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 <[email protected]> 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 <[email protected]> wrote:
>
>> I got some answers from the previous thread:
>> https://www.mail-archive.com/[email protected]/msg36578.html
>>
>> 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 <[email protected]> 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 <
>>> [email protected]> 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 <[email protected]> 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
>>>>>
>>>>>
>>>>>
>>>>
>>>
>>
>
