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
>>>>>>
>>>>>>
>>>>>>
>>>>>
>>>>
>>>
>>
>

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