[ccp4bb] MOLREP bug..

[Eleanor Dodson]

I give MOLREP am input mtz with space group R32:H or R32 or H32

(entered as R32:H)


But MOLREP claims the SG is


default_PST_limit : 0.250 of origin peak

   PST will not be used.

   If you like to use PST, use keyword PST = Y


 * Space group : H 3*

  No: 146 Sett:   2

  Cell: 185.735 185.735 112.709   90.00   90.00  120.00



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Re: [ccp4bb] Molrep

[Soisson, Stephen M]

Methinks this is sage reasoning on the part of Dr Dodson

Good luck
Steve

On May 27, 2017, at 6:46 AM, Eleanor Dodson 
> wrote:

no idea really - looks like a bug..
There is a limit on the Radius of gyration whch i thinks is
< 0 .5 * shortest_cell_edge..

Probably it is chosen as 27.85, then re-adjusted to allow for anisptropy, and 
not properly trapped.

You could try setting it yourself - there is a keyword - or ignore the "aniso 
correction" option

eleanor



On 26 May 2017 at 00:28, Dyda 
> wrote:
Dear All,

Does anyone know by any chance what to do when Molrep crashes with:

  Radius of gyration  :   27.85
  WARNING: Radius of integration  >42.40
  Radius of integration   :   42.40
  Resolution  :   29.824.00
 --- rfcoef for model ---
 --- rfcoef for Fobs ---
  NCS (from Self rotation Function): 1
  ERROR: in RFROT: RF overflow
  ERR: in CALC_SRF

This is with "anisothermal correction of Fobs" whatever that means.

It runs fine with "default scaling".

Data are very anisotropic, so "anisothermal correction of Fobs" sounded 
attractive.

Thanks.

Fred
 
[32m***
Fred Dyda, Ph.D.   Phone:301-402-4496
Laboratory of Molecular BiologyFax: 301-496-0201
DHHS/NIH/NIDDK 
e-mail:fred.d...@nih.gov
Bldg. 5. Room 303
Bethesda, MD 20892-0560  URGENT message e-mail: 
2022476...@mms.att.net
Google maps coords: 39.000597, -77.102102
http://www2.niddk.nih.gov/NIDDKLabs/IntramuralFaculty/DydaFred
*** 
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Re: [ccp4bb] Molrep

[Gerard Bricogne]

Dear Fred,

 Have you tried putting your data through the STARANISO server at 
 
 http://staraniso.globalphasing.org  ?


 With best wishes,
 
  Gerard.

--
On Thu, May 25, 2017 at 07:28:50PM -0400, Dyda wrote:
> Dear All,
> 
> Does anyone know by any chance what to do when Molrep crashes with:
> 
>   Radius of gyration  :   27.85
>   WARNING: Radius of integration  >42.40
>   Radius of integration   :   42.40
>   Resolution  :   29.824.00
>  --- rfcoef for model ---
>  --- rfcoef for Fobs ---
>   NCS (from Self rotation Function): 1
>   ERROR: in RFROT: RF overflow
>   ERR: in CALC_SRF
> 
> This is with "anisothermal correction of Fobs" whatever that means.
> 
> It runs fine with "default scaling".
> 
> Data are very anisotropic, so "anisothermal correction of Fobs" sounded 
> attractive.  
> 
> Thanks.
> 
> Fred
> ***
> Fred Dyda, Ph.D.   Phone:301-402-4496
> Laboratory of Molecular BiologyFax: 301-496-0201
> DHHS/NIH/NIDDK e-mail:fred.d...@nih.gov  
> Bldg. 5. Room 303 
> Bethesda, MD 20892-0560  URGENT message e-mail: 2022476...@mms.att.net
> Google maps coords: 39.000597, -77.102102
> http://www2.niddk.nih.gov/NIDDKLabs/IntramuralFaculty/DydaFred
> ***

-- 

 ===
 * *
 * Gerard Bricogne g...@globalphasing.com  *
 * *
 * Global Phasing Ltd. *
 * Sheraton House, Castle Park Tel: +44-(0)1223-353033 *
 * Cambridge CB3 0AX, UK   Fax: +44-(0)1223-366889 *
 * *
 ===

[ccp4bb] Molrep

[Dyda]

Dear All,

Does anyone know by any chance what to do when Molrep crashes with:

  Radius of gyration  :   27.85
  WARNING: Radius of integration  >42.40
  Radius of integration   :   42.40
  Resolution  :   29.824.00
 --- rfcoef for model ---
 --- rfcoef for Fobs ---
  NCS (from Self rotation Function): 1
  ERROR: in RFROT: RF overflow
  ERR: in CALC_SRF

This is with "anisothermal correction of Fobs" whatever that means.

It runs fine with "default scaling".

Data are very anisotropic, so "anisothermal correction of Fobs" sounded 
attractive.  

Thanks.

Fred
***
Fred Dyda, Ph.D.   Phone:301-402-4496
Laboratory of Molecular BiologyFax: 301-496-0201
DHHS/NIH/NIDDK e-mail:fred.d...@nih.gov  
Bldg. 5. Room 303 
Bethesda, MD 20892-0560  URGENT message e-mail: 2022476...@mms.att.net
Google maps coords: 39.000597, -77.102102
http://www2.niddk.nih.gov/NIDDKLabs/IntramuralFaculty/DydaFred
***

[ccp4bb] MOLREP phased translation function

[Kajander, Tommi A]

Hi,

is the phased translation function in MolRep still working under CCP4 - doenst 
seem to go forward with the old CCP4 GUI (i cant get any coordinated out phased 
or not)
and the new one (CCP4i2) doesnt seem to have that option? (in other words i 
cant get any solution written out as coordinates).

-

I just get eg something like :


--- convert "molrep.crd" to "molrep.pdb" ---
  Time:15h 57m 14s  Elapsed: 0h 27m 19s

 OPENED INPUT MTZ FILE
 Logical Name: /Users/tkajande/….../overall_best_refine_data.mtz   Filename: 
/Users/tkajande/…../overall_best_refine_data.mtz

 Data line--- LABIN F=FP SIGF=SIGFP

 OPENED INPUT MTZ FILE
 Logical Name: /Users/tkajande/……./overall_best_refine_data.mtz   Filename: 
/Users/tkajande/…../overall_best_refine_data.mtz

 SYMINFO file set to /Applications/ccp4-7.0/lib/data/syminfo.lib
 SYMINFO file set to /Applications/ccp4-7.0/lib/data/syminfo.lib
 SYMINFO file set to /Applications/ccp4-7.0/lib/data/syminfo.lib
 SYMINFO file set to /Applications/ccp4-7.0/lib/data/syminfo.lib
 SYMINFO file set to /Applications/ccp4-7.0/lib/data/syminfo.lib
 SYMINFO file set to /Applications/ccp4-7.0/lib/data/syminfo.lib
 SYMINFO file set to /Applications/ccp4-7.0/lib/data/syminfo.lib
 SYMINFO file set to /Applications/ccp4-7.0/lib/data/syminfo.lib

#CCP4I TERMINATION STATUS 1
#CCP4I TERMINATION TIME 18 Jan 2017  15:57:50
#CCP4I TERMINATION OUTPUT_FILES  XXX_42_molrep.doc XXX_42_molrep.xml 
XXX_42_rf.molrep_rf XXX_42_align.pdb
#CCP4I MESSAGE Task completed successfully



(probably not a good solution but also output file name does not match the one 
suggested..  starting to get bit tired of it...)

Thanks,
Tommi

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 sa...@igbmc.fr
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

[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 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

 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

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 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 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.htmld=AwMFaQc=-dg2m7zWuuDZ0MUcV7Sdqwr=uV9bK9zAIvRZlk7q6-YllAm=7kauOiFgNMhDGRtA1PkMFhKOYJHao8bdY2NU84DO36Us=LWP0S_qlKqdAsniO09EK3o72dfTWMQ42_JzTShSCZvQe=

 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

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 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   0.0000.000  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 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.htmld=AwMFaQc=-dg2m7zWuuDZ0MUcV7Sdqwr=uV9bK9zAIvRZlk7q6-YllAm=7kauOiFgNMhDGRtA1PkMFhKOYJHao8bdY2NU84DO36Us=LWP0S_qlKqdAsniO09EK3o72dfTWMQ42_JzTShSCZvQe=

 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

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 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.ukmailto: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 c.z...@yale.edumailto: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.edumailto:c.z...@yale.edu wrote:
I got some answers from the previous thread: 
https://www.mail-archive.com/ccp4bb@jiscmail.ac.uk/msg36578.htmlhttps://urldefense.proofpoint.com/v2/url?u=https-3A__www.mail-2Darchive.com_ccp4bb-40jiscmail.ac.uk_msg36578.htmld=AwMFaQc=-dg2m7zWuuDZ0MUcV7Sdqwr=uV9bK9zAIvRZlk7q6-YllAm=7kauOiFgNMhDGRtA1PkMFhKOYJHao8bdY2NU84DO36Us=LWP0S_qlKqdAsniO09EK3o72dfTWMQ42_JzTShSCZvQe=

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.edumailto: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.ukmailto: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.edumailto: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

[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 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

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 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

[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 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

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 c.z...@yale.edu 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 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

[ccp4bb] MOLREP self-rotation matrix

[Chen Zhao]

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

[ccp4bb] Molrep and Refmac5 errors

[Rajiv K Bedi]

Dear all,

I recently started using CCP4i (Windows 8) software for data processing and 
model building but I get the following error messages whenever I use molrep and 
refmac5:

MOLREP
#CCP4I TERMINATION STATUS 0  MOLREP(ccp4):  Error in label assignments in 
LABIN
#CCP4I TERMINATION TIME 08 Oct 2013  16:27:56
#CCP4I MESSAGE Task failed

REFMAC5
#CCP4I TERMINATION STATUS 0  Program received signal 11 (SIGSEGV): Segmentation 
fault.
#CCP4I TERMINATION TIME 08 Oct 2013  16:26:50
#CCP4I MESSAGE Task failed

I get those error with every data set I tried, therefore, I would be really 
appreciative if you could help me with it.

Thanks,
Rajiv

[ccp4bb] MolRep error

[Justyna Wojdyla]

Dear All,

I am trying to run MolRep with 'input fixed model' option and i am getting 
error message:

At line 1260 of file /usr/local/xtal/ccp4-6.2.0/src/molrep_/molrep.f
Fortran runtime error: End of record

I am using:
CCP4 6.2: MOLREP(ccp4) version 11.0.02 : 07/02/11

I found the updated version of the molrep binary for Windows system but could 
not see anything for linux. I'll be grateful for your help. 
Justyna

--
Dr Justyna Aleksandra Wojdyla
Department of Biology
University of York
Heslington, York, YO10 5DD
United Kingdom
Tel: +44 (0)1904 328818
Email: justyna.wojd...@york.ac.uk
EMAIL DISCLAIMER http://www.york.ac.uk/docs/disclaimer/email.htm

Re: [ccp4bb] MolRep error

[Garib N Murshudov]

you can try a version from this site:

http://www.ysbl.york.ac.uk/~alexei/molrep.html

If it does not work please let me know


regards
Garib


On 15 Mar 2012, at 12:45, Justyna Wojdyla jw...@york.ac.uk wrote:

 Dear All,
 
 I am trying to run MolRep with 'input fixed model' option and i am getting 
 error message:
 
 At line 1260 of file /usr/local/xtal/ccp4-6.2.0/src/molrep_/molrep.f
 Fortran runtime error: End of record
 
 I am using:
 CCP4 6.2: MOLREP(ccp4) version 11.0.02 : 07/02/11
 
 I found the updated version of the molrep binary for Windows system but could 
 not see anything for linux. I'll be grateful for your help. 
 Justyna
 
 --
 Dr Justyna Aleksandra Wojdyla
 Department of Biology
 University of York
 Heslington, York, YO10 5DD
 United Kingdom
 Tel: +44 (0)1904 328818
 Email: justyna.wojd...@york.ac.uk
 EMAIL DISCLAIMER http://www.york.ac.uk/docs/disclaimer/email.htm

Garib N Murshudov 
Structural Studies Division
MRC Laboratory of Molecular Biology
Hills Road 
Cambridge 
CB2 0QH UK
Email: ga...@mrc-lmb.cam.ac.uk 
Web http://www.mrc-lmb.cam.ac.uk

Re: [ccp4bb] molrep question - how get our ducks in a row?

[Eleanor Dodson]

PISA does just this - download pdb to ebi server; let iyt cluster molecules 
and read back the assembled fcoordinates - plus lots gf useful info..


Eleanor

On Feb 24 2012, David Shin wrote:


Hi Gloria,

It depends on if you mean hard as in thinking up a slick trick, or hard as
in maybe 20-30 mins of tedious work. I had the same problem with 18 in the
ASM, where the solution had scattered models, but didn't want to think
about it, so just used pymol.

1) open the first model with the original 6 models

2) then make separate files with each of the other subunits (with the CRYST
line) - with short names like m1.pdb, m2.pdb, m3.pdb etc. (this is so you
can read easily in the gui  later for saving)

3) then open m1.pdb

4) on the left, go to the A or action menu for m1 .pdb  generate 
symmetry mates   within 100 Angstroms (this can be smaller or larger, just
need to see them)

5) then you'll have the symmates on the screen and the list of each right
listed as m1_100-1-100 etc. So you can just click them on and off to see
which one you like, then save that molecule.

6) Then delete the symmates delete m1_*  so you can check

7) Open the saved symmate to check

8) go to step 3 for the next model, ie. m2.pdb

not a slick answer, but can be done when tired with minimal error.

On Thu, Feb 23, 2012 at 4:07 PM, Gloria Borgstahl 
gborgst...@gmail.comwrote:



Hello all,
We are solving a superstructure of a protein complex with 2 parts.
Built 6 of the first part and they are all sensibly stacked next to each
other.
Then we read this into molrep as the fixed model and solved for the
second part.
The solution was found but the 6 for the second model are in different
ASU's and unit cells.
What is the easiest way to get everyone together in one asu?

We can think of hard ways to do it, but any advice?
Thanks, Gloria








--
Professor Eleanor Dodson
YSNL, Dept of Chemistry
University of York
Heslington YO10 5YW
tel: 00 44 1904 328259
Fax: 00 44 1904 328266

Re: [ccp4bb] molrep question - how get our ducks in a row?

[Daniel Schlieper]

Hello Gloria,

I usually let Coot display the nearest symmetry molecules (as CA) and save 
those that fit: Option Save Symmetry Coordinates... and pick the 
molecule to save.


Best regards, Daniel
--
Daniel Schlieper email: daniel.schlie...@tuxomania.net
Biochemische Pflanzenphysiologie phone: +49 211 8115232
Heinrich-Heine-Universitaet  fax  : +49 211 8113569
40204 Duesseldorf, Germany   http://www.biologie.uni-duesseldorf.de

On Thu, 23 Feb 2012, Gloria Borgstahl wrote:


Hello all,
We are solving a superstructure of a protein complex with 2 parts.
Built 6 of the first part and they are all sensibly stacked next to each other.
Then we read this into molrep as the fixed model and solved for the
second part.
The solution was found but the 6 for the second model are in different
ASU's and unit cells.
What is the easiest way to get everyone together in one asu?

We can think of hard ways to do it, but any advice?
Thanks, Gloria

[ccp4bb] Molrep - Fortran runtime errors

[Jason Porta]

When using a multi-copy search/fitting two models in Molrep, I encounter a 
fortran runtime error. This happens at the stage where the second model is 
being read in. I see that there are some previous posts concerning this. I did 
try using a different version (as previous posters reported working) of molrep, 
but this is not working either. Here are two log outputs concerning the error:

1.) Fortran runtime error: Attempt to allocate negative amount of memory.  

2.) Possible integer overflow/usr/lab/people/jcp/xlinksc/trimmed.pdb 
has failed with error message
At line 1064 of file molrep_keywords.fh
Fortran runtime error: Bad real number in item 3 of list input

I am using Molrep version 11.0.02. All other modules work except for the 
multi-copy search.

Any help and/or suggestions are appreciated,

Best regards,
Jason P

[ccp4bb] molrep question - how get our ducks in a row?

[Gloria Borgstahl]

Hello all,
We are solving a superstructure of a protein complex with 2 parts.
Built 6 of the first part and they are all sensibly stacked next to each other.
Then we read this into molrep as the fixed model and solved for the
second part.
The solution was found but the 6 for the second model are in different
ASU's and unit cells.
What is the easiest way to get everyone together in one asu?

We can think of hard ways to do it, but any advice?
Thanks, Gloria

Re: [ccp4bb] molrep question - how get our ducks in a row?

[David Shin]

Hi Gloria,

It depends on if you mean hard as in thinking up a slick trick, or hard as
in maybe 20-30 mins of tedious work. I had the same problem with 18 in the
ASM, where the solution had scattered models, but didn't want to think
about it, so just used pymol.

1) open the first model with the original 6 models

2) then make separate files with each of the other subunits (with the CRYST
line) - with short names like m1.pdb, m2.pdb, m3.pdb etc. (this is so you
can read easily in the gui  later for saving)

3) then open m1.pdb

4) on the left, go to the A or action menu for m1 .pdb  generate 
symmetry mates   within 100 Angstroms (this can be smaller or larger, just
need to see them)

5) then you'll have the symmates on the screen and the list of each right
listed as m1_100-1-100 etc. So you can just click them on and off to see
which one you like, then save that molecule.

6) Then delete the symmates delete m1_*  so you can check

7) Open the saved symmate to check

8) go to step 3 for the next model, ie. m2.pdb

not a slick answer, but can be done when tired with minimal error.

On Thu, Feb 23, 2012 at 4:07 PM, Gloria Borgstahl gborgst...@gmail.comwrote:

 Hello all,
 We are solving a superstructure of a protein complex with 2 parts.
 Built 6 of the first part and they are all sensibly stacked next to each
 other.
 Then we read this into molrep as the fixed model and solved for the
 second part.
 The solution was found but the 6 for the second model are in different
 ASU's and unit cells.
 What is the easiest way to get everyone together in one asu?

 We can think of hard ways to do it, but any advice?
 Thanks, Gloria




-- 
David Shin, Ph.D
Lawrence Berkeley National Labs
1 Cyclotron Road
MS 83-R0101
Berkeley, CA 94720
USA

Re: [ccp4bb] molrep question - how get our ducks in a row?

[Johan Turkenburg]

Hi,

There is an option in the molrep interface (in the search parameters
tab) to output all models closest to the input coordinate file With a
bit of luck, that should do it.

Johan

On 24 February 2012 00:07, Gloria Borgstahl gborgst...@gmail.com wrote:
 Hello all,
 We are solving a superstructure of a protein complex with 2 parts.
 Built 6 of the first part and they are all sensibly stacked next to each 
 other.
 Then we read this into molrep as the fixed model and solved for the
 second part.
 The solution was found but the 6 for the second model are in different
 ASU's and unit cells.
 What is the easiest way to get everyone together in one asu?

 We can think of hard ways to do it, but any advice?
 Thanks, Gloria



-- 
Dr. Johan P. Turkenburg X-ray facilities manager
York Structural Biology Laboratory
University of York   Phone (+) 44 1904 328251
York YO10 5DD   UK  Fax   (+) 44 1904 328266

Note new email address johan.turkenb...@york.ac.uk

Re: [ccp4bb] MOLREP fails when using input fixed model

[Guenter Fritz]

Dear Zhong Chen and CCP4 users,
I get the very same error on a Centos 5 box. Is there a solution yet?
Best regards,
Guenter

Dear all,
   Recently, I used MOLREP to molecular replacement.
 My OS is fedora 14 and CCP4 version is the newest one ccp4-6.2.0 .
 When I run a pdb file and mtz by MOLREP without input fixed model, everything is right. 
  However, when I run it by MOLREP when using input fixed model. 
 The error is attached below.

 At line 1260 of file /usr/local/xtal/ccp4-6.2.0/src/molrep_/molrep.f
Fortran runtime error: End of record
 Actually, my ccp4 is installed at /home/software/ccp4, not at  
/usr/local/xtal/ccp4-6.2.0/src/molrep_/molrep.f, which does not exist in my 
linux.
In addition, I tried several published structures and tried to test MOLREP  by 
input fixed model method .The error are same.
 Moreover, I tried to run it in windows XP   using input fixed model,  Molrep 
run well.
 
 I thought that it is a bug in this version of MOLREP.

 Any comments are welcome.
  with best wishes
zhong chen
--
zhongzhou chen 
Room 2071, research center in life sciences,

 No. 2 yuanmingyuan west road, Haidian District, Beijing, 100193  P.R. China
Tel: (86)-10-62734078



--
PD Dr. Günter Fritz
Fachbereich Biologie
Universität Konstanz

[ccp4bb] Solved: [ccp4bb] MOLREP fails when using input fixed model

[Guenter Fritz]

Sorry,
I should have had a look also at the CCP4 site:
updated version of molrep from Aug 8.
http://www.ccp4.ac.uk/updates/linux/ccp4-6.2.0/bin/
Cheers
Guenter

Dear Zhong Chen and CCP4 users,
I get the very same error on a Centos 5 box. Is there a solution yet?
Best regards,
Guenter

Dear all,
   Recently, I used MOLREP to molecular replacement.
 My OS is fedora 14 and CCP4 version is the newest one ccp4-6.2.0 .
 When I run a pdb file and mtz by MOLREP without input fixed model, 
everything is right.   However, when I run it by MOLREP when using 
input fixed model.  The error is attached below.

 At line 1260 of file /usr/local/xtal/ccp4-6.2.0/src/molrep_/molrep.f
Fortran runtime error: End of record
 Actually, my ccp4 is installed at /home/software/ccp4, not at  
/usr/local/xtal/ccp4-6.2.0/src/molrep_/molrep.f, which does not exist 
in my linux.
In addition, I tried several published structures and tried to test 
MOLREP  by input fixed model method .The error are same.
 Moreover, I tried to run it in windows XP   using input fixed 
model,  Molrep run well.
 
 I thought that it is a bug in this version of MOLREP.

 Any comments are welcome.
  with best wishes
zhong chen
--
zhongzhou chen Room 2071, research center in life sciences,
 No. 2 yuanmingyuan west road, Haidian District, Beijing, 100193  
P.R. China

Tel: (86)-10-62734078

[ccp4bb] MOLREP TFcntrst

[Sven Dahms]

Dear all,

Does anyone know the definition of the TFcntrst value in MOLREPv10.2.35 and 
the difference of TFcntrst to Cntrst?

an example from a MOLREP log-file:

  Time_elapsed: 0h  0m 18s Remained: 0h  0m 40s
 Sol_ RF TF   Tf/sig  TFcntrst  PFind  PFPFmin  wRfac Scor Scor_max Cntrst
 Sol___1__1   25.38  2.848   1.00  1.00   1.00  0.725  0.143  0.143   0.00
 Sol___2_12   30.78  2.136   1.00  1.00   1.00  0.736  0.120  0.143   0.00
 Sol___3_11   24.33  2.538   1.00  1.00   1.00  0.733  0.124  0.143   0.00
 Sol___4__1   29.08  8.246   1.00  1.00   1.00  0.665  0.266  0.266   0.00
 Sol___5__1   34.66  7.999   1.00  1.00   1.00  0.666  0.265  0.266   0.00
 Sol___6_14   27.33  2.200   1.00  1.00   1.00  0.724  0.135  0.266   0.00
...

If anyone could help me, I'd be very grateful. Thanks!

Sven
-- 
Empfehlen Sie GMX DSL Ihren Freunden und Bekannten und wir
belohnen Sie mit bis zu 50,- Euro! https://freundschaftswerbung.gmx.de

[ccp4bb] MOLREP no output!

[Eric Karg]

Dear all,

I'm using MOLREP in CCP4 for MR. The problem is that it doesn't output a pdb 
file although the last contrast value written in the log file is 3.13! Are 
there certain criteria which have to be fulfilled before it gives a pdb file or 
is it a bug?

Thanks for your help!

Eric

[ccp4bb] MOLREP fails when using input fixed model

[dengzq1987]

Dear all,
   Recently, I used MOLREP to molecular replacement.
 My OS is fedora 14 and CCP4 version is the newest one ccp4-6.2.0 .
 When I run a pdb file and mtz by MOLREP without input fixed model, everything 
is right. 
  However, when I run it by MOLREP when using input fixed model. 
 The error is attached below.
 At line 1260 of file /usr/local/xtal/ccp4-6.2.0/src/molrep_/molrep.f
Fortran runtime error: End of record
 Actually, my ccp4 is installed at /home/software/ccp4, not at  
/usr/local/xtal/ccp4-6.2.0/src/molrep_/molrep.f, which does not exist in my 
linux.
In addition, I tried several published structures and tried to test MOLREP  by 
input fixed model method .The error are same.
 Moreover, I tried to run it in windows XP   using input fixed model,  Molrep 
run well.

 I thought that it is a bug in this version of MOLREP.
 Any comments are welcome.
  with best wishes
zhong chen
 
--
zhongzhou chen 
Room 2071, research center in life sciences,
 No. 2 yuanmingyuan west road, Haidian District, Beijing, 100193  P.R. China
Tel: (86)-10-62734078


15_molrep.log
Description: Binary data

[ccp4bb] Molrep and Coot bugs

[Soisson, Stephen M]

Hello all-

(Paging Paul and Alexei)

I recently came across a difficulty in Coot and Molrep in parsing PDB
files containing insertion residues of the type where the residue number
is the same but with an A, B, etc appendage.

For example, PDB file 2CMR has several instances of the following type:

Chain H:

ATOM   2169  N   LEU H  82  16.387  -4.529  38.070  1.00 25.36
N  
ATOM   2170  CA  LEU H  82  15.979  -3.226  38.555  1.00 25.57
C  
ATOM   2171  C   LEU H  82  15.316  -3.389  39.922  1.00 26.75
C  
ATOM   2172  O   LEU H  82  14.360  -4.111  40.078  1.00 25.74
O  
ATOM   2173  CB  LEU H  82  15.023  -2.596  37.544  1.00 25.63
C  
ATOM   2174  CG  LEU H  82  14.413  -1.206  37.737  1.00 26.28
C  
ATOM   2175  CD1 LEU H  82  15.420  -0.136  37.660  1.00 27.77
C  
ATOM   2176  CD2 LEU H  82  13.343  -0.983  36.660  1.00 28.33
C  
ATOM   2177  N   SER H  82A 15.825  -2.655  40.902  1.00 28.60
N  
ATOM   2178  CA  SER H  82A 15.372  -2.752  42.281  1.00 29.89
C  
ATOM   2179  C   SER H  82A 14.393  -1.640  42.642  1.00 29.70
C  
ATOM   2180  O   SER H  82A 14.078  -0.798  41.806  1.00 29.43
O  
ATOM   2181  CB  SER H  82A 16.596  -2.727  43.180  1.00 29.86
C  
ATOM   2182  OG  SER H  82A 17.038  -4.056  43.307  1.00 34.03
O  
ATOM   2183  N   SER H  82B 13.887  -1.673  43.880  1.00 30.63
N  
ATOM   2184  CA  SER H  82B 12.924  -0.673  44.398  1.00 30.48
C  
ATOM   2185  C   SER H  82B 11.938  -0.229  43.358  1.00 30.29
C  
ATOM   2186  O   SER H  82B 11.818   0.962  43.102  1.00 29.95
O  
ATOM   2187  CB  SER H  82B 13.654   0.570  44.911  1.00 31.02
C  
ATOM   2188  OG  SER H  82B 14.509   0.257  45.981  1.00 32.62
O  
ATOM   2189  N   LEU H  82C 11.231  -1.180  42.758  1.00 31.07
N  
ATOM   2190  CA  LEU H  82C 10.297  -0.869  41.674  1.00 31.04
C  
ATOM   2191  C   LEU H  82C  9.143   0.028  42.133  1.00 31.96
C  
ATOM   2192  O   LEU H  82C  8.499  -0.235  43.149  1.00 31.17
O  
ATOM   2193  CB  LEU H  82C  9.736  -2.138  41.050  1.00 30.89
C  
ATOM   2194  CG  LEU H  82C 10.733  -2.983  40.270  1.00 30.03
C  
ATOM   2195  CD1 LEU H  82C 10.151  -4.334  40.056  1.00 29.26
C  
ATOM   2196  CD2 LEU H  82C 11.157  -2.335  38.918  1.00 28.52
C
ATOM   2197  N   ARG H  83   8.901   1.084  41.361  1.00 32.25
N  
ATOM   2198  CA  ARG H  83   7.794   1.992  41.566  1.00 33.17
C  
ATOM   2199  C   ARG H  83   6.921   1.896  40.344  1.00 32.91
C  
ATOM   2200  O   ARG H  83   7.302   1.285  39.340  1.00 32.53
O  
ATOM   2201  CB  ARG H  83   8.311   3.411  41.795  1.00 33.79
C  
ATOM   2202  CG  ARG H  83   8.658   3.653  43.274  1.00 38.22
C  
ATOM   2203  CD  ARG H  83   9.368   4.995  43.632  1.00 42.93
C  
ATOM   2204  NE  ARG H  83  10.363   5.464  42.651  1.00 45.96
N  
ATOM   2205  CZ  ARG H  83  11.557   4.897  42.402  1.00 47.45
C  
ATOM   2206  NH1 ARG H  83  11.954   3.792  43.028  1.00 48.29
N  
ATOM   2207  NH2 ARG H  83  12.359   5.445  41.501  1.00 48.14
N  


Coot Bug:  file reads and displays fine, but when you do real space
fitting on any of the insertion residues (say residue 82B), the fitting
is actually done on residue 82.

Molrep Bug:  This one is particularly troublesome, as the file is not
parsed correctly, residues end up being re-numbered, and the numbering
is not sequential.  

Example Molrep Output:

ATOM   3696  N   LEU A  84   7.810  42.393   1.658  1.00 20.00
AN
ATOM   3697  CA  LEU A  84   9.191  42.617   1.283  1.00 20.00
AC
ATOM   3698  C   LEU A  84   9.316  42.523  -0.237  1.00 20.00
AC
ATOM   3699  O   LEU A  84   8.968  41.536  -0.839  1.00 20.00
AO
ATOM   3700  CB  LEU A  84  10.070  41.578   1.978  1.00 20.00
AC
ATOM   3701  CG  LEU A  84  11.590  41.538   1.815  1.00 20.00
AC
ATOM   3702  CD1 LEU A  84  12.251  42.705   2.420  1.00 20.00
AC
ATOM   3703  CD2 LEU A  84  12.123  40.253   2.463  1.00 20.00
AC
ATOM   3704  N   SER A  85   9.870  43.569  -0.836  1.00 20.00
AN
ATOM   3705  CA  SER A  85   9.985  43.683  -2.282  1.00 20.00
AC
ATOM   3706  C   SER A  85  11.376  43.304  -2.777  1.00 20.00
AC
ATOM   3707  O   SER A  85  12.243  42.955  -1.980  1.00 20.00
AO
ATOM   3708  CB  SER A  85   9.627  45.107  -2.670  1.00 20.00
AC
ATOM   3709  OG  SER A  85   8.233  45.144  -2.850  1.00 20.00
AO
ATOM   3710  N   SER A  86  11.564  43.336  -4.101  1.00 20.00
AN
ATOM   3711  CA  SER A  86  12.851  42.998  -4.754  1.00 20.00
AC
ATOM   3712  C   SER A  86  13.564  41.867  -4.074  1.00 20.00
AC
ATOM   3713  O   SER A  86  14.714  42.019  -3.684  1.00 20.00
AO
ATOM   3714  CB  SER A  86  13.791  44.206  -4.761  1.00 20.00
AC
ATOM   3715  OG  SER A  86  13.247  45.274  -5.494  1.00 20.00
AO
ATOM   3716  N   LEU A  87  12.888  40.733  -3.930  1.00 20.00
AN
ATOM 

Re: [ccp4bb] molrep NOSG=-1 (space group checking)

[Eleanor Dodson]

I guess the only real choice is P2 21 21 or P21 21 21 -  the absences 
alng h00 could be a result of the pseudo-translation.


I cant explain the score - maybe there is something in the documentation?
But I am afraid after refinement in P212121 the resultant model is sure 
to give the best score in that SG.


Eleanor
PS - I believe in belt-and-braces. What SG did PHASER suggest with the 
original model?

When two programs agree one feels more confident

 On 03/15/2011 05:30 PM, Francis E Reyes wrote:

Hi all


I'm checking all space groups under P222 for data that contains a
pseudotranslation. The data integrates in P222 but a 26% PST peak
(0.500, 0.000, 0.23) makes this look like a C2221 cell (see previous
CCP4bb post subject: Let's talk pseudotranslational symmetry (or maybe
it's bad data). I was able to get a solution (2 molecules per ASU
related by PST) in P 21 21 21, and able to build into additional density
and refine to R/Rfree of 0.274/0.317 for 3.5A data. There still a few
uninterpretable blobs (a linker region of about 6 residues) left.

I'm now trying to do the MR of the refined model in all combinations of
P222 via MOLREP (NOSG=-1).

Now I'm trying to interpret the output of molrep.

--- Space Group Checking. ---
I,Nsg,Scor,Cntr: 1 16 P 2 2 2 0.375 5.521
I,Nsg,Scor,Cntr: 2 17 P 2 2 21 0.415 12.143
I,Nsg,Scor,Cntr: 3 1017 P 21 2 2 0.337 1.722
I,Nsg,Scor,Cntr: 4 2017 P 2 21 2 0.327 14.237
I,Nsg,Scor,Cntr: 5 18 P 21 21 2 0.419 5.169
I,Nsg,Scor,Cntr: 6 2018 P 21 2 21 0.414 10.808
I,Nsg,Scor,Cntr: 7 3018 P 2 21 21 0.463 12.357
I,Nsg,Scor,Cntr: 8 19 P 21 21 21 0.621 18.538
Time: 11h 22m 8s Elapsed: 0h 11m 30s
MOLREP(ccp4): Failure

[1] Is there somewhere in the man page or documentation that explains
how 'Scor' is computed?

[2] Based on the results above, it seems that P 21 21 21 is the correct
s.g.?

[3] Why the failure?

Thanks!

F



-
Francis E. Reyes M.Sc.
215 UCB
University of Colorado at Boulder

gpg --keyserver pgp.mit.edu --recv-keys 67BA8D5D

8AE2 F2F4 90F7 9640 28BC 686F 78FD 6669 67BA 8D5D

[ccp4bb] molrep NOSG=-1 (space group checking)

[Francis E Reyes]

Hi all


I'm checking all space groups under P222 for data that contains a  
pseudotranslation. The data integrates in P222 but a 26% PST peak  
(0.500, 0.000, 0.23) makes this look like a C2221 cell (see previous  
CCP4bb post subject:  Let's talk pseudotranslational symmetry (or  
maybe it's bad data). I was able to get a solution (2 molecules per  
ASU related by PST) in P 21 21 21, and able to build into additional  
density and refine to R/Rfree of 0.274/0.317 for 3.5A data.  There  
still a few uninterpretable blobs (a linker region of about 6  
residues) left.


I'm now trying to do the MR of the refined model in all combinations  
of P222 via MOLREP (NOSG=-1).


Now I'm trying to interpret the output of molrep.

  --- Space Group Checking. ---
  I,Nsg,Scor,Cntr:1   16   P 2 2 2  0.375   
5.521
  I,Nsg,Scor,Cntr:2   17   P 2 2 21 0.415  
12.143
  I,Nsg,Scor,Cntr:3 1017   P 21 2 2 0.337   
1.722
  I,Nsg,Scor,Cntr:4 2017   P 2 21 2 0.327  
14.237
  I,Nsg,Scor,Cntr:5   18   P 21 21 20.419   
5.169
  I,Nsg,Scor,Cntr:6 2018   P 21 2 210.414  
10.808
  I,Nsg,Scor,Cntr:7 3018   P 2 21 210.463  
12.357
  I,Nsg,Scor,Cntr:8   19   P 21 21 21   0.621  
18.538

  Time:11h 22m  8s  Elapsed: 0h 11m 30s
 MOLREP(ccp4):  Failure

[1]  Is there somewhere in the man page or documentation that explains  
how 'Scor' is computed?


[2] Based on the results above, it seems that P 21 21 21 is the  
correct s.g.?


[3] Why the failure?

Thanks!

F



-
Francis E. Reyes M.Sc.
215 UCB
University of Colorado at Boulder

gpg --keyserver pgp.mit.edu --recv-keys 67BA8D5D

8AE2 F2F4 90F7 9640 28BC  686F 78FD 6669 67BA 8D5D

[ccp4bb] Molrep with two models

[Christian Roth]

Dear all,

I tried MolRep with a two domain protein. I have cut the two domain as one 
domain rotates which prevent a search with the complete model. After I finished 
the first run. I put this solution as fixed input model in the second molrep 
run 
with the second domain. The resulting solution positioned the tow expected 
molecules, but not nearby the two already found domains. Interestingly a 
symmetry mate would be at the correct position. I could manually write out the 
coordinates of the symmetry molecule to put the two domains together, but I 
thought Molrep would position it close to the already found domains because 
they belong together and in fact they are one polypeptide chain. 
Why does this not happen? Do I have to incorporate additional information or 
constrains for the Molrep run?

Thanks and Best Regards

Christian

Re: [ccp4bb] Molrep with two models

[Ed Pozharski]

http://www.ysbl.york.ac.uk/~alexei/molrep.html#stick

On Thu, 2011-02-17 at 19:32 +0100, Christian Roth wrote:
 Dear all,
 
 I tried MolRep with a two domain protein. I have cut the two domain as one 
 domain rotates which prevent a search with the complete model. After I 
 finished 
 the first run. I put this solution as fixed input model in the second molrep 
 run 
 with the second domain. The resulting solution positioned the tow expected 
 molecules, but not nearby the two already found domains. Interestingly a 
 symmetry mate would be at the correct position. I could manually write out 
 the 
 coordinates of the symmetry molecule to put the two domains together, but I 
 thought Molrep would position it close to the already found domains because 
 they belong together and in fact they are one polypeptide chain. 
 Why does this not happen? Do I have to incorporate additional information or 
 constrains for the Molrep run?
 
 Thanks and Best Regards
 
 Christian

-- 
I'd jump in myself, if I weren't so good at whistling.
   Julian, King of Lemurs

Re: [ccp4bb] Molrep with two models

[Vellieux Frederic]

The molecular replacement program does not know about your molecule 
being a single polypeptide chain. The problem is fit two bodies 
therefore the program fits two bodies. The centre of mass of whatever 
you wish to position is placed the standard asymmetric unit used by 
the program. If it happens that the center of mass of the second domain 
- linked to the (already positioned) first domain by the polypeptide 
linkages - does not fall within that asymmetric unit, then it won't be 
this one that will be provided in the resulting pdb file. An equivalent 
will be provided. Checking the symmetry equivalents (including limited 
translations) and writing out the correct equivalent to replace that 
you do not wish to have is the way to go. Just as you did. In case of a 
search using the entire molecule, this problem does not occur.


And if you go from a molecular replacement solution provided by program 
X to an automatic model rebuilding program called Y, these two programs 
will not necessarily use the same conventions. Hence you may end up with 
the model after automatic model rebuilding that does not superimpose 
with the input file coming from molecular replacement. Same reason there.


Does that answer your question?

Fred.

Christian Roth wrote:

Dear all,

I tried MolRep with a two domain protein. I have cut the two domain as one 
domain rotates which prevent a search with the complete model. After I finished 
the first run. I put this solution as fixed input model in the second molrep run 
with the second domain. The resulting solution positioned the tow expected 
molecules, but not nearby the two already found domains. Interestingly a 
symmetry mate would be at the correct position. I could manually write out the 
coordinates of the symmetry molecule to put the two domains together, but I 
thought Molrep would position it close to the already found domains because 
they belong together and in fact they are one polypeptide chain. 
Why does this not happen? Do I have to incorporate additional information or 
constrains for the Molrep run?


Thanks and Best Regards

Christian


  

[ccp4bb] Molrep 11.0

[Alexei Vagin]

Molrep 11.0 is available from here:

http://www.ysbl.york.ac.uk/~alexei/molrep.html

Several improvements recently, but the main news is

a new algorithm of Multi-copy search.

Instead of searching for two copies and then for the next two etc.
the program constructs larger multimers (3mers,4mers,5mers,...,
as large as it can) and checks them by the translation function.
It takes time (30 mins to a couple of hours dependent on
the resolution, size of cell, space group) but it is much faster
than the previous implementation.

Re: [ccp4bb] Molrep error - bug 3790

[Charles Ballard]

Dear Jonathan

this sounds like a known issue with the version on molrep that was  
released with ccp4 version 6.1.1 (so if you are having the problem  
with 6.1.3 then it has got back in).   For some reason we did not get  
to the bottom of the file path gets doubled up, /home/caruthej/bo3/ 
ccp4/bo3P1_11_molrep_/home/caruthej/bo3/ccp4/ 
bo3P1_11_molrep_trfn_scr.crd , we have the /home twice.  The  
suggested work around is to upgrade to 6.1.3 .  If you do not wish to  
upgrade fully at this point just download the new version and replace  
the molrep in $CCP4/bin


Sorry for the problem

Charles Ballard
CCP4

On 26 Feb 2010, at 19:31, Jonathan Marvin Caruthers wrote:


All:



Can anyone help me out here?  I'm trying to get Molrep to run but  
it seems to be crashing while trying to open some file after it's  
done the rotation function search.  I'm getting the following error:


**

  Number of RF peaks :  30
 thetaphi chialphabeta   gamma   
RfRf/sigma
 Sol_RF   144.61  -44.03  112.01  272.52   71.21  180.58 
0.3240E+05 10.69
 Sol_RF   262.99  136.68  133.64   93.36  109.980.00 
0.3154E+05 10.40
 Sol_RF   3   111.50 -133.69  138.32   92.40  120.82  179.79 
0.2804E+05  9.25
 Sol_RF   4   139.89   46.56  102.16  273.12   60.170.00 
0.2556E+05  8.43
 Sol_RF   5   147.85   44.94   96.78  271.31   46.891.43 
0.1701E+05  5.61
 Sol_RF   6   119.97 -108.35  162.70   88.58  117.83  125.29 
0.1673E+05  5.52
 Sol_RF   756.80  141.24  140.27  107.82  103.815.34 
0.1650E+05  5.44
 Sol_RF   855.15  142.30  142.33  111.46  101.916.87 
0.1601E+05  5.28
 Sol_RF   954.36  143.15  143.09  113.35  100.887.05 
0.1563E+05  5.16
 Sol_RF  10   115.41 -108.41  160.88   93.02  125.92  129.84 
0.1562E+05  5.15
 Sol_RF  1155.10  137.38  127.36   96.53   94.641.77 
0.1554E+05  5.13
 Sol_RF  12   142.36   34.36  113.03  254.24   61.235.51 
0.1539E+05  5.08
 Sol_RF  13   115.81 -141.38  155.86   64.78  123.37  167.54 
0.1516E+05  5.00
 Sol_RF  14   147.45   78.25  143.98  279.34   61.55  302.85 
0.1501E+05  4.95
 Sol_RF  15   116.29 -141.01  153.70   66.80  121.63  168.82 
0.1500E+05  4.95
 Sol_RF  1675.23  164.12  119.33   97.66  113.14  309.42 
0.1461E+05  4.82
 Sol_RF  17   150.03   57.40   91.74  285.64   42.03  350.83 
0.1450E+05  4.78
 Sol_RF  1849.18  -35.04   85.65  266.17   61.92  156.24 
0.1437E+05  4.74
 Sol_RF  19   139.72   66.72  124.31  281.42   69.74  327.98 
0.1434E+05  4.73
 Sol_RF  2060.59  -24.12   79.57  268.13   67.75  136.36 
0.1434E+05  4.73
 Sol_RF  21   118.54 -105.41  168.98   86.00  121.95  116.82 
0.1429E+05  4.71
 Sol_RF  22   109.08 -138.84  156.70   73.40  135.51  171.08 
0.1422E+05  4.69
 Sol_RF  2337.48  -33.22   75.56  268.37   43.78  154.81 
0.1417E+05  4.67
 Sol_RF  24   118.00 -105.87  171.24   83.39  123.37  115.14 
0.1411E+05  4.65
 Sol_RF  25   119.13 -105.81  169.16   85.22  120.83  116.84 
0.1410E+05  4.65
 Sol_RF  26   117.07 -130.56  136.98   90.32  111.87  171.45 
0.1403E+05  4.63
 Sol_RF  27   142.78   18.10  126.65  230.35   65.43   14.15 
0.1400E+05  4.62
 Sol_RF  28   135.68   14.72  139.96  221.71   82.06   12.27 
0.1399E+05  4.62
 Sol_RF  29   146.60   71.15  139.06  275.24   62.10  312.94 
0.1397E+05  4.61
 Sol_RF  3058.45  -20.76   81.24  273.41   67.39  134.93 
0.1392E+05  4.59

  Final number of peaks :  30
 INFO:Relations between peaks see in molrep.doc
  NCS_model (from Model Self rotation Function): 1
  Program will use NCS =: 1
 Sol_
 Sol_--- Multi-copy Search ---
 Sol_
 Sol_ Resmin,Resmax :   77.324.00
 Sol_ Radius_giration:  30.442
  Radius_max :  56.282
 Sol_ Chi,Delta  :   0.000  10.000
 Sol_ Dist_min,max,Dpar_max  :30.442  1000.000  1000.000
 Sol_
 Sol_--- First monomer search ---
 Sol_
 Sol_ RF TF   Tf/sigTFcntrst PKind PKmax PKmin   Rfac  Scor  
Scor_max Cntrst
 Open failed: Unit:   8, File: /home/caruthej/bo3/ccp4/ 
bo3P1_11_molrep_/home/caruthej/bo3/ccp4/ 
bo3P1_11_molrep_trfn_scr.crd (logical: /home/caruthej/bo3/ccp4/ 
bo3P1_11_molrep_/home/caruthej/bo3/ccp4/bo3P1_11_molrep_trfn_scr.crd)
 MOLREP(ccp4):   Open failed: File: /home/caruthej/bo3/ccp4/ 
bo3P1_11_molrep_/home/caruthej/bo3/ccp4/bo3P1_11_molrep_trfn_scr.crd

Times: User:  82.2s System:1.2s Elapsed: 1:35
/pre
/html
** 
*

* Information from CCP4Interface script
** 
*
The program run with command: /usr/local/ccp4-6.1.0/ccp4-6.1.0/bin/ 
molrep PATH_SCR /home/caruthej/bo3/ccp4/bo3P1_11_molrep_ PATH_OUT  
/home/caruthej/bo3/ccp4/bo3P1_11_molrep_ HKLIN /home/caruthej/ 
bo3/P1/ccp4/merged.mtz MODEL 

Re: [ccp4bb] Molrep error -

[Chavas Leo]

Dear Jon --

it looks to me that it is trying to open a file that does not exist  
because of the path name... I'm not an expert in MolRep, but you  
defined PATH_SCR and PATH_OUT with the same names; the problem might  
then be that it tried to open a file located in the PATH_SCR/ 
PATH_OUT... (or the opposite). Perhaps if you try the following it  
could work:


/usr/local/ccp4-6.1.0/ccp4-6.1.0/bin/molrep PATH_SCR /home/caruthej/ 
bo3/ccp4/ PATH_OUT bo3P1_11_molrep_ HKLIN /home/caruthej/bo3/P1/ 
ccp4/merged.mtz MODEL /home/caruthej/bo3/P1/cns/model.pdb


Sorry if it doesn't help.

Kind regards.

-- Leo --

On 27 Feb 2010, at 04:31, Jonathan Marvin Caruthers wrote:

The program run with command: /usr/local/ccp4-6.1.0/ccp4-6.1.0/bin/ 
molrep PATH_SCR /home/caruthej/bo3/ccp4/bo3P1_11_molrep_ PATH_OUT  
/home/caruthej/bo3/ccp4/bo3P1_11_molrep_ HKLIN /home/caruthej/ 
bo3/P1/ccp4/merged.mtz MODEL /home/caruthej/bo3/P1/cns/model.pdb



Chavas Leonard, Ph.D.
Assistant Professor

Structural Biology Research Center
Photon Factory
High Energy Research Organization (KEK)
305-0801 Tsukuba Oho 1-1
Japan

Tel: +81(0)29-864-5642 (4901)
Fax: +81(0)29-864-2801
e-mail: leonard.cha...@kek.jp

Science Advisory Board (BIT Life Sciences)
Editorial Board (JAA)

http://pfweis.kek.jp/~leo

[ccp4bb] Molrep error -

[Jonathan Marvin Caruthers]

All:



Can anyone help me out here?  I'm trying to get Molrep to run but it seems to 
be crashing while trying to open some file after it's done the rotation 
function search.  I'm getting the following error:

**

  Number of RF peaks :  30
 thetaphi chialphabeta   gamma  RfRf/sigma
 Sol_RF   144.61  -44.03  112.01  272.52   71.21  180.580.3240E+05 10.69
 Sol_RF   262.99  136.68  133.64   93.36  109.980.000.3154E+05 10.40
 Sol_RF   3   111.50 -133.69  138.32   92.40  120.82  179.790.2804E+05  9.25
 Sol_RF   4   139.89   46.56  102.16  273.12   60.170.000.2556E+05  8.43
 Sol_RF   5   147.85   44.94   96.78  271.31   46.891.430.1701E+05  5.61
 Sol_RF   6   119.97 -108.35  162.70   88.58  117.83  125.290.1673E+05  5.52
 Sol_RF   756.80  141.24  140.27  107.82  103.815.340.1650E+05  5.44
 Sol_RF   855.15  142.30  142.33  111.46  101.916.870.1601E+05  5.28
 Sol_RF   954.36  143.15  143.09  113.35  100.887.050.1563E+05  5.16
 Sol_RF  10   115.41 -108.41  160.88   93.02  125.92  129.840.1562E+05  5.15
 Sol_RF  1155.10  137.38  127.36   96.53   94.641.770.1554E+05  5.13
 Sol_RF  12   142.36   34.36  113.03  254.24   61.235.510.1539E+05  5.08
 Sol_RF  13   115.81 -141.38  155.86   64.78  123.37  167.540.1516E+05  5.00
 Sol_RF  14   147.45   78.25  143.98  279.34   61.55  302.850.1501E+05  4.95
 Sol_RF  15   116.29 -141.01  153.70   66.80  121.63  168.820.1500E+05  4.95
 Sol_RF  1675.23  164.12  119.33   97.66  113.14  309.420.1461E+05  4.82
 Sol_RF  17   150.03   57.40   91.74  285.64   42.03  350.830.1450E+05  4.78
 Sol_RF  1849.18  -35.04   85.65  266.17   61.92  156.240.1437E+05  4.74
 Sol_RF  19   139.72   66.72  124.31  281.42   69.74  327.980.1434E+05  4.73
 Sol_RF  2060.59  -24.12   79.57  268.13   67.75  136.360.1434E+05  4.73
 Sol_RF  21   118.54 -105.41  168.98   86.00  121.95  116.820.1429E+05  4.71
 Sol_RF  22   109.08 -138.84  156.70   73.40  135.51  171.080.1422E+05  4.69
 Sol_RF  2337.48  -33.22   75.56  268.37   43.78  154.810.1417E+05  4.67
 Sol_RF  24   118.00 -105.87  171.24   83.39  123.37  115.140.1411E+05  4.65
 Sol_RF  25   119.13 -105.81  169.16   85.22  120.83  116.840.1410E+05  4.65
 Sol_RF  26   117.07 -130.56  136.98   90.32  111.87  171.450.1403E+05  4.63
 Sol_RF  27   142.78   18.10  126.65  230.35   65.43   14.150.1400E+05  4.62
 Sol_RF  28   135.68   14.72  139.96  221.71   82.06   12.270.1399E+05  4.62
 Sol_RF  29   146.60   71.15  139.06  275.24   62.10  312.940.1397E+05  4.61
 Sol_RF  3058.45  -20.76   81.24  273.41   67.39  134.930.1392E+05  4.59
  Final number of peaks :  30
 INFO:Relations between peaks see in molrep.doc
  NCS_model (from Model Self rotation Function): 1
  Program will use NCS =: 1
 Sol_
 Sol_--- Multi-copy Search ---
 Sol_
 Sol_ Resmin,Resmax :   77.324.00
 Sol_ Radius_giration:  30.442
  Radius_max :  56.282
 Sol_ Chi,Delta  :   0.000  10.000
 Sol_ Dist_min,max,Dpar_max  :30.442  1000.000  1000.000
 Sol_
 Sol_--- First monomer search ---
 Sol_
 Sol_ RF TF   Tf/sigTFcntrst PKind PKmax PKmin   Rfac  Scor Scor_max Cntrst
 Open failed: Unit:   8, File: 
/home/caruthej/bo3/ccp4/bo3P1_11_molrep_/home/caruthej/bo3/ccp4/bo3P1_11_molrep_trfn_scr.crd
 (logical: 
/home/caruthej/bo3/ccp4/bo3P1_11_molrep_/home/caruthej/bo3/ccp4/bo3P1_11_molrep_trfn_scr.crd)
 MOLREP(ccp4):   Open failed: File: 
/home/caruthej/bo3/ccp4/bo3P1_11_molrep_/home/caruthej/bo3/ccp4/bo3P1_11_molrep_trfn_scr.crd
   
Times: User:  82.2s System:1.2s Elapsed: 1:35  
/pre
/html
***
* Information from CCP4Interface script
***
The program run with command: /usr/local/ccp4-6.1.0/ccp4-6.1.0/bin/molrep 
PATH_SCR /home/caruthej/bo3/ccp4/bo3P1_11_molrep_ PATH_OUT 
/home/caruthej/bo3/ccp4/bo3P1_11_molrep_ HKLIN 
/home/caruthej/bo3/P1/ccp4/merged.mtz MODEL 
/home/caruthej/bo3/P1/cns/model.pdb 
has failed with error message
Last system error message: No such file or directory
 MOLREP(ccp4):   Open failed: File: 
/home/caruthej/bo3/ccp4/bo3P1_11_molrep_/home/caruthej/bo3/ccp4/bo3P1_11_molrep_trfn_scr.crd
   
***


#CCP4I TERMINATION STATUS 0 Last system error message: No such file or 
directory  MOLREP(ccp4):   Open failed: File: 
/home/caruthej/bo3/ccp4/bo3P1_11_molrep_/home/caruthej/bo3/ccp4/bo3P1_11_molrep_trfn_scr.crd
   
#CCP4I TERMINATION TIME 26 Feb 2010  11:34:11
#CCP4I MESSAGE Task failed

*

It appears to be trying to open 

Re: [ccp4bb] Molrep error -

[James Stroud]

Often times these types of errors arise from the lack of write  
permissions to the directory in question or the lack of a directory  
altogether. The clue is here/The clue is here:


  /home/caruthej/bo3/ccp4/bo3P1_11_molrep_/home/caruthej/bo3/ccp4/

James


On Feb 26, 2010, at 11:31 AM, Jonathan Marvin Caruthers wrote:


All:



Can anyone help me out here?  I'm trying to get Molrep to run but it  
seems to be crashing while trying to open some file after it's done  
the rotation function search.  I'm getting the following error:


**

 Number of RF peaks :  30
thetaphi chialphabeta   gamma  Rf 
Rf/sigma
Sol_RF   144.61  -44.03  112.01  272.52   71.21  180.58 
0.3240E+05 10.69
Sol_RF   262.99  136.68  133.64   93.36  109.980.00 
0.3154E+05 10.40
Sol_RF   3   111.50 -133.69  138.32   92.40  120.82  179.79 
0.2804E+05  9.25
Sol_RF   4   139.89   46.56  102.16  273.12   60.170.00 
0.2556E+05  8.43
Sol_RF   5   147.85   44.94   96.78  271.31   46.891.43 
0.1701E+05  5.61
Sol_RF   6   119.97 -108.35  162.70   88.58  117.83  125.29 
0.1673E+05  5.52
Sol_RF   756.80  141.24  140.27  107.82  103.815.34 
0.1650E+05  5.44
Sol_RF   855.15  142.30  142.33  111.46  101.916.87 
0.1601E+05  5.28
Sol_RF   954.36  143.15  143.09  113.35  100.887.05 
0.1563E+05  5.16
Sol_RF  10   115.41 -108.41  160.88   93.02  125.92  129.84 
0.1562E+05  5.15
Sol_RF  1155.10  137.38  127.36   96.53   94.641.77 
0.1554E+05  5.13
Sol_RF  12   142.36   34.36  113.03  254.24   61.235.51 
0.1539E+05  5.08
Sol_RF  13   115.81 -141.38  155.86   64.78  123.37  167.54 
0.1516E+05  5.00
Sol_RF  14   147.45   78.25  143.98  279.34   61.55  302.85 
0.1501E+05  4.95
Sol_RF  15   116.29 -141.01  153.70   66.80  121.63  168.82 
0.1500E+05  4.95
Sol_RF  1675.23  164.12  119.33   97.66  113.14  309.42 
0.1461E+05  4.82
Sol_RF  17   150.03   57.40   91.74  285.64   42.03  350.83 
0.1450E+05  4.78
Sol_RF  1849.18  -35.04   85.65  266.17   61.92  156.24 
0.1437E+05  4.74
Sol_RF  19   139.72   66.72  124.31  281.42   69.74  327.98 
0.1434E+05  4.73
Sol_RF  2060.59  -24.12   79.57  268.13   67.75  136.36 
0.1434E+05  4.73
Sol_RF  21   118.54 -105.41  168.98   86.00  121.95  116.82 
0.1429E+05  4.71
Sol_RF  22   109.08 -138.84  156.70   73.40  135.51  171.08 
0.1422E+05  4.69
Sol_RF  2337.48  -33.22   75.56  268.37   43.78  154.81 
0.1417E+05  4.67
Sol_RF  24   118.00 -105.87  171.24   83.39  123.37  115.14 
0.1411E+05  4.65
Sol_RF  25   119.13 -105.81  169.16   85.22  120.83  116.84 
0.1410E+05  4.65
Sol_RF  26   117.07 -130.56  136.98   90.32  111.87  171.45 
0.1403E+05  4.63
Sol_RF  27   142.78   18.10  126.65  230.35   65.43   14.15 
0.1400E+05  4.62
Sol_RF  28   135.68   14.72  139.96  221.71   82.06   12.27 
0.1399E+05  4.62
Sol_RF  29   146.60   71.15  139.06  275.24   62.10  312.94 
0.1397E+05  4.61
Sol_RF  3058.45  -20.76   81.24  273.41   67.39  134.93 
0.1392E+05  4.59

 Final number of peaks :  30
INFO:Relations between peaks see in molrep.doc
 NCS_model (from Model Self rotation Function): 1
 Program will use NCS =: 1
Sol_
Sol_--- Multi-copy Search ---
Sol_
Sol_ Resmin,Resmax :   77.324.00
Sol_ Radius_giration:  30.442
 Radius_max :  56.282
Sol_ Chi,Delta  :   0.000  10.000
Sol_ Dist_min,max,Dpar_max  :30.442  1000.000  1000.000
Sol_
Sol_--- First monomer search ---
Sol_
Sol_ RF TF   Tf/sigTFcntrst PKind PKmax PKmin   Rfac  Scor  
Scor_max Cntrst
Open failed: Unit:   8, File: /home/caruthej/bo3/ccp4/ 
bo3P1_11_molrep_/home/caruthej/bo3/ccp4/bo3P1_11_molrep_trfn_scr.crd  
(logical: /home/caruthej/bo3/ccp4/bo3P1_11_molrep_/home/caruthej/bo3/ 
ccp4/bo3P1_11_molrep_trfn_scr.crd)
MOLREP(ccp4):   Open failed: File: /home/caruthej/bo3/ccp4/ 
bo3P1_11_molrep_/home/caruthej/bo3/ccp4/bo3P1_11_molrep_trfn_scr.crd

Times: User:  82.2s System:1.2s Elapsed: 1:35
/pre
/html
***
* Information from CCP4Interface script
***
The program run with command: /usr/local/ccp4-6.1.0/ccp4-6.1.0/bin/ 
molrep PATH_SCR /home/caruthej/bo3/ccp4/bo3P1_11_molrep_ PATH_OUT  
/home/caruthej/bo3/ccp4/bo3P1_11_molrep_ HKLIN /home/caruthej/bo3/ 
P1/ccp4/merged.mtz MODEL /home/caruthej/bo3/P1/cns/model.pdb

has failed with error message
Last system error message: No such file or directory
MOLREP(ccp4):   Open failed: File: /home/caruthej/bo3/ccp4/ 
bo3P1_11_molrep_/home/caruthej/bo3/ccp4/bo3P1_11_molrep_trfn_scr.crd

***


#CCP4I TERMINATION STATUS 0 Last system error message: No such file  
or directory  

Re: [ccp4bb] MOLREP

[Eleanor Dodson]

How can that be!  Are you also providing a sequence?

Eleanor

Tommi Kajander wrote:

Hi,
I have been using a dimer as a search model in MOLREP (there will be 
several in AU),
for some reason the program tends to break the dimer into monomers 
wihtout asking me..
how is this determined in the program... a more detailed manual would 
be nice, also on the output
as the different contrasts and their meaning appear bit cryptic to me. 
(i am beginning to get the hang of it

but its still bit fuzzy..)

Also if i am searching for number of say these dimers and there is a 
speudo-translation vector
should it be used all the time? (i would assume not all the searched 
unit are related necessarily by the
translational NCS) (to make it even merrier, there is both proper 
speudo centering and just translational
NCS  .. and you can only specify one vector... if we are lucky its 
also twinned...


thanks for comments,
Tommi

Re: [ccp4bb] MOLREP

[Eleanor Dodson]

Then I suspect the sequence is overriding the model.

My preferred approach.
Get a sequence alignment from somewhere and use CHAINSAW to edit the 
model you want to use. That is documented!  And it will edit both 
monomers in turn I believe..


Then you will have a dimer with the appropriate sequence editing done 
for you.


Now give that toMOLREP without any sequence. Now I am pretty sure it 
will use your whole model.
It will determine the non-cryst tramslation and apply it automatically 
to all copies I guess but if you have strong NCT then it usually more or 
less relates allmolecules..

.

Pseudo centring - what do you mean by that?

Twinning - Aaagh
Eleanor


tommi kajander wrote:
yes i am, i haven't got a clue, it always seems to be doing somethig 
other than i want it to..
to be honest the manual is prety obsolete and non-existent, would be 
nice if the authors provided

more info on current vresion.

tommi


On 1.10.2009, at 11.10, Eleanor Dodson wrote:


How can that be!  Are you also providing a sequence?

Eleanor

Tommi Kajander wrote:

Hi,
I have been using a dimer as a search model in MOLREP (there will be 
several in AU),
for some reason the program tends to break the dimer into monomers 
wihtout asking me..
how is this determined in the program... a more detailed manual 
would be nice, also on the output
as the different contrasts and their meaning appear bit cryptic to 
me. (i am beginning to get the hang of it

but its still bit fuzzy..)

Also if i am searching for number of say these dimers and there is a 
speudo-translation vector
should it be used all the time? (i would assume not all the searched 
unit are related necessarily by the
translational NCS) (to make it even merrier, there is both proper 
speudo centering and just translational
NCS  .. and you can only specify one vector... if we are lucky its 
also twinned...


thanks for comments,
Tommi







Tommi Kajander, Ph.D.
Macromolecular X-ray Crystallography
Research Program in Structural Biology and Biophysics
Institute of Biotechnology
P.O. Box 65 (Street: Viikinkaari 1, 4th floor)
University of Helsinki
FIN-00014 Helsinki, Finland
Tel. +358-9-191 58903
Fax  +358-9-191 59940

[ccp4bb] MOLREP

[Tommi Kajander]

Hi,
I have been using a dimer as a search model in MOLREP (there will be  
several in AU),
for some reason the program tends to break the dimer into monomers  
wihtout asking me..
how is this determined in the program... a more detailed manual would  
be nice, also on the output
as the different contrasts and their meaning appear bit cryptic to me.  
(i am beginning to get the hang of it

but its still bit fuzzy..)

Also if i am searching for number of say these dimers and there is a  
speudo-translation vector
should it be used all the time? (i would assume not all the searched  
unit are related necessarily by the
translational NCS) (to make it even merrier, there is both proper  
speudo centering and just translational
NCS  .. and you can only specify one vector... if we are lucky its  
also twinned...


thanks for comments,
Tommi

Re: [ccp4bb] molrep can't find *_trfn_scr.crd

[Stein, ND (Norman)]

Hi Francis

This is a known problem. Molrep is prepending the path name twice to the
file name, which means that when it subsequently looks for the file, it
cannot find it. You can fix the problem by downloading the latest source
code version of molrep from Alexei's site:

http://www.ysbl.york.ac.uk/~alexei/molrep.html#installation

Alternatively you can pick up a Molrep 10.2.31 binary for Linux from

ftp://ftp.ccp4.ac.uk/nds/molrep_10.2.31/molrep  

Norman Stein
CCP4

-Original Message-
From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On Behalf Of
Francis E Reyes
Sent: 29 June 2009 18:15
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] molrep can't find *_trfn_scr.crd

When doing a multi-copy search, after the first rotation is done it
seems to be looking for a _121_molrep_trfn_scr.crd file in my /tmp
directory that it can't find just prior to doing the first monomer
search.

Anyone have any ideas?
thanks

FR

-
Francis Reyes M.Sc.
215 UCB
University of Colorado at Boulder

gpg --keyserver pgp.mit.edu --recv-keys 67BA8D5D

8AE2 F2F4 90F7 9640 28BC  686F 78FD 6669 67BA 8D5D
--
Scanned by iCritical.

[ccp4bb] molrep can't find *_trfn_scr.crd

[Francis E Reyes]

When doing a multi-copy search, after the first rotation is done it  
seems to be looking for a _121_molrep_trfn_scr.crd file in my /tmp  
directory that it can't find just prior to doing the first monomer  
search.


Anyone have any ideas?
thanks

FR

-
Francis Reyes M.Sc.
215 UCB
University of Colorado at Boulder

gpg --keyserver pgp.mit.edu --recv-keys 67BA8D5D

8AE2 F2F4 90F7 9640 28BC  686F 78FD 6669 67BA 8D5D

Re: [ccp4bb] MolRep of coiled coils

[Thomas Edwards]

Sorry - I should have added that, yes, there are 2 identical peptide chains 
that should be parallel coiled-coil.
Any advice gratefully received.
Ed


-Original Message-
From: cockburn [mailto:[EMAIL PROTECTED]
Sent: Fri 3/28/2008 1:35 PM
To: Thomas Edwards
Subject: Re: [ccp4bb] MolRep of coiled coils
 
Hi Thomas,
Does your coiled-coil consist of two polypeptide chains, and are their 
sequences identical? Do you expect it to be a parallel or anti-parallel 
coiled-coil?
Yours
Joe

Thomas Edwards a écrit :
 Dear BB,

 I am attempting molecular replacement with a 2.8A data set from crystals of a 
 coiled coil of about 150 residues.
 Probably p21212 but maybe p2221.

 So far, Phaser, MolRep, Amore, Mr Bump, have not provided a good solution as 
 judged by Z-scores, CCs, Rfactors, and whether there is any density outside 
 the model (there should be - I'm using a slightly shorter model to search 
 with).

 One possible problem is that the coiled coil may not be straight. It may have 
 a slight curve to it.
 I have used models from the PDB that are straight or slightly curved, so far 
 with no success.
 I have tried a few different resolution cutoffs too.
 I have tried single helix chains or dimeric coiled coils.

 Is there anything special about MR with coiled coils?
 Can anybody provide any tips/hints on MR with coiled coils??

 Thanks
 Ed
   

Re: [ccp4bb] MolRep of coiled coils

[M T]

My short experience with coiled-coil is that molecular replacement can
be difficult for classical software (due to the very anysotropic
shape of the protein).
In our case (a short parallel dimeric coiled-coil), molecular
replacement trials using AMoRe or MOLREP were unsuccessful. We solved
the structure using EPMR (evolutionary search molecular replacement
software).
http://www.msg.ucsf.edu/local/programs/epmr/epmr.html

Michel.

Re: [ccp4bb] MolRep of coiled coils

[Das, Debanu]

Hi Thomas,
   MR of coiled coils can be quite tricky including considerations of being 
curved, etc. If conventional MR is failing (assuming you have tried different 
kinds of parameter and search model tweaks, you can also play around with the 
search thresholds in phaser), you may try the following:

If you have multiple copies in the asu, you may try to find the orientation of 
the NCS axis. If you think that the molecules may be aligned along a particular 
direction, you can then generate a list of rotation search angles manually in 
fine increments (couple of degrees) and then force a translation search around 
all these rotation angles and then follow it up with a packing function search. 
This is like a brute force rotation/translation search across all rotation 
angles. Therefore identification of the ncs axis/molecular orientation will 
provide some search time advantage.
You can do this in PHASER. Check out the manual to run stand alone scripts for 
these steps.

Although different from the above, the follg. reference may provide useful 
reading:
Gonzalez L Jr, Brown RA, Richardson D, Alber T.
Crystal structures of a single coiled-coil peptide in two oligomeric states 
reveal the basis for structural polymorphism.
Nat Struct Biol. 1996 Dec;3(12):1002-9.

Also check tropomysin structure MR attempts from Carolyn Cohen's group.

Regards,
Debanu.
--
Debanu Das,
Structure Determination Core,
Joint Center for Structural Genomics.
Stanford Synchrotron Radiation Laboratory,
Menlo Park, CA.


-Original Message-
From: CCP4 bulletin board on behalf of Thomas Edwards
Sent: Fri 3/28/2008 5:57 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] MolRep of coiled coils
 
Dear BB,

I am attempting molecular replacement with a 2.8A data set from crystals of a 
coiled coil of about 150 residues.
Probably p21212 but maybe p2221.

So far, Phaser, MolRep, Amore, Mr Bump, have not provided a good solution as 
judged by Z-scores, CCs, Rfactors, and whether there is any density outside the 
model (there should be - I'm using a slightly shorter model to search with).

One possible problem is that the coiled coil may not be straight. It may have a 
slight curve to it.
I have used models from the PDB that are straight or slightly curved, so far 
with no success.
I have tried a few different resolution cutoffs too.
I have tried single helix chains or dimeric coiled coils.

Is there anything special about MR with coiled coils?
Can anybody provide any tips/hints on MR with coiled coils??

Thanks
Ed

Re: [ccp4bb] MolRep of coiled coils

[James Holton]

MR on CCs is generally a pain.  The problem is that sliding any CC along 
its own supertwist (say by one heptad) will give you a solution that 
lines up very well with the right model.  There are a lot of solutions 
of this type, so you basically have a multitude of models that are all 
okay and the right one is not that much better than any of them.  
Hence, the Z-score is low.  This problem gets even worse if your CC 
crystallizes end-to-end with another copy of itself (CCs like to do that).


I'd be willing to bet that you actually already have the right 
solution.  Take the best one from your favorite program and start 
refining it.  Do rigid body first and keep re-applying rigid-body 
refinement until the model stops moving.  This is important.  Don't just 
stop when the Rcryst flattens out.  Let the MODEL settle down.  Then 
break the CC in half.  Rigid-body each half until they stop moving.  
Keep sub-dividing like this.  Eventually, you will be refining 
individual heptads from each chain.  This is a poor-man's way to do 
rubber body refinement which should let you refine a bent CC.  rubber 
body refinement in general lets you make much bigger leaps in 
coordinate space than all-atom refinement.  Using this methodology, I 
was once able to solve an antiparallel trimer CC using a parallel trimer 
as the starting model.  (the reversed chain was apparent in the refined 
map, but not in the starting map).


It can also be useful to start with idealized coiled-coil models.  The 
PDB does not always contain what you want.  I wrote a little jiffy 
program for generating an idealized coiled-coil in PDB format here:

http://bl831.als.lbl.gov/~jamesh/scripts/supertwist.awk
The top of this file (text) contains instructions on how to use it.  The 
idealized CC MR method proved useful in solving this structure:

R. Howard et. al. Neuron 53(5), 663-75.
and the methodology is described in that paper.  Using idealized models 
allows you to scan over the various superhelical parameters and then 
plot the Z-score, CC, or whatever you like vs the parameter.  Once you 
have optimized each parameter, you can do a multi-dimensional MR 
meta-search over a small range of all the parameters.


-James Holton
MAD Scientist


Thomas Edwards wrote:

Dear BB,

I am attempting molecular replacement with a 2.8A data set from crystals of a 
coiled coil of about 150 residues.
Probably p21212 but maybe p2221.

So far, Phaser, MolRep, Amore, Mr Bump, have not provided a good solution as 
judged by Z-scores, CCs, Rfactors, and whether there is any density outside the 
model (there should be - I'm using a slightly shorter model to search with).

One possible problem is that the coiled coil may not be straight. It may have a 
slight curve to it.
I have used models from the PDB that are straight or slightly curved, so far 
with no success.
I have tried a few different resolution cutoffs too.
I have tried single helix chains or dimeric coiled coils.

Is there anything special about MR with coiled coils?
Can anybody provide any tips/hints on MR with coiled coils??

Thanks
Ed
  

[ccp4bb] Molrep fails to run

[Mike Xishan]

Dear all
sorry if this query has already been asked. Whenever, I run a job for
molecular replacement in Molrep program using ccp4i, it fails to run and
shows the following error.
Child killed: segementation violation

I would appreciate for suggestions to fix this eror.

xishan

Re: [ccp4bb] Molrep fails to run

[Stein, ND (Norman)]

Dear Xishan
 
Can you tell me what version of CCP4 you are running and on which
platform? Have you been able to run other programs through ccp4i
successfully?
Does the molrep job fail immediately or does it produce any output
before failing? If the latter, it would be very useful to see all the
output.
 
Norman Stein
CCP4 



From: CCP4 bulletin board [mailto:[EMAIL PROTECTED] On Behalf Of
Mike Xishan
Sent: 25 February 2008 11:28
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] Molrep fails to run


Dear all
sorry if this query has already been asked. Whenever, I run a job for
molecular replacement in Molrep program using ccp4i, it fails to run and
shows the following error.
Child killed: segementation violation
 
I would appreciate for suggestions to fix this eror.
 
xishan

[ccp4bb] MOLREP for space group F432

[Manfred S. Weiss]

Dear CCP4ers,

has anybody ever noticed a strange behaviour of MOLREP in space
group F432 (no. 209)? It seems as if the rotation function works
ok, but translation functions take about 100 times the time they
should.

Cheers, Manfred.


*  *
*Dr. Manfred S. Weiss  *
*  *
* Team Leader  *
*  *
* EMBL Hamburg OutstationFon: +49-40-89902-170 *
* c/o DESY, Notkestr. 85 Fax: +49-40-89902-149 *
* D-22603 Hamburg   Email: [EMAIL PROTECTED] *
* GERMANY   Web: www.embl-hamburg.de/~msweiss/ *
*  *

Re: [ccp4bb] MOLREP for space group F432

[Garib Murshudov]

In the previous email I missed index.jsp. Here is the correct url for  
programs (including molrep). So again


In newer version of molrep cubic space groups are handled much  
faster. Here is the url where you can download molrep


http://www.ysbl.york.ac.uk/YSBLPrograms/index.jsp

regards
Garib

On 17 Sep 2007, at 10:10, Manfred S. Weiss wrote:


Dear CCP4ers,

has anybody ever noticed a strange behaviour of MOLREP in space
group F432 (no. 209)? It seems as if the rotation function works
ok, but translation functions take about 100 times the time they
should.

Cheers, Manfred.


*  *
*Dr. Manfred S. Weiss  *
*  *
* Team Leader  *
*  *
* EMBL Hamburg OutstationFon: +49-40-89902-170 *
* c/o DESY, Notkestr. 85 Fax: +49-40-89902-149 *
* D-22603 Hamburg   Email: [EMAIL PROTECTED] *
* GERMANY   Web: www.embl-hamburg.de/~msweiss/ *
*  *

[ccp4bb] Molrep question

[Cynthia Czyrphony]

Hi all,

I'm using molrep with an MTZ file as input, so according to the manual I
should end up with a formatted CIFF file with the F_observed, but I only get
a pdb file for the coordinates. Any idea of what I'm doing wrong?

Thanks in advance,

Cynthia

[ccp4bb] MolRep with Phaser using a partial existing solution

[Jay Thompson]

Hi,

I have a question with molecular replacement using Phaser.  I'm trying to
solve a complex and I have a partial molecular replacement solution solved
using another program.  This solution is correct and makes up ~50% of the
entire complex.  I wanted to fix this solution and search for another small
fragment of the complex using Phaser.  I've been reading the Phaser manual
and it seems that I cannot input a pdb with this partial solution and tell
the program to fix this molecule.  It seems that fixed solutions can be only
input by putting in its Euler angles and fractional coordinate
translations.  Is this correct that I cannot input a pdb and fix it?  If I
cannot do this, then is there a quick way to identify the euler angles and
coordinate translations for Phaser.

Thanks a lot!!

Jay

Re: [ccp4bb] MolRep with Phaser using a partial existing solution

[Tim Grune]

Hello,

you could try to let phaser search for the first fragment, too. That way it 
should produce a file ending with '.sol' which you can pass to phaser for the 
second search (bottom at the ccp4-gui, Define search sets...).

Otherwise, if you do not want to move the first fragment, both the Euler 
angles and the translation should be 0 0 0.

Tim

On Friday 18 May 2007 11:24, Jay Thompson wrote:
 Hi,

 I have a question with molecular replacement using Phaser.  I'm trying to
 solve a complex and I have a partial molecular replacement solution solved
 using another program.  This solution is correct and makes up ~50% of the
 entire complex.  I wanted to fix this solution and search for another small
 fragment of the complex using Phaser.  I've been reading the Phaser manual
 and it seems that I cannot input a pdb with this partial solution and tell
 the program to fix this molecule.  It seems that fixed solutions can be
 only input by putting in its Euler angles and fractional coordinate
 translations.  Is this correct that I cannot input a pdb and fix it?  If I
 cannot do this, then is there a quick way to identify the euler angles and
 coordinate translations for Phaser.

 Thanks a lot!!

 Jay

-- 
Tim Grune
Australian Synchrotron
800 Blackburn Road
Clayton, VIC 3168
Australia


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Re: [ccp4bb] MolRep with Phaser using a partial existing solution

[Tim Grune]

Hi,

what resolution range do you use? You can try reducing it a little. 
How big is your cell?
Tim

On Friday 18 May 2007 13:46, Jay Thompson wrote:
 Hi,

 Thanks for the suggestions and quick reply.  Suggestions work great!

 But I have another problem and looking back at the ccp4bb, I see that
 Elenor had a similar problem late last year.  The error message is as
 follows:


 BFONT COLOR=#FF8800
 --
 OUT OF MEMORY ERROR: St9bad_alloc
 --
 /FONT/B

 !--SUMMARY_END--
 
 EXIT STATUS: FAILURE
 

 CPU Time: 0 days 0 hrs 19 mins 53.80 secs (1193.80 secs)
 Finished: Thu May 17 20:28:14 2007

 /pre
 /html

 The only suggestion from the ccp4bb threads that I could see was to try
 running it on a different computer with more memory.  I've tried running
 the job on two different Mac G5 and I get the same error message.  The
 computers that I have are pretty new and have 2 GB of SDRAM.  I'm surprised
 that I have a memory problem.  I'm also using the Phaser 1.3.3 (I'm
 assuming this is the latest version).  Thanks for all your help, in
 advance.

 Jay

 On 5/17/07, Jay Thompson [EMAIL PROTECTED] wrote:
  Hi,
 
  I have a question with molecular replacement using Phaser.  I'm trying to
  solve a complex and I have a partial molecular replacement solution
  solved using another program.  This solution is correct and makes up ~50%
  of the entire complex.  I wanted to fix this solution and search for
  another small fragment of the complex using Phaser.  I've been reading
  the Phaser manual and it seems that I cannot input a pdb with this
  partial solution and tell the program to fix this molecule.  It seems
  that fixed solutions can be only input by putting in its Euler angles and
  fractional coordinate
  translations.  Is this correct that I cannot input a pdb and fix it?  If
  I cannot do this, then is there a quick way to identify the euler angles
  and coordinate translations for Phaser.
 
  Thanks a lot!!
 
  Jay

-- 
Tim Grune
Australian Synchrotron
800 Blackburn Road
Clayton, VIC 3168
Australia


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