Hi Eleanor, Thank you so much for your test! However, I am not starting with a PDB file. What I am doing self-RF on is just the Patterson map. So my problem is to convert the output Euler angles to orthogonal matrix.
Thanks a lot for your time, Chen On Tue, May 19, 2015 at 5:26 AM, Eleanor Dodson <eleanor.dod...@york.ac.uk> wrote: > Actually it is pretty easy: > > Here is the log of pdbset > > [ccp4@roo job_55]$ pdbset xyzin part.pdb > ... > > Logical name: XYZIN File name: part.pdb > PDB file is being opened on unit 1 for INPUT. > > MATRICES DERIVED FROM CRYST1 CARD IN COORDINATE FILE > > > RF RO > > 0.016 0.009 -0.000 -0.000 61.922 -30.961 0.000 -0.000 > -0.000 0.019 -0.000 0.000 0.000 53.626 0.000 0.000 > 0.000 -0.000 0.004 0.000 0.000 0.000 248.752 -0.000 > -0.000 0.000 -0.000 1.000 -0.000 0.000 -0.000 1.000 > > rota euler 10 20 30 > Data line--- rota euler 10 20 30 > end > Data line--- end > > Logical name: XYZOUT File name: XYZOUT > PDB file is being opened on unit 2 for OUTPUT. > > > Coordinates will be transformed as follows: > > ( 0.714610 -0.613092 0.336824 ) ( x ) ( 0.000 ) > ( 0.633718 0.771281 0.059391 ) ( y ) + ( 0.000 ) > ( -0.296198 0.171010 0.939693 ) ( z ) ( 0.000 ) > > .... > > Of course you still have to worry about the orthogonalisation code used > for the SELFROT search. > > polarrfn tells you what is chosen > > For triclinic, orthorhombic ext the choice is usually > > Z || c* X || a and Y chosen to make an orthogonal set > > > But for monoclinic it is often set > > Z || b* X || a and Y chosen to make an orthogonal set > > Eleanor > > > > On 18 May 2015 at 18:57, Chen Zhao <c.z...@yale.edu> wrote: > >> Sorry for the spaming... Just want to correct that I plan to say covert >> the MOLREP self-RF Euler angle to RESOLVE (not SOLVE) orthogonal matrix... >> >> On Mon, May 18, 2015 at 1:44 PM, Chen Zhao <c.z...@yale.edu> wrote: >> >>> I got some answers from the previous thread: >>> https://www.mail-archive.com/ccp4bb@jiscmail.ac.uk/msg36578.html >>> <https://urldefense.proofpoint.com/v2/url?u=https-3A__www.mail-2Darchive.com_ccp4bb-40jiscmail.ac.uk_msg36578.html&d=AwMFaQ&c=-dg2m7zWuuDZ0MUcV7Sdqw&r=uV9bK9zAIvRZlk7q6-YllA&m=7kauOiFgNMhDGRtA1PkMFhKOYJHao8bdY2NU84DO36U&s=LWP0S_qlKqdAsniO09EK3o72dfTWMQ42_JzTShSCZvQ&e=> >>> >>> But I just want to make sure what I am doing... >>> >>> Thanks a lot, >>> Chen >>> >>> On Mon, May 18, 2015 at 1:36 PM, Chen Zhao <c.z...@yale.edu> wrote: >>> >>>> Hi Eleanor, >>>> >>>> Yeah, the relationship of the XYZ with the unit cell axes is tricky >>>> too. Although I can get some clues by looking at the position of the >>>> crystallographic symmetry axes on the XY plane, it is better if I could >>>> find a definite answer... >>>> >>>> Thank you, >>>> Chen >>>> >>>> On Mon, May 18, 2015 at 1:24 PM, Eleanor Dodson < >>>> eleanor.dod...@york.ac.uk> wrote: >>>> >>>>> Hmm - there are programs which give you the matrix associated with >>>>> Eulerian or Polar angles. I think one is pdbset.. >>>>> >>>>> Or there is documentation in polarrfn or rotmat which describes how to >>>>> do it.. >>>>> >>>>> But remember there are conventions about which axes correspond to the >>>>> orthogonal X Y Z axes used to define the angles >>>>> >>>>> Eleanor >>>>> >>>>> >>>>> On 18 May 2015 at 17:04, Chen Zhao <c.z...@yale.edu> wrote: >>>>> >>>>>> Hi all, >>>>>> >>>>>> I am now trying to convert the NCS axis expressed by theta, phi, chi >>>>>> (or alpha, beta, gamma) from MOLREP to an orthogonal matrix in order to >>>>>> feed into SOLVE. Would anybody suggest me a correct way to do it? >>>>>> >>>>>> Thank you so much in advance! >>>>>> >>>>>> Best, >>>>>> Chen >>>>>> >>>>>> >>>>>> >>>>> >>>> >>> >> >
