual coordinate files, apply
> transformation and merge them back. However, is there an easier way out?
>
> Best wishes,
> Kaushik
>
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