Dear all,
Thank you so much for your valuable thoughts. The problem is gone after I used rotation matrix instead of O matrix. Now DM is running fine. Thanks. Best regards, Joe ---------- Forwarded message ---------- From: Stein, ND (Norman) <[EMAIL PROTECTED]> Date: Jul 31, 2007 8:13 AM Subject: RE: [ccp4bb] problem in running DM (NCS averaging) To: JOE CRYSTAL <[EMAIL PROTECTED]> Cc: [EMAIL PROTECTED] Hi Your first error seems to have been caused by invalid input. The program seems to have read the lines AVERAGE REFI and LABOUT ... correctly, so the problem input is in the lines between these two. It looks as if there might be two such lines; one of these is presumably LABIN.... Are there any typos in these input lines? Regrading your second error, have you supplied all the necessary data in the CCP4i gui? in particular, have you specified a rotation and translation defining the NCS operator. (the Define NCS Symmetry section in the gui; you may have to scroll down to see all of it). Norman Stein CCP4 ------------------------------ *From:* CCP4 bulletin board [mailto:[EMAIL PROTECTED] *On Behalf Of *JOE CRYSTAL *Sent:* 30 July 2007 17:09 *To:* [email protected] *Subject:* [ccp4bb] problem in running DM (NCS averaging) Dear all, I tried to run DM for NCS averaging (DM module in CCP4i 6.0.2 installed under Windows XP), but the running failed at different stages with various error message as listed below. I was told it could be an installation problem, but I don't know how to fix it. I am wondering if you have encountered such problems before. I am very thankful for any help and comments. Thanks in advance. Error Message 1: ********************************************************************************************************************* #CCP4I JOB_ID 69 #CCP4I SCRATCH C:/Ccp4Temp/ #CCP4I PID 772 </pre> <B><FONT COLOR="#FF0000"><!--SUMMARY_BEGIN--> <html> <!-- CCP4 HTML LOGFILE --> <hr> <!--SUMMARY_END--></FONT></B> <a name="dmdm"><h1>dm 2.1</h1></a> <B><FONT COLOR="#FF0000"><!--SUMMARY_BEGIN--> <pre> ############################################################### ############################################################### ############################################################### ### CCP4 6.0 : dm version 6.0 : ## ############################################################### User: Chen Run date: 30/ 7/2007 Run time: 10:27:58 Please reference: Collaborative Computational Project, Number 4. 1994. "The CCP4 Suite: Programs for Protein Crystallography". Acta Cryst. D50, 760-763. as well as any specific reference in the program write-up. <!--SUMMARY_END--></FONT></B> </pre> <a href="http://www.yorvic.york.ac.uk/~cowtan/dm/refs.html<http://www.yorvic.york.ac.uk/%7Ecowtan/dm/refs.html>">dm reference:</a> <blockquote> K. Cowtan (1994), dm: An automated procedure for phase improvement by density modification. Joint CCP4 and ESF-EACBM Newsletter on Protein Crystallography, 31, p34-38. </blockquote><p> <a name="tocdm"><h2>Contents</h2></a> <ul> <li><a href="#commanddm">Command input</a> <li><a href="#commentsdm">Comments</a> <li><a href="#mtzindm">MTZ input</a> <li><a href="#datachkdm">Data Checking</a> <li><a href="#datascldm">Data Scaling</a> <li><a href="#solmskdm">Solvent Mask</a> <li><a href="#cyc0001dm">First Cycle</a> <li><a href="#dataoutdm">Output</a> </ul> <a name="commanddm"><h2>Command Input</h2></a> <pre> Data line--- <a href="C:\CCP4-Packages\ccp4-6.0.2\html/dm.html#mode">MODE </a> SOLV AVER Data line--- <a href="C:\CCP4-Packages\ccp4-6.0.2\html/dm.html#combine">COMBINE </a> PERT Data line--- <a href="C:\CCP4-Packages\ccp4-6.0.2\html/dm.html#ncsmask">NCSMASK </a> SIZE 10 Data line--- <a href="C:\CCP4-Packages\ccp4-6.0.2\html/dm.html#scheme">SCHEME </a> ALL Data line--- <a href="C:\CCP4-Packages\ccp4-6.0.2\html/dm.html#ncycle">NCYCLE </a> AUTO Data line--- <a href="C:\CCP4-Packages\ccp4-6.0.2\html/dm.html#solc">SOLCONT </a> 0.5 Data line--- <a href="C:\CCP4-Packages\ccp4-6.0.2\html/dm.html#average">AVERAGE </a> REFI *** Warning Invalid keyword *** Warning Invalid sub-keyword in position 2 *** Warning Invalid keyword *** Warning Invalid sub-keyword in position 2 *** Warning Invalid keyword *** Warning Invalid sub-keyword in position 2 *** Warning Invalid keyword *** Warning Invalid sub-keyword in position 2 *** Warning Invalid keyword *** Warning Invalid sub-keyword in position 2 *** Warning Invalid keyword *** Warning Invalid sub-keyword in position 2 *** Warning Invalid sub-keyword in position 3 *** Warning Invalid sub-keyword in position 4 *** Warning Invalid sub-keyword in position 5 *** Warning Invalid sub-keyword in position 6 *** Warning Invalid sub-keyword in position 7 *** Warning Invalid sub-keyword in position 8 *** Warning Invalid sub-keyword in position 9 Data line--- <a href="C:\CCP4-Packages\ccp4-6.0.2\html/dm.html#labout">LABOUT </a> FDM=FDM PHIDM=PHIDM FOMDM=FOMDM <B><FONT COLOR="#FF0000"><!--SUMMARY_BEGIN--> dm: Input error (see above) Times: User: 0.0s System: 0.0s Elapsed: 0:00 </pre> </html> <!--SUMMARY_END--></FONT></B> *************************************************************************** * Information from CCP4Interface script *************************************************************************** The program run with command: dm HKLIN "D:/xtalwork/DM21/delM_arpwarp/work1/7_solvent_refmac7.mtz" HKLOUT "D:/xtalwork/DM21/delM_arpwarp/work1/7_solvent_dm4.mtz" SOLOUT "D:/xtalwork/DM21/delM_arpwarp/work1/7_solvent_dm2.msk" NCSIN1 "D:/xtalwork/DM21/delM_arpwarp/work1/A.msk" VUOUT D:/xtalwork/DM21/delM_arpwarp/work1/delM_69_ncs.odat has failed with error message dm: Input error (see above) *************************************************************************** #CCP4I TERMINATION STATUS 0 " dm: Input error (see above)" #CCP4I TERMINATION TIME 30 Jul 2007 10:27:58 #CCP4I MESSAGE Task failed Error Message 2: +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ <a name="ncsmskdm"><h3>Initial Averaging Mask</h3></a> <B><FONT COLOR="#FF0000"><!--SUMMARY_BEGIN--> *************************************************************************** * Information from CCP4Interface script *************************************************************************** The program run with command: dm HKLIN "D:/xtalwork/DM21/delM_arpwarp/work1/7_solvent_refmac7.mtz" HKLOUT "D:/xtalwork/DM21/delM_arpwarp/work1/7_solvent_dm3.mtz" SOLOUT "D:/xtalwork/DM21/delM_arpwarp/work1/7_solvent_dm2.msk" NCSOUT "D:/xtalwork/tmp/delM_63_ncs.msk" has failed with error message forrtl: severe (157): Program Exception - access violation Image PC Routine Line Source ntdll.dll 7C911E58 Unknown Unknown Unknown ntdll.dll 7C910D5C Unknown Unknown Unknown dm.exe 004A8FFF Unknown Unknown Unknown *************************************************************************** #CCP4I TERMINATION STATUS 0 "forrtl: severe (157): Program Exception - access violation Image PC Routine Line Source ntdll.dll 7C911E58 Unknown Unknown Unknown ntdll.dll 7C910D5C Unknown Unknown Unknown dm.exe 004A8FFF Unknown Unknown Unknown" #CCP4I TERMINATION TIME 29 Jul 2007 21:34:02 #CCP4I TERMINATION OUTPUT_FILES D:/xtalwork/tmp/delM_63_ncs.msk TEMPORARY #CCP4I MESSAGE Task failed
