Re: [ccp4bb] loop building with ARP/wARP - REFMAC/gfortran problem? and work-around
Hello, Further investigation (and lots of help from Huw Jenkins) has confirmed that the following error: ### CCP4 6.2: Refmac_5.6.0117 version 5.6.0117 : 13/06/11## QUITTING ... ARP/wARP module stopped with an error message: REFMAC5 occurs to most ARP/wARP classic model building jobs when used with the Fink CCP4 version 6.2.0-102. Also, as suggested yesterday on this board, the error occurs when CCP4 has been compiled with gcc/gfortran 4.6.1. There are two main workarounds at the moment. The easiest is to turn off conditional restraints as shown in the image linked below: http://min.us/moKdRlW4l The other is to compile Refmac with gfortran version 4.4. This error only appears in the lastest Fink compiled version of CCP4 - the DMG installed binaries of CCP4 do not exhibit this problem. We are trying to find the underlying cause of the problem and I hope that this error isn't causing too much inconvenience. Saul Hazledine On Sep 6, 2011, at 4:48 PM, Huw Jenkins wrote: On 25 Aug 2011, at 14:12, Gregory Bowman wrote: When I try to run ARP/wARP classic for loop building, I get the following message in the logfile: QUITTING ... ARP/wARP module stopped with an error message: REFMAC I get the same error running auto_tracing.sh from ARP/wARP 7.2. (CCP4 6.2.0, OS X 10.6.8) As a work-around getting ARP/wARP to use the refmac binary from http://www.ysbl.york.ac.uk/~garib/refmac/data/refmac_experimental/refmac5.6_macintel.tar.gz (version 5.6.0119) allows ARP/wARP to run. Some information that may help work out what the problem is below: The only helpful error message I get in the logs is: At line 723 of file /sw64/src/fink.build/ccp4-6.2.0-102/ccp4-6.2.0/src/refmac5_/read_extra_restraints.f (unit = 9, file = '/tmp/huwtj/refmac5_temp1.53659_BOND_R') Fortran runtime error: Sequential READ or WRITE not allowed after EOF marker, possibly use REWIND or BACKSPACE ### CCP4 6.2: Refmac_5.6.0117 version 5.6.0117 : 13/06/11## QUITTING ... ARP/wARP module stopped with an error message: REFMAC5 At first I thought this was a 32/64bit issue but after compiling CCP4 as 32bit I get exactly the same error: At line 723 of file /sw/src/fink.build/ccp4-6.2.0-102/ccp4-6.2.0/src/refmac5_/read_extra_restraints.f (unit = 9, file = '/tmp/huwtj/refmac5_temp1.81086_BOND_R') Fortran runtime error: Sequential READ or WRITE not allowed after EOF marker, possibly use REWIND or BACKSPACE ### CCP4 6.2: Refmac_5.6.0117 version 5.6.0117 : 13/06/11## QUITTING ... ARP/wARP module stopped with an error message: REFMAC5 In both cases this is CCP4 built/installed by fink on OS X 10.6.8. When I try to compile refmac from the latest source code with gfortran 4.6.1 I get a lot of warnings (which go away if I add -fno-whole-file to XFFLAGS) and the executable produced fails in the same way when called by auto_tracing.sh. This suggests to me it's a compiler issue not any differences between refmac 5.6.0117 and 5.6.0119, unfortunately that's about the limit of my understanding. Hopefully some of that is useful to someone! Huw
Re: [ccp4bb] loop building with ARP/wARP - REFMAC/gfortran problem? and work-around
On 25 Aug 2011, at 14:12, Gregory Bowman wrote: When I try to run ARP/wARP classic for loop building, I get the following message in the logfile: QUITTING ... ARP/wARP module stopped with an error message: REFMAC I get the same error running auto_tracing.sh from ARP/wARP 7.2. (CCP4 6.2.0, OS X 10.6.8) As a work-around getting ARP/wARP to use the refmac binary from http://www.ysbl.york.ac.uk/~garib/refmac/data/refmac_experimental/refmac5.6_macintel.tar.gz (version 5.6.0119) allows ARP/wARP to run. Some information that may help work out what the problem is below: The only helpful error message I get in the logs is: At line 723 of file /sw64/src/fink.build/ccp4-6.2.0-102/ccp4-6.2.0/src/refmac5_/read_extra_restraints.f (unit = 9, file = '/tmp/huwtj/refmac5_temp1.53659_BOND_R') Fortran runtime error: Sequential READ or WRITE not allowed after EOF marker, possibly use REWIND or BACKSPACE ### CCP4 6.2: Refmac_5.6.0117 version 5.6.0117 : 13/06/11## QUITTING ... ARP/wARP module stopped with an error message: REFMAC5 At first I thought this was a 32/64bit issue but after compiling CCP4 as 32bit I get exactly the same error: At line 723 of file /sw/src/fink.build/ccp4-6.2.0-102/ccp4-6.2.0/src/refmac5_/read_extra_restraints.f (unit = 9, file = '/tmp/huwtj/refmac5_temp1.81086_BOND_R') Fortran runtime error: Sequential READ or WRITE not allowed after EOF marker, possibly use REWIND or BACKSPACE ### CCP4 6.2: Refmac_5.6.0117 version 5.6.0117 : 13/06/11## QUITTING ... ARP/wARP module stopped with an error message: REFMAC5 In both cases this is CCP4 built/installed by fink on OS X 10.6.8. When I try to compile refmac from the latest source code with gfortran 4.6.1 I get a lot of warnings (which go away if I add -fno-whole-file to XFFLAGS) and the executable produced fails in the same way when called by auto_tracing.sh. This suggests to me it's a compiler issue not any differences between refmac 5.6.0117 and 5.6.0119, unfortunately that's about the limit of my understanding. Hopefully some of that is useful to someone! Huw
Re: [ccp4bb] loop building with ARP/wARP - REFMAC/gfortran problem? and work-around
On 06/09/11 16:48, Huw Jenkins wrote: On 25 Aug 2011, at 14:12, Gregory Bowman wrote: When I try to run ARP/wARP classic for loop building, I get the following message in the logfile: QUITTING ... ARP/wARP module stopped with an error message: REFMAC I get the same error running auto_tracing.sh from ARP/wARP 7.2. (CCP4 6.2.0, OS X 10.6.8) As a work-around getting ARP/wARP to use the refmac binary from http://www.ysbl.york.ac.uk/~garib/refmac/data/refmac_experimental/refmac5.6_macintel.tar.gz (version 5.6.0119) allows ARP/wARP to run. Some information that may help work out what the problem is below: The only helpful error message I get in the logs is: At line 723 of file /sw64/src/fink.build/ccp4-6.2.0-102/ccp4-6.2.0/src/refmac5_/read_extra_restraints.f (unit = 9, file = '/tmp/huwtj/refmac5_temp1.53659_BOND_R') Fortran runtime error: Sequential READ or WRITE not allowed after EOF marker, possibly use REWIND or BACKSPACE ### CCP4 6.2: Refmac_5.6.0117 version 5.6.0117 : 13/06/11## QUITTING ... ARP/wARP module stopped with an error message: REFMAC5 At first I thought this was a 32/64bit issue but after compiling CCP4 as 32bit I get exactly the same error: At line 723 of file /sw/src/fink.build/ccp4-6.2.0-102/ccp4-6.2.0/src/refmac5_/read_extra_restraints.f (unit = 9, file = '/tmp/huwtj/refmac5_temp1.81086_BOND_R') Fortran runtime error: Sequential READ or WRITE not allowed after EOF marker, possibly use REWIND or BACKSPACE ### CCP4 6.2: Refmac_5.6.0117 version 5.6.0117 : 13/06/11## QUITTING ... ARP/wARP module stopped with an error message: REFMAC5 In both cases this is CCP4 built/installed by fink on OS X 10.6.8. When I try to compile refmac from the latest source code with gfortran 4.6.1 I get a lot of warnings (which go away if I add -fno-whole-file to XFFLAGS) and the executable produced fails in the same way when called by auto_tracing.sh. This suggests to me it's a compiler issue not any differences between refmac 5.6.0117 and 5.6.0119, unfortunately that's about the limit of my understanding. Hopefully some of that is useful to someone! Huw Hi Huw, I recently found the same problem and solved it by compiling refmac 5.6.0119 using gnu compilers from the 4.4 series (4.4.6 I think). I'm attaching the makefiles I used. However, this will only work if you compile the whole ccp4 suite with the same compilers... To do it I ran: source ...wherever_CCP4_is.../include/ccp4.setup-sh FC=gfortran F77=gfortran CC=gcc-4 CXX=g++-4 ./configure --with-netlib-lapack 21 | tee configure.log make 21 | tee make.log make install 21 | tee install.log Using Apple lapack libraries didn't work. HTH. -- Miguel Architecture et Fonction des Macromolécules Biologiques (UMR6098) CNRS, Universités d'Aix-Marseille I II Case 932, 163 Avenue de Luminy, 13288 Marseille cedex 9, France Tel: +33(0) 491 82 55 93 Fax: +33(0) 491 26 67 20 mailto:miguel.ortiz-lombar...@afmb.univ-mrs.fr http://www.afmb.univ-mrs.fr/Miguel-Ortiz-Lombardia makerefmac.tgz Description: GNU Zip compressed data
[ccp4bb] loop building with ARP/wARP
Hi all, I have a large disordered loop (33aa) for a 2.0 Å dataset for which the rest of the structure is well-defined, and phases are decent (Rwork=19.6, Rfree=24.6). I can see some broken up density at one end, but have been unable to convincingly build into into this region manually. I would like to try arp/warp to improve density or possibly extend the loop termini but have been thwarted by some technical problems and would appreciate any advice. I've installed ccp4 6.2.0 on Mac OS X (10.6.8) with fink, both as 32-bit and 64-bit to allow me to run ARP/wARP (version 7.1) from the ccp4i GUI. I've been unable to get loopy to work, and also the standard ARP/wARP classic. When I run ARP/wARP Loops (a.k.a. loopy), I get the message in the log file: Couldn't find any loop to build, loopy will simple copy the pdb file. The program is able to read the sequence .pir file and match it to the structure, and seems from the sequence alignment to identify the regions of the sequence for which there is no structure. I'm guessing that I'm not putting some obvious parameter into the GUI/starting script, but I don't know what that might be. The script generated from the GUI (21_loopy.def) is pasted below. When I try to run ARP/wARP classic for loop building, I get the following message in the logfile: QUITTING ... ARP/wARP module stopped with an error message: REFMAC *** Look for error message in the file: /Users/gbowman/Greg/20_warpNtrace_refine.last.log At the end of the warpNtrace_refine.last.log file, the program reports what seem to be close contacts. Since I don't see this in the structure, and don't have any problems or errors like this when I refine the structure with REMAC, is this from rebuilding, and is this the problem that halts REFMAC? Thanks! Greg = = = = = = 20_warpNtrace_refine.last.log = = = = = = snip Input file :restraints.pdb NUMBER OF MONOMERS IN THE LIBRARY : 11465 with complete description: 11465 NUMBER OF MODIFICATIONS:53 NUMBER OF LINKS:66 I am reading libraries. Please wait. - energy parameters - monomers description (links mod ) BFONT COLOR=#FF!--SUMMARY_BEGIN-- !--SUMMARY_END--/FONT/B Number of atoms:2463 Number of residues : 859 Number of chains : 3 I am reading library. Please wait. mon_lib.cif INFO: link is found (not be used) dist= 1.907 ideal_dist= 1.432 ch:AA res: 8 GLY at:CA .-ch:AA res: 50 TYR at:OH . INFO: link is found (not be used) dist= 2.126 ideal_dist= 1.645 ch:AA res: 13 ARG at:NH1 .-ch:AA res: 54 MET at:SD . INFO: link is found (not be used) dist= 1.820 ideal_dist= 1.462 ch:AA res: 13 ARG at:NH1 .-ch:AA res: 54 MET at:CE . INFO: link is found (not be used) dist= 1.757 ideal_dist= 1.395 ch:AA res: 13 ARG at:NE .-ch:AA res: 119 PHE at:CD1 . INFO: link is found (not be used) dist= 1.572 ideal_dist= 1.462 ch:AA res: 13 ARG at:NH2 .-ch:AA res: 125 LEU at:CD2 . INFO: link is found (not be used) dist= 1.751 ideal_dist= 1.513 ch:AA res: 33 ILE at:CG2 .-ch:AA res: 39 PRO at:CG . INFO: link is found (not be used) dist= 1.451 ideal_dist= 1.513 ch:AA res: 33 ILE at:CG2 .-ch:AA res: 39 PRO at:CD . INFO: link is found (not be used) dist= 1.759 ideal_dist= 1.524 ch:AA res: 58 LYS at:CD .-ch:AA res: 130 LEU at:CB . INFO: link is found (not be used) dist= 1.725 ideal_dist= 1.513 ch:AA res: 58 LYS at:CD .-ch:AA res: 130 LEU at:CD1 . INFO: link is found (not be used) dist= 1.578 ideal_dist= 1.524 ch:AA res: 83 ARG at:CD .-ch:AA res: 101 PRO at:CG . INFO: link is found (not be used) dist= 1.843 ideal_dist= 1.457 ch:AA res: 83 ARG at:NE .-ch:AA res: 101 PRO at:CB . INFO: link is found (not be used) dist= 0.666 ideal_dist= 1.457 ch:AA res: 83 ARG at:NE .-ch:AA res: 101 PRO at:CG . INFO: link is found (not be used) dist= 1.275 ideal_dist= 1.510 ch:AA res: 83 ARG at:CZ .-ch:AA res: 101 PRO at:CB . INFO: link is found (not be used) dist= 1.102 ideal_dist= 1.510 ch:AA res: 83 ARG at:CZ .-ch:AA res: 101 PRO at:CG . INFO: link is found (not be used) dist= 1.191 ideal_dist= 1.457 ch:AA res: 83 ARG at:NH1 .-ch:AA res: 101 PRO at:CA . INFO: link is found (not be used) dist= 0.690 ideal_dist= 1.457
Re: [ccp4bb] loop building with ARP/wARP
Dear Greg, Try ARP/wARP 7.2, released a few days ago, which is better, more stable and should have improved flash of error messages to the log files. ARP/wARP Loopy will not build a 33-residue loop at once, but Classic model building may get the gap shortened. Go to www.arp-warp.org for download. In parallel, from the same page you can submit Classic protein model building for remote execution in Hamburg, which also has ARP/wARP 7.2 installed. Please get back if problems remain. With best regards, Victor Quoting Gregory Bowman gdbow...@jhu.edu: Hi all, I have a large disordered loop (33aa) for a 2.0 Å dataset for which the rest of the structure is well-defined, and phases are decent (Rwork=19.6, Rfree=24.6). I can see some broken up density at one end, but have been unable to convincingly build into into this region manually. I would like to try arp/warp to improve density or possibly extend the loop termini but have been thwarted by some technical problems and would appreciate any advice. I've installed ccp4 6.2.0 on Mac OS X (10.6.8) with fink, both as 32-bit and 64-bit to allow me to run ARP/wARP (version 7.1) from the ccp4i GUI. I've been unable to get loopy to work, and also the standard ARP/wARP classic. When I run ARP/wARP Loops (a.k.a. loopy), I get the message in the log file: Couldn't find any loop to build, loopy will simple copy the pdb file. The program is able to read the sequence .pir file and match it to the structure, and seems from the sequence alignment to identify the regions of the sequence for which there is no structure. I'm guessing that I'm not putting some obvious parameter into the GUI/starting script, but I don't know what that might be. The script generated from the GUI (21_loopy.def) is pasted below. When I try to run ARP/wARP classic for loop building, I get the following message in the logfile: QUITTING ... ARP/wARP module stopped with an error message: REFMAC *** Look for error message in the file: /Users/gbowman/Greg/20_warpNtrace_refine.last.log At the end of the warpNtrace_refine.last.log file, the program reports what seem to be close contacts. Since I don't see this in the structure, and don't have any problems or errors like this when I refine the structure with REMAC, is this from rebuilding, and is this the problem that halts REFMAC? Thanks! Greg = = = = = = 20_warpNtrace_refine.last.log = = = = = = snip Input file :restraints.pdb NUMBER OF MONOMERS IN THE LIBRARY : 11465 with complete description: 11465 NUMBER OF MODIFICATIONS:53 NUMBER OF LINKS:66 I am reading libraries. Please wait. - energy parameters - monomers description (links mod ) BFONT COLOR=#FF!--SUMMARY_BEGIN-- !--SUMMARY_END--/FONT/B Number of atoms:2463 Number of residues : 859 Number of chains : 3 I am reading library. Please wait. mon_lib.cif INFO: link is found (not be used) dist= 1.907 ideal_dist= 1.432 ch:AA res: 8 GLY at:CA .-ch:AA res: 50 TYR at:OH . INFO: link is found (not be used) dist= 2.126 ideal_dist= 1.645 ch:AA res: 13 ARG at:NH1 .-ch:AA res: 54 MET at:SD . INFO: link is found (not be used) dist= 1.820 ideal_dist= 1.462 ch:AA res: 13 ARG at:NH1 .-ch:AA res: 54 MET at:CE . INFO: link is found (not be used) dist= 1.757 ideal_dist= 1.395 ch:AA res: 13 ARG at:NE .-ch:AA res: 119 PHE at:CD1 . INFO: link is found (not be used) dist= 1.572 ideal_dist= 1.462 ch:AA res: 13 ARG at:NH2 .-ch:AA res: 125 LEU at:CD2 . INFO: link is found (not be used) dist= 1.751 ideal_dist= 1.513 ch:AA res: 33 ILE at:CG2 .-ch:AA res: 39 PRO at:CG . INFO: link is found (not be used) dist= 1.451 ideal_dist= 1.513 ch:AA res: 33 ILE at:CG2 .-ch:AA res: 39 PRO at:CD . INFO: link is found (not be used) dist= 1.759 ideal_dist= 1.524 ch:AA res: 58 LYS at:CD .-ch:AA res: 130 LEU at:CB . INFO: link is found (not be used) dist= 1.725 ideal_dist= 1.513 ch:AA res: 58 LYS at:CD .-ch:AA res: 130 LEU at:CD1 . INFO: link is found (not be used) dist= 1.578 ideal_dist= 1.524 ch:AA res: 83 ARG at:CD .-ch:AA res: 101 PRO at:CG . INFO: link is found (not be used) dist= 1.843 ideal_dist= 1.457 ch:AA res: 83 ARG at:NE .-ch:AA res: 101 PRO at:CB . INFO: link is found (not be used) dist= 0.666 ideal_dist= 1.457 ch:AA
