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
