[sharp-discuss] FFT problem during solvent flattening

[Clemens Vonrhein]

Dear Taro,

looks like a permission error - I'm not sure which file it can't open
though. Maybe you can attach the whole log file?

Another reason might be NFS related: sometimes, the script just runs
to fast. And if anything is funny with your filesystems (ie. your
logfiles etc directories are not local to the machine where you
actually run the job) things can go funny. So make sure to have NFS
configured correctly. Another thing could be that the time one the the
two machines is different - try configuring ntp/xntp. Obviously, if
you run the whole thing completely local (httpd and sharpfiles
directory) then this does not apply.

What happens if you try and run the job again? Does it always stop
with the same error? Or does it sometimes work?

Cheers

Clemens


On Wed, Jun 29, 2005 at 11:25:06AM +0900, ttamada wrote:
> Dear all,
>  
> I am trying to run a solvent flattening protocol through the Phase
> Improvement Control Panel but I get the error message bellow. SOLOMON
> (including FFT) and DM runs fine from a ccp4i (linux).
> Any suggestions are appreciated!
>  
> Taro
> 
>  
> 
>  ###############################################################
> 
>  ###############################################################
> 
>  ###############################################################
> 
>  ### CCP4 5.0: FFT                version 5.0       : 26/01/04##
> 
>  ###############################################################
> 
>  User: sharp  Run date: 29/ 6/2005 Run time: 11:33:16 
> 
>  
> 
>  
> 
>  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--- LABI F1=Fcent PHI=PHIcent
> 
>  Data line--- RESO 38.341 3.50
> 
>  Data line--- XYZL ASU
> 
>  Map limits will be set to the CCP4 asymmetric unit
> 
>  Data line--- END
> 
>  
> 
> OPENED INPUT MTZ FILE 
> 
> Logical Name: HKLIN   Filename: eden-unique.mtz 
> 
> ...
> 
> * Column Labels :
> 
> H K L NUMORB FB PHIB FOM HX HY FH PHIH FP SIGFP HLA HLB HLC HLD HL0 Fcent
> PHIcent FOMcent Fmap PHImap FHref PHIHref FreeR_flag
> 
> ...
> 
> Spacegroup information obtained from library file: 
> 
> Logical Name: SYMINFO   Filename: /home/sharp/database/syminfo.lib
> 
> ...
> 
> Axis order in map: fast=Y,  medium= X,  slow(section)= Z
> 
> Permutation of axes: (program=input)  x= X,  y= Y,  z= Z
> 
>  
> 
> >>>>>> CCP4 library signal library_file:Cannot open file (Error)
> 
>          raised in ccp4_file_open <<<<<<
> 
> >>>>>> CCP4 library signal library_file:Null pointer passed (Error)
> 
>          raised in ccp4_file_mode <<<<<<
> 
> >>>>>> CCP4 library signal library_file:Null pointer passed (Error)
> 
>          raised in ccp4_file_writechar <<<<<<
> 
> >>>>>> CCP4 library signal library_file:Null pointer passed (Error)
> 
>          raised in ccp4_file_mode <<<<<<
> 
>  
> 
> --------------------------------------------------
> Taro Tamada, Ph.D.
> Senior Scientist
> Structural Biology Group, Neutron Science Research Center,
> Japan Atomic Energy Research Institute (JAERI)
> Tokai-mura, Naka-gun, Ibaraki 319-1195, Japan
> Phone.: +81-29-282-6736, Fax:+81-29-284-3822
> E-mail: ttamada at neutrons.tokai.jaeri.go.jp
> --------------------------------------------------
> 
>  
> 

> _______________________________________________
> sharp-discuss mailing list
> sharp-discuss at globalphasing.com
> http://www.globalphasing.com/mailman/listinfo/sharp-discuss


-- 

***************************************************************
* Clemens Vonrhein, Ph.D.     vonrhein AT GlobalPhasing DOT com
*
*  Global Phasing Ltd.
*  Sheraton House, Castle Park 
*  Cambridge CB3 0AX, UK
*--------------------------------------------------------------
* BUSTER Development Group      (http://www.globalphasing.com)
***************************************************************