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Subject: ---solved---Fwd: problem in running DM (NCS averaging)
From: JOE CRYSTAL gchen2 {- at -} GMAIL {- dot -} COM
Date: 2007-07-31
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)
Date: Jul 31, 2007 8:13 AM
Subject: RE: [ccp4bb] problem in running DM (NCS averaging)
To: JOE CRYSTAL
Cc: ccp4@dl.ac.uk
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:CCP4BB@JISCMAIL.AC.UK] *On Behalf Of *JOE
CRYSTAL
*Sent:* 30 July 2007 17:09
*To:* CCP4BB@JISCMAIL.AC.UK
*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
dm 2.1
###############################################################
###############################################################
###############################################################
### 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.
dm
reference:
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.
Contents
Command Input
Data line--- MODE
SOLV AVER
Data line--- href="C:CCP4-Packagesccp4-6.0.2html/dm.html#combine">COMBINE
PERT
Data line--- href="C:CCP4-Packagesccp4-6.0.2html/dm.html#ncsmask">NCSMASK
SIZE 10
Data line--- SCHEME
ALL
Data line--- NCYCLE
AUTO
Data line--- SOLCONT
0.5
Data line--- href="C:CCP4-Packagesccp4-6.0.2html/dm.html#average">AVERAGE
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--- LABOUT
FDM=FDM PHIDM=PHIDM FOMDM=FOMDM
dm: Input error (see above)
Times: User: 0.0s System: 0.0s Elapsed: 0:00
***************************************************************************
* 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:
+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
Initial Averaging Mask
***************************************************************************
* 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
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