From: Jacob Keller
Date: 6 September 2011 22:34
Dear Crystallographers,
in trying to convert a mmcif to mtz, I get the logfile below. I looked
in the directory, and there is a file cf_mm.dic, but this is
presumably not the same as the similar .lib file. Any thoughts about
this? Did the file somehow get lost? Also, I recently did this same
conversion to another file without problems...
Jacob Keller
#CCP4I VERSION CCP4Interface 2.1.0
#CCP4I SCRIPT LOG import
#CCP4I DATE 06 Sep 2011 16:29:11
#CCP4I USER 'UNKNOWN'
#CCP4I PROJECT 3mgl
#CCP4I JOB_ID 3
#CCP4I SCRATCH C:/Ccp4Temp
#CCP4I HOSTNAME chloe
#CCP4I PID 2728
<html> <!-- CCP4 HTML LOGFILE -->
<hr>
<pre>
###############################################################
###############################################################
###############################################################
### CCP4 6.2: cif2mtz version 6.2 : 16/11/09##
###############################################################
User: Jacob Run date: 6/ 9/2011 Run time: 16:29:19
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.
Data line--- title [No title given]
Data line--- symmetry P4212
Spacegroup information obtained from library file:
Logical Name: SYMINFO Filename:
C:\CCP4-Packages\ccp4-6.2.0\lib\data\syminfo.lib
Data line--- cell 90.91 90.91 65.21 90.0 90.0 90.0
Data line--- end
>>>> CCIF signal CCIF_FOPEN (severity: SEVERE ERROR/FATAL) <<<<
(Raised in zzs_undump)
Cannot open file C:\CCP4-Packages\ccp4-6.2.0\lib\data\cif_mmdic.lib for reading!
***************************************************************************
* Information from CCP4Interface script
***************************************************************************
The program run with command: cif2mtz HKLIN
"C:/Users/Jacob/Desktop/structures/PDB_3mgl/3mgl-sf.cif" HKLOUT
"C:/Ccp4Temp/3mgl_3_1_mtz.tmp"
has failed with error message
child process exited abnormally
***************************************************************************
#CCP4I TERMINATION STATUS 0 "child process exited abnormally"
#CCP4I TERMINATION TIME 06 Sep 2011 16:29:19
#CCP4I MESSAGE Task failed
--
*******************************************
Jacob Pearson Keller
Northwestern University
Medical Scientist Training Program
*******************************************
----------
From: Martyn Winn
Yes, the program does need the (binary) data file cif_mmdic.lib which is
created from the cif_mm.dic file.
This should be in the directory C:\CCP4-Packages\ccp4-6.2.0\lib and NOT
C:\CCP4-Packages\ccp4-6.2.0\lib\data as you have.
Which suggests that the environment variable MMCIFDIC is set wrongly.
And if I look at my windows installation .... mmm yes it is set wrong
and cif2mtz indeed fails. Edit it in system -> advanced -> environment
variables (or whatever ....), restart ccp4i, and voila it works!
So sorry, this looks like a cock-up in the windows distribution :(
HTH
Martyn
* *
* Dr. Martyn Winn *
* *
* STFC Daresbury Laboratory, Daresbury, Warrington, WA4 4AD, U.K. * *
***********************************************************************
----------
From: Jacob Keller
Much obliged!
Thanks,
Jacob
Date: 6 September 2011 22:34
Dear Crystallographers,
in trying to convert a mmcif to mtz, I get the logfile below. I looked
in the directory, and there is a file cf_mm.dic, but this is
presumably not the same as the similar .lib file. Any thoughts about
this? Did the file somehow get lost? Also, I recently did this same
conversion to another file without problems...
Jacob Keller
#CCP4I VERSION CCP4Interface 2.1.0
#CCP4I SCRIPT LOG import
#CCP4I DATE 06 Sep 2011 16:29:11
#CCP4I USER 'UNKNOWN'
#CCP4I PROJECT 3mgl
#CCP4I JOB_ID 3
#CCP4I SCRATCH C:/Ccp4Temp
#CCP4I HOSTNAME chloe
#CCP4I PID 2728
<html> <!-- CCP4 HTML LOGFILE -->
<hr>
<pre>
###############################################################
###############################################################
###############################################################
### CCP4 6.2: cif2mtz version 6.2 : 16/11/09##
###############################################################
User: Jacob Run date: 6/ 9/2011 Run time: 16:29:19
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.
Data line--- title [No title given]
Data line--- symmetry P4212
Spacegroup information obtained from library file:
Logical Name: SYMINFO Filename:
C:\CCP4-Packages\ccp4-6.2.0\lib\data\syminfo.lib
Data line--- cell 90.91 90.91 65.21 90.0 90.0 90.0
Data line--- end
>>>> CCIF signal CCIF_FOPEN (severity: SEVERE ERROR/FATAL) <<<<
(Raised in zzs_undump)
Cannot open file C:\CCP4-Packages\ccp4-6.2.0\lib\data\cif_mmdic.lib for reading!
***************************************************************************
* Information from CCP4Interface script
***************************************************************************
The program run with command: cif2mtz HKLIN
"C:/Users/Jacob/Desktop/structures/PDB_3mgl/3mgl-sf.cif" HKLOUT
"C:/Ccp4Temp/3mgl_3_1_mtz.tmp"
has failed with error message
child process exited abnormally
***************************************************************************
#CCP4I TERMINATION STATUS 0 "child process exited abnormally"
#CCP4I TERMINATION TIME 06 Sep 2011 16:29:19
#CCP4I MESSAGE Task failed
--
*******************************************
Jacob Pearson Keller
Northwestern University
Medical Scientist Training Program
*******************************************
----------
From: Martyn Winn
Yes, the program does need the (binary) data file cif_mmdic.lib which is
created from the cif_mm.dic file.
This should be in the directory C:\CCP4-Packages\ccp4-6.2.0\lib and NOT
C:\CCP4-Packages\ccp4-6.2.0\lib\data as you have.
Which suggests that the environment variable MMCIFDIC is set wrongly.
And if I look at my windows installation .... mmm yes it is set wrong
and cif2mtz indeed fails. Edit it in system -> advanced -> environment
variables (or whatever ....), restart ccp4i, and voila it works!
So sorry, this looks like a cock-up in the windows distribution :(
HTH
Martyn
***********************************************************************
* *
* Dr. Martyn Winn *
* *
* STFC Daresbury Laboratory, Daresbury, Warrington, WA4 4AD, U.K. * *
***********************************************************************
----------
From: Jacob Keller
Much obliged!
Thanks,
Jacob
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