Thanks Alexander, I got the solution #2 below as well from my colleague Johan Raber :)
Cheers, Martin ############ solution #2 ########################## Hi Martin, A colleague of mine suggested this could be a known OS bug related to opening files on a read-only mounted file system (such as /software on Triolith). We have a workaround for this until that bug is fixed by RedHat. Please try to do: $ export LD_PRELOAD=/software/tools/ldpreload/openrocrwrap/libopenrocrwrapsilent.so before running CCP4i again, and tell us if this fixed the problem. /Johan -----Original Message----- From: Alexander Batyuk [mailto:bat...@bioc.uzh.ch] Sent: den 15 maj 2013 10:34 To: Martin Moche Subject: Re: [ccp4bb] Refmac error Dear Martin, I think we solved it by changing the file's permissions (for mon_lib_list.cif) to rwxrwxrwx Best wishes, Alex On 15 May 2013, at 10:25, Martin Moche <martin.mo...@ki.se> wrote: > Dear colleagues, > > I have the same problems as Peer Mittl once had. > > Was this solved and what was the solution? > > Running arpWarp the job terminates with the message: > Refmac_5.7.0032: Open failed: File: > /software/apps/ccp4/ccp4-6.3.0/lib/data/monomers/list/mon_lib_list.cif > > > However the mon_lib_list.cif is readable to my user? > [x_marmo@triolith3 CCP4]$ more > /software/apps/ccp4/ccp4-6.3.0/lib/data/monomers/list/mon_lib_list.cif > global_ > _lib_name mon_lib > _lib_version 5.39 > _lib_update 06/11/12 > #--------------------------------- > > > > Here is the output of the ls -l command suggested by Tim Gruene > [x_marmo@triolith3 CCP4]$ ls -l > /software/apps/ccp4/ccp4-6.3.0/lib/data/monomers/list/mon_lib_list.cif > -rw-r--r-- 1 raber nsc 1078257 May 15 08:15 > /software/apps/ccp4/ccp4-6.3.0/lib/data/monomers/list/mon_lib_list.cif > > > > > At the end of the warpNtrace logfile is the following information: > [x_marmo@triolith3 CCP4]$ tail -22 > /home/x_marmo/MexR/CCP4/2_warpNtrace_refine.last.log > B value outliers 10.000 > NCS outliers 20.000 > --------------------------------------------------------------- > > Input file :arp_0.pdb_start > Size of lib_com.fh(bytes) : 118100416 > Open failed: Unit: 7, File: > /software/apps/ccp4/ccp4-6.3.0/lib/data/monomers/list/mon_lib_list.cif > (logical: > /software/apps/ccp4/ccp4-6.3.0/lib/data/monomers/list/mon_lib_list.cif) > <B><FONT COLOR="#FF0000"><!--SUMMARY_BEGIN--> > Refmac_5.7.0032: Open failed: File: > /software/apps/ccp4/ccp4-6.3.0/lib/data/monomers/list/mon_lib_list.cif > > Times: User: 0.3s System: 0.0s Elapsed: 0:00 > </pre> > </html> > <!--SUMMARY_END--></FONT></B> > > <B><FONT COLOR="#FF0000"><!--SUMMARY_BEGIN--> > QUITTING ... ARP/wARP module stopped with an error message: > REFMAC5 > > *** Look for error message in the file: > /home/x_marmo/MexR/CCP4/2_warpNtrace_refine.last.log > [x_marmo@triolith3 CCP4]$ > > > > What is wrong here? > > Best regards, > Martin -- Alex Batyuk The Plueckthun Lab www.bioc.uzh.ch/plueckthun
