Re: [ccp4bb] refmac5 error message

- Protein crystallography

Main steps:

- Protein purification
- Crystallisation

Special:

- Programs for crystallography
- X-ray detectors

Basic tutorials:

   - Chemistry
   - Protein
   - Peptide
   - Amino Acids

Xtal community:

- CCP4BB

CCP4bb navigation

CCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999

Previous message:
Subject: refmac5 error message
From: Vesna Serrano vsserran {- at -} NCSU {- dot -} EDU
Date: 2009-08-06

Next message:
Subject: Re: Zinc or Iron binding protein, that is a question!
From: "George M {- dot -} Sheldrick" gsheldr {- at -} SHELX {- dot -} UNI-AC {- dot -} GWDG {- dot -} DE
Date: 2009-08-06

Subject: Re: refmac5 error message
From: Ezra Peisach epeisach {- at -} GMAIL {- dot -} COM
Date: 2009-08-06

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
>
>
>


>
>  ###############################################################
>  ###############################################################
>  ###############################################################
>  ### 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
>

>
> ***************************************************************************
> * 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

CCP4bb navigation

CCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999

Previous message:
Subject: refmac5 error message
From: Vesna Serrano vsserran {- at -} NCSU {- dot -} EDU
Date: 2009-08-06