Sorry for a "bug" with the previous (empty) mail . Here is the message :
Dear Chen, there is a very old program CONVROT (Urzhumtseva & Urzhumtsev, 1997, J.Appl.Cryst) that you can dowload from http://www-ibmc.u-strasbg.fr/arn/Site_UPR9002/Sites.html (or if you want I can send you a copy off-list). It converts any kind of angles (rotation description) to any other kind of rotation descriptions including the matrices. If you have difficulties to install it as a whole GUI program, for your particular problem you may use only the main fortran program convrot.for. A new python version will come soon I hope. Best regards, Sacha Urzhumtsev ________________________________ De : CCP4 bulletin board <CCP4BB@JISCMAIL.AC.UK> de la part de Chen Zhao <c.z...@yale.edu> Envoyé : mardi 19 mai 2015 16:11 À : CCP4BB@JISCMAIL.AC.UK Objet : Re: [ccp4bb] MOLREP self-rotation matrix 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<mailto: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<mailto: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<mailto: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<mailto: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<mailto: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<mailto: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
