Re: [ccp4bb] MOLREP self-rotation matrix

[Chen Zhao]

Hi Sacha,

Thanks you for your advice! I tried it and it does work. And thank you for
your effort on this tool. It is really helpful!

Have a nice day,
Chen

On Wed, May 20, 2015 at 3:11 AM, Alexandre OURJOUMTSEV 
wrote:

>  Dear Chen,
>
>
>
> Thank you for your confirmation (it is a pleasure, not everybody does it!).
>
>
>
> I am glad that it works for you.
>
> Now, if you wish/can spend 5 minutes more, you may (see
> http://www-ibmc.u-strasbg.fr/arn/Site_UPR9002/convrot/Convrot.html):
>
>  -  Do the same (I mean – compile) three other fortran programs
> of that package
>
> -  Correct THE FIRST LINE of convrot5.tcl so that it indicates
> the correct PATH to the command 'wish' of the Tcl/tk libraries (directory
> where you have this program at your computer)
>
>
>
> Then normally the GUI version should work; it is more convenient than the
> on-line fortran version alone.
>
>
>
> We understand that this is an obsolete way working with programs and by
> this reason we are finishing its more modern python version (practically
> done…). As for everybody, the problem is absence of time to do this !
>
>
>
> Have a nice day, and good luck !
>
>
> Sacha
>
>
>
>
>
> *De :* Chen Zhao [mailto:c.z...@yale.edu]
> *Envoyé :* mardi 19 mai 2015 18:00
> *À :* Alexandre OURJOUMTSEV
> *Objet :* Re: [ccp4bb] MOLREP self-rotation matrix
>
>
>
> Dear Sacha,
>
> I am able to run the program now. Thank you so much!
>
> Have a nice day,
>
> Chen
>
>
>

Re: [ccp4bb] MOLREP self-rotation matrix

[Alexandre OURJOUMTSEV]

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  de la part de Chen Zhao 

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 
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   0.0000.000  53.626   0.000   0.000
0.000  -0.000   0.004   0.0000.000   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 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 
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 
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 
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 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

Re: [ccp4bb] MOLREP self-rotation matrix

[Alexandre OURJOUMTSEV]

Re: [ccp4bb] MOLREP self-rotation matrix

[Chen Zhao]

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 
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  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   0.0000.000  53.626   0.000   0.000
>>> 0.000  -0.000   0.004   0.0000.000   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  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  wrote:

> I got some answers from the previous thread:
> https://www.mail-archive.com/ccp4bb@jiscmail.ac.uk/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  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  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



>>>
>>
>

>>>
>>
>

Re: [ccp4bb] MOLREP self-rotation matrix

[Chen Zhao]

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 
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   0.0000.000  53.626   0.000   0.000
> 0.000  -0.000   0.004   0.0000.000   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  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  wrote:
>>
>>> I got some answers from the previous thread:
>>> https://www.mail-archive.com/ccp4bb@jiscmail.ac.uk/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  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  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
>>
>>
>>
>

>>>
>>
>

Re: [ccp4bb] MOLREP self-rotation matrix

[Eleanor Dodson]

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   0.0000.000  53.626   0.000   0.000
0.000  -0.000   0.004   0.0000.000   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  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  wrote:
>
>> I got some answers from the previous thread:
>> https://www.mail-archive.com/ccp4bb@jiscmail.ac.uk/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  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  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
>
>
>

>>>
>>
>

Re: [ccp4bb] MOLREP self-rotation matrix

[Chen Zhao]

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  wrote:

> I got some answers from the previous thread:
> https://www.mail-archive.com/ccp4bb@jiscmail.ac.uk/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  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  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



>>>
>>
>

Re: [ccp4bb] MOLREP self-rotation matrix

[Chen Zhao]

I got some answers from the previous thread:
https://www.mail-archive.com/ccp4bb@jiscmail.ac.uk/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  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  > 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  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
>>>
>>>
>>>
>>
>

Re: [ccp4bb] MOLREP self-rotation matrix

[Chen Zhao]

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 
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  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
>>
>>
>>
>

Re: [ccp4bb] MOLREP self-rotation matrix

[Eleanor Dodson]

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  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
>
>
>