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 </pre> </html> ------------- 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.
