Hah, this sounds good. I will try it out! Thank you so much!
Best, Chen On Tue, May 19, 2015 at 10:22 AM, Eleanor Dodson <eleanor.dod...@york.ac.uk> wrote: > Any set of coordinates will do .. > pdbset just converts the eulerian or polar angles to a matrix.. > > In the example I gave > rota euler 10 20 30 > > corresponds to matrix. > ( 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 ) > > > On 19 May 2015 at 15:11, Chen Zhao <c.z...@yale.edu> wrote: > >> 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 >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>> >>>>>> >>>>> >>>> >>> >> >
