[ccp4bb] phaser 2.3.0 floating point exception
Dear Randy and the Phaser team, Phaser 2.3.0 brought us several enhancement, but similar to Alexander Schiffer's experience, Phaser has failed several times now with a floating point exception error at different stages of automated MR: it has stopped in the beginning of RF and then in a new run it stopped in the middle of TF. The remedy is to explicitly lower the resolution of the input data (that was a 1.2 A resolution data with a smallish unit cell). I can provide the log files and the mtz file if necessary. Sincerely, Petr --- Petr Leiman EPFL IPSB-LBBS BSP-415 CH-1015 Lausanne, Suisse http://lbbs.epfl.ch
[ccp4bb] CCP4MG 2.5.0 troublesome start
Dear all, with the new MG version the program wants to start the previous session giving me an empty window without any buttons no matter how hard I delete or rename previous .CCP4MG files (presumably containing the status files etc...). As a result I cannot start new MG under my login ... Any ideas? Jan -- Jan Dohnalek, Ph.D Institute of Macromolecular Chemistry Academy of Sciences of the Czech Republic Heyrovskeho nam. 2 16206 Praha 6 Czech Republic Tel: +420 296 809 390 Fax: +420 296 809 410
Re: [ccp4bb] phaser 2.3.0 floating point exception
Dear Petr, Yes, please do send the log files, MTZ file and anything else needed to run the job that shows the problem, so we can track it down. It's probably best to send them off-line. We couldn't reproduce Alexander's problem, but he tells me that it only occurs when the script is started from a mono application (and I confess that I don't really know yet what that means). Once the problem he ran into has been defined a bit better, we can look into whether it's something we can fix on our end. Regards, Randy Read On 6 Sep 2011, at 08:25, Petr Leiman wrote: Dear Randy and the Phaser team, Phaser 2.3.0 brought us several enhancement, but similar to Alexander Schiffer's experience, Phaser has failed several times now with a floating point exception error at different stages of automated MR: it has stopped in the beginning of RF and then in a new run it stopped in the middle of TF. The remedy is to explicitly lower the resolution of the input data (that was a 1.2 A resolution data with a smallish unit cell). I can provide the log files and the mtz file if necessary. Sincerely, Petr --- Petr Leiman EPFL IPSB-LBBS BSP-415 CH-1015 Lausanne, Suisse http://lbbs.epfl.ch -- Randy J. Read Department of Haematology, University of Cambridge Cambridge Institute for Medical Research Tel: + 44 1223 336500 Wellcome Trust/MRC Building Fax: + 44 1223 336827 Hills RoadE-mail: rj...@cam.ac.uk Cambridge CB2 0XY, U.K. www-structmed.cimr.cam.ac.uk
[ccp4bb] CCPALC: not enough memory
hello, it seems i am recently getting the above error quite a lot in mapmask. i have searched for a solution, but only found the problem mentioned a few times with no precise solution indicated. would there be a way to find out HOW MUCH memory mapmask is hoping for ? i do have 2 Gb of memory and 3 Gb of swap, and limit says cputime unlimited filesize unlimited datasize unlimited stacksize8192 kbytes coredumpsize 0 kbytes memoryuseunlimited vmemoryuse unlimited descriptors 1024 memorylocked 64 kbytes maxproc unlimited mapmask itself dies in the middle of running and without error message to its log file. thanks ingo
Re: [ccp4bb] CCPALC: not enough memory
Can you send the command script, and mapdump output for any input maps? Also, if you are entering a PDB file, the cell, spacegroup, and an idea of range of X, Y, and Z values? On 09/06/2011 09:56 AM, Ingo P. Korndoerfer wrote: hello, it seems i am recently getting the above error quite a lot in mapmask. i have searched for a solution, but only found the problem mentioned a few times with no precise solution indicated. would there be a way to find out HOW MUCH memory mapmask is hoping for ? i do have 2 Gb of memory and 3 Gb of swap, and limit says cputime unlimited filesize unlimited datasize unlimited stacksize8192 kbytes coredumpsize 0 kbytes memoryuseunlimited vmemoryuse unlimited descriptors 1024 memorylocked 64 kbytes maxproc unlimited mapmask itself dies in the middle of running and without error message to its log file. thanks ingo
Re: [ccp4bb] CCPALC: not enough memory
OK, here's the solution (also to BB in case anyone else has this problem). The PDB file appears to come from CNS. The coordinate file contains the following atoms: ATOM 2244 CG LEU A 452.000.000.000 1.00 0.00 A ATOM 2245 CD1 LEU A 452.000.000.000 1.00 0.00 A ATOM 2246 CD2 LEU A 452.000.000.000 1.00 0.00 A These coordinates are no doubt dummy values of some sort. But, interpreted as coordinates, they are so far from the rest of the model that attempting to build a mask around them and the rest of the model would take a vast file. The PDB file header contains the following lines generated by CNS: REMARK unknown coordinates for atom: ALEU 452 CG REMARK unknown coordinates for atom: ALEU 452 CD1 REMARK unknown coordinates for atom: ALEU 452 CD2 That suggests to me that the problem may have been with the file input to CNS. You'd have to look at your input file to work out exactly what is going on. In the meantime, deleting these atoms or autofitting the sidechain in coot ought to fix it. Hope that solves it, Kevin On 09/06/2011 09:56 AM, Ingo P. Korndoerfer wrote: hello, it seems i am recently getting the above error quite a lot in mapmask. i have searched for a solution, but only found the problem mentioned a few times with no precise solution indicated. would there be a way to find out HOW MUCH memory mapmask is hoping for ? i do have 2 Gb of memory and 3 Gb of swap, and limit says cputime unlimited filesize unlimited datasize unlimited stacksize8192 kbytes coredumpsize 0 kbytes memoryuseunlimited vmemoryuse unlimited descriptors 1024 memorylocked 64 kbytes maxproc unlimited mapmask itself dies in the middle of running and without error message to its log file. thanks ingo
Re: [ccp4bb] CCPALC: not enough memory
I have seen these type of cases. They cause problem. They may come from O, from cns or other programs. Origins may even not be known. My solution was that if an atom has coordinates 9998.000 or more then consider them absent (i.e. set occupancies 0). On 6 Sep 2011, at 14:30, Kevin Cowtan wrote: OK, here's the solution (also to BB in case anyone else has this problem). The PDB file appears to come from CNS. The coordinate file contains the following atoms: ATOM 2244 CG LEU A 452.000.000.000 1.00 0.00 A ATOM 2245 CD1 LEU A 452.000.000.000 1.00 0.00 A ATOM 2246 CD2 LEU A 452.000.000.000 1.00 0.00 A These coordinates are no doubt dummy values of some sort. But, interpreted as coordinates, they are so far from the rest of the model that attempting to build a mask around them and the rest of the model would take a vast file. The PDB file header contains the following lines generated by CNS: REMARK unknown coordinates for atom: ALEU 452 CG REMARK unknown coordinates for atom: ALEU 452 CD1 REMARK unknown coordinates for atom: ALEU 452 CD2 That suggests to me that the problem may have been with the file input to CNS. You'd have to look at your input file to work out exactly what is going on. In the meantime, deleting these atoms or autofitting the sidechain in coot ought to fix it. Hope that solves it, Kevin On 09/06/2011 09:56 AM, Ingo P. Korndoerfer wrote: hello, it seems i am recently getting the above error quite a lot in mapmask. i have searched for a solution, but only found the problem mentioned a few times with no precise solution indicated. would there be a way to find out HOW MUCH memory mapmask is hoping for ? i do have 2 Gb of memory and 3 Gb of swap, and limit says cputime unlimited filesize unlimited datasize unlimited stacksize8192 kbytes coredumpsize 0 kbytes memoryuseunlimited vmemoryuse unlimited descriptors 1024 memorylocked 64 kbytes maxproc unlimited mapmask itself dies in the middle of running and without error message to its log file. thanks ingo Garib N Murshudov Structural Studies Division MRC Laboratory of Molecular Biology Hills Road Cambridge CB2 0QH UK Email: ga...@mrc-lmb.cam.ac.uk Web http://www.mrc-lmb.cam.ac.uk
Re: [ccp4bb] How to help crystal grow bigger
Dear SnowDeer, Just how small is too small? If you have access to a microfocus beamline you might find you can collect decent diffraction data from crystals with dimensions in the single digit microns. Fishing tiny crystals is difficult, but something like the MicroMesh tennis racquet mounts can help. Having multiple crystals on the same pin is in fact a rather helpful way of screening lots of samples. Please don't discount your crystals _only_ because they are small! Shameless plug: there is a review on microcrystallography here that you might find interesting. http://www.tandfonline.com/doi/abs/10.1080/0889311X.2010.527964 Best wishes -- David On 5 September 2011 09:06, SnowDeer huanxu...@gmail.com wrote: Dear All: Recently I am working on a protein which can already grow nice pyramid-like crystals after the condition was optimized, while the crystals are too small to be picked up. The crystals grew quite fast and densely, so I tried to put 100ul paraffin oil inside the 600ul reservoir solution or put the plate under 16 degree to slow down the evaporation, while the crystals were still the same. I also tried macro or micro seeding with or without the paraffin oil. Macroseeding would give a larger crystal (not very nice) with many small crystals in the drop even I washed the seeds carefully. For microseeding, the same small crystals grew. I don't have many experiences in crystallography, so I have no idea how to make it grow bigger... Any suggestion is most welcome. Thanks. SnowDeer
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] peptide crystallization question
Dear all I am interested in crystallizing a 5 residue peptide. I have no prior experience in this field although I have crystallized larger proteins (5--60 kDa). Do people use regular screens used in macromolecular crystallization such as Hamptons, wizards etc? Any suggestions are greatly appreciated. Also, can anyone point me to some relevant literature ? Thanks. Ritcha
Re: [ccp4bb] peptide crystallization question
On Tue, 2011-09-06 at 11:51 -0500, Chaudhary, Ritcha wrote: Do people use regular screens used in macromolecular crystallization such as Hamptons, wizards etc? Probably not - I believe short peptides are crystallized mostly via various evaporation techniques (but I am very curious to hear what those with more experience with this will suggest). It should also form a stable structure, otherwise it will either not crystallize or the form you get won't be representative of solution structure. Which begs the question - why not NMR? -- After much deep and profound brain things inside my head, I have decided to thank you for bringing peace to our home. Julian, King of Lemurs
Re: [ccp4bb] peptide crystallization question
Dear Ritcha, we have crystallised various peptides, especially circular ones, both from regular screens used in MX and from specially prepared screens (i.e. different organic solvents). We tend to use slow evaporation from under mineral oil in Terazaki plates (i.e. microbatch). We have also failed to crystallise many peptides, perhaps due to their inherent flexibility, perhaps due to our incompetence. I also did not have previous experience in crystallising peptides. What to try first depends on your peptide. If you have a lot of material, you can just try many, many conditions. If you have it as a solid or can obtain it as a solid by evaporation, you can quickly determine solubility in different solvents. We find 50% methanol useful in many cases. If you try volatile solvents first, you can then evaporate them and re-use the peptide. From your sequence, you should know if your peptide is hydrophilic, hydrophobic, aromatic, basic, acidic, etc. Based on these properties dissolve at high concentration in like solvent and set up crystallisation trials with solutions likely to precipitate it out slowly, i.e. somewhat unlike. If your peptide is very hydrophobic, you may need to use hydrophobic solvent incompatible with normal plastics. In these cases we use glass containers. If you have organic chemists nearby, talk to them - many of them have experience in crystallising organic compounds and can give you good ideas for crystallising peptides. Greetings, Mark Mark J van Raaij On 6 Sep 2011, at 18:51, Chaudhary, Ritcha wrote: Dear all I am interested in crystallizing a 5 residue peptide. I have no prior experience in this field although I have crystallized larger proteins (5--60 kDa). Do people use regular screens used in macromolecular crystallization such as Hamptons, wizards etc? Any suggestions are greatly appreciated. Also, can anyone point me to some relevant literature ? Thanks. Ritcha
[ccp4bb] Multi-Pole Approach to Structural Biology
Dear Colleague, Due to many requests, we have extended the deadline for submission of abstracts for contributed talks within: International Conference Multi-Pole Approach to Structural Biology November 16-19, 2011 | Warsaw, Poland Information, programme and registration: http://iimcb.genesilico.pl/multipole/ The purpose of this international conference is to discuss the advances of structural biology that have been promoted through interdisciplinary research, with contributions of scientists significantly linked to Poland. However, the conference will be entirely in English and we encourage both national and international participants to register and attend. *Invited speakers represent mostly biocrystallography and structural bioinformatics, but the scope of the entire conference, and in particular the contributed presentations are expected to cover a much broader area of life sciences!* Topics include, but are not limited to: molecular and cell biology (also focus on function rather than structure), biochemistry, biophysics, -omics, evolutionary biology, systems biology, and computational biology. A special panel discussion will be organized by the Foundation for Polish Science. We encourage both senior and junior scientists to submit abstracts covering any aspects of life sciences, to be considered for talks and/or posters. The extended deadline for abstracts/talks is September 15th, 2011 Selected talks will be announced before September 21st. Early registration deadline is also September 15th, 2011 regular fee: 500 PLN = 125 Euro student fee: 300 PLN = 75 Euro Payments for early registrations: until September 30th Late registration and poster abstracts will continue to be accepted until the limit of the venue is reached. We would also greatly appreciate if you could forward this announcement to anybody who may be interested, and if you post the attached poster at a message board in your institution. Yours sincerely, Janusz Bujnicki Zbigniew Dauter Mariusz Jaskólski Wladek Minor Alexander Wlodawer
[ccp4bb] converting mmcif to mtz failure
Dear Crystallographers, in trying to convert a mmcif to mtz, I get the logfile below. I looked in the directory, and there is a file cf_mm.dic, but this is presumably not the same as the similar .lib file. Any thoughts about this? Did the file somehow get lost? Also, I recently did this same conversion to another file without problems... Jacob Keller #CCP4I VERSION CCP4Interface 2.1.0 #CCP4I SCRIPT LOG import #CCP4I DATE 06 Sep 2011 16:29:11 #CCP4I USER 'UNKNOWN' #CCP4I PROJECT 3mgl #CCP4I JOB_ID 3 #CCP4I SCRATCH C:/Ccp4Temp #CCP4I HOSTNAME chloe #CCP4I PID 2728 html !-- CCP4 HTML LOGFILE -- hr pre ### ### ### ### CCP4 6.2: cif2mtz version 6.2 : 16/11/09## ### User: Jacob Run date: 6/ 9/2011 Run time: 16:29:19 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. Data line--- title [No title given] Data line--- symmetry P4212 Spacegroup information obtained from library file: Logical Name: SYMINFO Filename: C:\CCP4-Packages\ccp4-6.2.0\lib\data\syminfo.lib Data line--- cell 90.91 90.91 65.21 90.0 90.0 90.0 Data line--- end CCIF signal CCIF_FOPEN (severity: SEVERE ERROR/FATAL) (Raised in zzs_undump) Cannot open file C:\CCP4-Packages\ccp4-6.2.0\lib\data\cif_mmdic.lib for reading! *** * Information from CCP4Interface script *** The program run with command: cif2mtz HKLIN C:/Users/Jacob/Desktop/structures/PDB_3mgl/3mgl-sf.cif HKLOUT C:/Ccp4Temp/3mgl_3_1_mtz.tmp has failed with error message child process exited abnormally *** #CCP4I TERMINATION STATUS 0 child process exited abnormally #CCP4I TERMINATION TIME 06 Sep 2011 16:29:19 #CCP4I MESSAGE Task failed -- *** Jacob Pearson Keller Northwestern University Medical Scientist Training Program cel: 773.608.9185 email: j-kell...@northwestern.edu ***
