Re: [ccp4bb] ncs phased refinement

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

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Subject: Pseudo Merohedral twining in C2 space group?
From: Xiaolei MA xiaolei {- dot -} ma {- at -} GMAIL {- dot -} COM
Date: 2007-12-08

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

Subject: Re: ncs phased refinement
From: "Winn, MD (Martyn)" m {- dot -} d {- dot -} winn {- at -} DL {- dot -} AC {- dot -} UK
Date: 2007-12-08

This is standard gotcha number 17, you are picking up "ncsmask" from XtalView rather
than the CCP4 one, see

http://www.ccp4.ac.uk/problems/general-probs.php#general_wrong_prog

Basically, you need to fix the path in some way so that the CCP4 one comes first.
check with "which -a ncsmask"

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

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

Previous message:
Subject: Pseudo Merohedral twining in C2 space group?
From: Xiaolei MA xiaolei {- dot -} ma {- at -} GMAIL {- dot -} COM
Date: 2007-12-08

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