Re: [ccp4bb] ncs phased refinement

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CCP4bb <-- 2007 <-- December 2007 <-- 08 December 2007

Previous message:
Subject: Re: Pseudo Merohedral twining in C2 space group?
From: Juergen Bosch jbosch {- at -} U {- dot -} WASHINGTON {- dot -} EDU
Date: 2007-12-08

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Subject: Postdoctoral position/Cold Spring Harbor Laboratory
From: Hiro Furukawa furukawa {- at -} CSHL {- dot -} EDU
Date: 2007-12-09

Subject: Re: ncs phased refinement
From: Tim Gruene tg {- at -} SHELX {- dot -} UNI-AC {- dot -} GWDG {- dot -} DE
Date: 2007-12-08

> Basically, you need to fix the path in some way so that the CCP4 one comes first.
^^^^^^^^^^^
The ccp4 setup file contains a variable 'ccp4_first_in_path' which you can
set to one to ensure ccp4 is 'first in path'. You also need to make sure
that this setup file is sourced after you set up the path for XtalView.
Tim

>
> HTH
> Martyn
>
> -----Original Message-----
> From: CCP4 bulletin board on behalf of Raja Dey
> Sent: Sat 12/8/2007 12:39 AM
> To: CCP4BB@JISCMAIL.AC.UK
> Subject: [ccp4bb] ncs phased refinement
>
> Hi All,
> I was trying to run NCS Phased refinement in the gui of CCP4 ( Refmac_5.2.0005) and getting the following error. I just pasted below the last part of the log file. Any help is greatly appreciated.
>
> Tarak
>
>
> ROTATION MATRIX
> -0.567 -0.405 0.717
> -0.385 -0.639 -0.665
> 0.728 -0.654 0.206
>
>
>
>
>
>
>
>
> PATTERSON SPHERICAL POLARS OMEGA PHI CHI OMEGA TO AXIS ZO PHI FROM AXIS XO TO AXIS YO
>
>
> WHEN BETA=0 CAN ONLY DEFINE ALPHA + GAMMA .
> WHEN BETA = 180 CAN ONLY DEFINE GAMMA - ALPHA.
>
>
> CROWTHER ALPHA BETA GAMMA 137.15697 -78.11038 41.90139
> SPHERICAL POLARS OMEGA PHI CHI 39.04911 -42.37222 179.26884
> DIRECTION COSINES OF ROTATION AXIS 0.46554 -0.42468 0.77661
>
>
> Angle between rotation axis and Centroid vector 87.88194
>
>
>
>
> ***** Note: Since this angle between rotation axis and Centroid vector is near to 90.0 this may represent a pure rotation ***
> LSQKAB: Normal Termination
> Times: User: 0.0s System: 0.0s Elapsed: 0:00
>
>
>
>
>
>
> ------------- NCS Mask -------------------
> unable to open phase file
> ***************************************************************************
> * Information from CCP4Interface script
> ***************************************************************************
> The program run with command: ncsmask XYZIN /home/raja/liang/native/p6522/b-sharpen/b-sharpen_1_12_chainI_pdb.tmp MSKOUT /home/raja/liang/native/p6522/b-sharpen/b-sharpen_1_15_msk.tmp
> has failed with error message
> child process exited abnormally
> ***************************************************************************
>
>
>
>
> #CCP4I TERMINATION STATUS 0 "child process exited abnormally"
> #CCP4I TERMINATION TIME 07 Dec 2007 16:13:00
> #CCP4I MESSAGE Task failed
>
>
>
>
> Raja Dey, Ph.D.
> Research Associate
> Molecular and Computational Biology
> University of Southern California
> 1050 Childs Way, Los Angeles, CA 90089
>
>
> ---------------------------------
> Forgot the famous last words? Access your message archive online. Click here.
>

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CCP4bb <-- 2007 <-- December 2007 <-- 08 December 2007

Previous message:
Subject: Re: Pseudo Merohedral twining in C2 space group?
From: Juergen Bosch jbosch {- at -} U {- dot -} WASHINGTON {- dot -} EDU
Date: 2007-12-08

Next message:
Subject: Postdoctoral position/Cold Spring Harbor Laboratory
From: Hiro Furukawa furukawa {- at -} CSHL {- dot -} EDU
Date: 2007-12-09