Vesna Serrano wrote:
> Dear all,
> I am using Refmac_5.5.0088 in CCP4 6.1.0, linux version. The program runs
> well normally, but all of a sudden it failed with the following message:
> Refmac_5.5.0088: Open failed: File: /tmp/vesna/refmac5_temp1.06489.txt.
> Here is the log file of the run:
>
> #CCP4I VERSION CCP4Interface 2.0.4
> #CCP4I SCRIPT LOG refmac5
> #CCP4I DATE 05 Aug 2009 02:04:38
> #CCP4I USER vesna
> #CCP4I PROJECT wtDHPAB
> #CCP4I JOB_ID 19
> #CCP4I SCRATCH /tmp/vesna
> #CCP4I HOSTNAME localhost.localdomain
> #CCP4I PID 6486
>
> <html> <!-- CCP4 HTML LOGFILE -->
> <hr>
> <pre>
>
> ###############################################################
> ###############################################################
> ###############################################################
> ### CCP4 6.1: Refmac_5.5.0088 version 5.5.0088 : 08/12/08##
> ###############################################################
> User: unknown Run date: 5/ 8/2009 Run time: 02:04:38
>
>
> 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.
>
> $TEXT:Reference1: $$ comment $$
> "Refinement of Macromolecular Structures by the Maximum-Likelihood
> Method:"
> G.N. Murshudov, A.A.Vagin and E.J.Dodson,(1997)
> Acta Crystallogr. D53, 240-255
> EU Validation contract: BIO2CT-92-0524
>
> $$
> $SUMMARY :Reference1: $$ Refmac: $$
> :TEXT:Reference1: $$
>
> Open failed: Unit: 7, File: /tmp/vesna/refmac5_temp1.06489.txt
> (logical: /tmp/vesna/refmac5_temp1.06489.txt)
> Refmac_5.5.0088: Open failed: File: /tmp/vesna/refmac5_temp1.06489.txt
> Times: User: 0.0s System: 0.0s Elapsed: 0:00
> </pre>
> </html>
> ***************************************************************************
> * Information from CCP4Interface script
> ***************************************************************************
> The program run with command: /usr/local/xtal/ccp4-6.1.1/bin/refmac5 XYZIN
> "/home/vesna/wtDHPAB/ABwt4ID50-adj1.pdb" XYZOUT
> "/home/vesna/wtDHPAB/wtDHPAB_19_2_pdb_1.tmp" HKLIN
> "/home/vesna/wtDHPAB/full_ABwtID4.mtz" HKLOUT
> "/home/vesna/wtDHPAB/wtDHPAB_19_3_mtz_1.tmp" LIBOUT
> "/home/vesna/wtDHPAB/wtDHPAB_19_lib.cif"
> has failed with error message
> Last system error message: Permission denied
> Refmac_5.5.0088: Refmac_5.5.0088
> ***************************************************************************
>
>
> #CCP4I TERMINATION STATUS 0 Last system error message: Permission denied
> Refmac_5.5.0088: Open failed: File: /tmp/vesna/refmac5_temp1.06489.txt
> #CCP4I TERMINATION TIME 05 Aug 2009 02:04:38
> #CCP4I MESSAGE Task failed
>
>
> I would very much appreciate help in solving this problem.
>
> Regards,
>
> Vesna Serrano
>
> Dept. of Chemistry
> NC State Univ.
> Raleigh, NC 27695
>
Can you write to the directory /tmp/vesna? Does it exist? The last
error is permission denied... This could happen if something wiped the
files in /tmp - including the directory, or if someone else created the
directory there and you cannot write to it.... I would check "ls -ld
/tmp/vesna" to see that the directory exists and the permissions are
correct.
Another possibility is that someone changed the permissions on the
directory /tmp - and made it not world writable... "ls -ld /tmp" would
tell you if this was the problem.
Good luck...
Ezra
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