Re: [ccp4bb] MrBump Behaves Strangely
Dear Jacob, Thanks for reporting this problem. Can you tell me what version of CCP4 you are using? As an alternative, you can use MrBUMP via the CCP4-online service which is available from here: www.ccp4.ac.uk/ccp4online It's still in development and only goes as far as the Refmac step but it does process the search models in parallel so it can be a lot quicker than running MrBUMP locally. Best wishes, Ronan On 03/02/15 17:22, Keller, Jacob wrote: Dear Crystallographers, I am trying to get MrBump to complete a partial solution, but on my windows7 machine, the CCP4i interface essentially freezes (cannot see logfiles therein, nothing responds, although it does not completely die), and those log files which I think are the correct ones have ceased changing. Nevertheless, the process continues on 2 cores and 800 MB RAM as phaser.exe. Is something broken here, maybe phaser has gone incognito mode, or something else? It's happened the last few days any time I've tried to run MrBump. Any thoughts? ...And please spare me any parathyrophobia--we don't need to beat that dead horse! JPK *** Jacob Pearson Keller, PhD Looger Lab/HHMI Janelia Research Campus 19700 Helix Dr, Ashburn, VA 20147 email: kell...@janelia.hhmi.org ***
[ccp4bb] CCP4 Study Weekend 2015 Advances in Experimental Phasing - Live Web Streaming
Dear All, The webcast for this year's CCP4 Study Weekend on Advances in Experimental Phasing taking place on the 8/9 of January will be available from the STFC Webinars page: http://www.stfc.ac.uk/webinars A programme for the meeting can be found here: http://www.ccp4.ac.uk/events/CCP4_2015/programme.html Best wishes, Ronan
Re: [ccp4bb] I am struggling to compile fasta36
Dear Pietro, Tim's solution should work for you. If not please let me know. From CCP4 6.5.0 (due very soon), the default sequence search tool in MrBUMP will be Phmmer which will be included in the suite on all supported operating systems. So there won't be the need to download fasta separately. Best wishes, Ronan On 15/12/14 16:47, Tim Gruene wrote: Dear Pietro, zlib is the C compression library. You must have some version of libz.so installed in order to link againt it. Regards, Tim On 12/15/2014 05:36 PM, Pietro Roversi wrote: Dear all, I apologise for the dullness of the question, but I am struggling to compile the fasta36 binary that I need to run MrBump: emmaWT:/software/fasta-36.3.7/src sudo make -f ../make/Makefile.linux64_sse2 all gcc -g -O -msse2 -o ../bin/fasta36 comp_mthr9.o work_thr2.o pthr_subs2.o compacc2_t.o showbest.o build_ares.o re_getlib.o mshowalign2_t.o htime.o apam.o doinit.o init_fa.o drop_nfa.o wm_align.o calcons_fa.o scale_se.o karlin.o lgetlib.o lgetaa_m.o c_dispn.o ncbl2_mlib.o lib_sel.o url_subs.o mrandom.o -lm -lz -lpthread /usr/bin/ld: cannot find -lz collect2: error: ld returned 1 exit status make: *** [fasta36] Error 1 Googling for this -lz ld flag does not seem to hit anything immediately relevant in the top pages. Please help! Pietro Sent from my Desktop Dr. Pietro Roversi Oxford University Biochemistry Department - Glycobiology Division South Parks Road Oxford OX1 3QU England - UK Tel. 0044 1865 275339
[ccp4bb] Reminder: CCP4 Study Weekend 2015 - Travel bursary application deadline is 31st of October
*The CCP4 Study Weekend (7 - 9 January 2015)* *East Midlands Conference Centre, University of Nottingham* ** *Wednesday 7 - MX User Meeting* *Thursday 8 / Friday 9 - CCP4 Study Weekend* ** *Advances in Experimental Phasing* ** *We cordially invite you to participate in the 2015 CCP4 Study Weekend at the the East Midlands Conference Centre, University of Nottingham. The annual CCP4 Study Weekend is a chance to shake off the post-New Year torpor, and work hard and play hard with your fellow crystallographers. Once again, we have put together an exciting scientific programme for the Thursday and Friday, either side of the traditional conference dinner. Please also check out the satellite meetings which may be of interest. The Study Weekend is a chance to catch up with old friends, but is also a chance to meet the CCP4 staff who will be there to present and demonstrate the latest software and to answer questions - please say hello!* ** *This year, the topic for the Study Weekend is Advances in Experimental Phasing. In keeping with previous CCP4 meetings, the lectures will focus on the presentation and discussion of advanced methods and techniques developed and used by the leaders in the field. *** *Scientific Organisers* *Thomas Schneider - EMBL Hamburg (Germany)* *Airlie McCoy - University of Cambridge (UK)* *Further details of the program and the registration are at **http://www.cse.scitech.ac.uk/events/CCP4_2015* *Please note that we have a limited number of travel bursaries available to international students to help with the cost of traveling to the UK. The deadline for applicants looking to avail of these bursaries is the /31st of October, 2014/**, so please get your application in before then. * *Terms and Conditions apply. Please read the cancellation policy before applying.* -- Scanned by iCritical.
Re: [ccp4bb] MrBump doesn't work (6.4.0 update)
Hi Marjolein, I'm glad to hear that. You may also be interested in the new CCP4 online service which hosts, among other applications, a MrBUMP service. One of the main advantages it has is that it uses HHPred to search for MR search models which can produce better models than the simple Fasta search performed in the older MrBUMP. You can access it here: www.ccp4.ac.uk/ccp4online Best wishes, Ronan On 19/08/14 12:22, Marjolein Thunnissen wrote: Hii Ronan, Hi, Embarrassingly enough, my problem has disappeared...I guess indeed it was the update, as I updated ccp4 today and now I tried and it works! Thanks! Marjolein On 19 Aug 2014, at 12:28, Ronan Keegan ronan.kee...@stfc.ac.uk mailto:ronan.kee...@stfc.ac.uk wrote: Hi Marjolein, Thanks for your email and sorry to hear about your problems with MrBUMP. Can you please tell me what OS you are using (Linux, Mac etc.)? Also us your CCP4 installation completely up to date? There should 20 updates in total installed. The last one has some important fixes for MrBUMP. Best wishes, Ronan On 19/08/14 09:28, Marjolein Thunnissen wrote: Hi I just encountered the same problem as described in the message below. I tried to search but couldn’t find an answer, but was a solution for this problem found? Thanks Marjolein On 04 Aug 2014, at 03:59, Eze Chivi ezech...@outlook.com.ar mailto:ezech...@outlook.com.ar wrote: Hello, I have a problem with the update 6.4.0 of ccp4: MrBump does not start, it freezes in the message Please wait...drawing task window mrbump and the error expected integer but got . Sometimes, MrBump starts, but drop-down menu doesn't work. Same problem in Linux or Windows versions. Thank you Ezequiel Mail Attachment.png * **Marjolein Thunnissen* Science Coordinator MX MAX IV Laboratory Lund University P.O. Box 118, SE-221 00 Lund, Sweden Visiting address: Ole Römers väg 1, 223 63 Lund Telephone: +46 766 32 04 17 www.maxlab.lu.se http://www.maxlab.lu.se/ -- Scanned by iCritical. * **Marjolein Thunnissen* Science Coordinator MX MAX IV Laboratory Lund University P.O. Box 118, SE-221 00 Lund, Sweden Visiting address: Ole Römers väg 1, 223 63 Lund Telephone: +46 766 32 04 17 www.maxlab.lu.se http://www.maxlab.lu.se/ -- Scanned by iCritical.
Re: [ccp4bb] AMPLE failure
Hi Robert, Thanks for your interest in AMPLE and reporting this bug. There is a small bug that has come about as a result of the latest MRBUMP update last week that causes this problem. We're preparing a fix for it which should be in the next ccp4 update towards the end of this week or early next week. In the meantime I can send you (off list) the latest version of the code that you can manually install. Best wishes, Ronan On 12/07/14 18:58, Robert Kirchdoerfer wrote: Hi, I'm trying to run AMPLE from ccp4-6.4.0 on Linux Ubuntu. It looks like it found all the program dependencies that it needs and Rosetta looks like it ran okay and I think MRBUMP looks alright, but then the program stopped with the following error message: MR and shelx DONE ALL DONE (in 1.64101706141 hours) Saved results as file: /home/rob/Crystal/108_B7U_3/ccp4/ROSETTA_MR_1/resultsd.pkl *** * Information from CCP4Interface script *** The program run with command: /home/rob/Xstal_Programs/ccp4v640/destination/ccp4-6.4.0/bin/ccp4-python -u /home/rob/Xstal_Programs/ccp4v640/destination/ccp4-6.4.0/bin/ample -mtz /home/rob/Crystal/108_B7U_3/ccp4/XDS_ASCII_scaled2.mtz -fasta /home/rob/Crystal/108_B7U_3/phenix/RNK149.fasta -nmodels 1000 -name MVD0 -run_dir /home/rob/Crystal/108_B7U_3/ccp4 -nproc 8 -make_models True -rosetta_dir /home/rob/Xstal_Programs/Rosetta/rosetta-3.5 -frags_3mers /home/rob/Crystal/108_B7U_3/ccp4/aat000_03_05.200_v1_3 -frags_9mers /home/rob/Crystal/108_B7U_3/ccp4/aat000_09_05.200_v1_3 -make_frags False -F F_XDSdataset -SIGF SIGF_XDSdataset -FREE FreeR_flag -early_terminate True -use_shelxe True -use_arpwarp False has failed with error message Traceback (most recent call last): File /home/rob/Xstal_Programs/ccp4v640/destination/ccp4-6.4.0/bin/ample, line 838, in summary = amopt.final_summary() File /home/rob/Xstal_Programs/ccp4v640/destination/ccp4-6.4.0/share/ample/python/ample_options.py, line 197, in final_summary result_summary.append( getattr( result, title2attr[ h ] ) ) KeyError: 'SHELXE_ACL' Any thoughts on how I might troubleshoot this? Thanks and Best wishes, Rob -- Scanned by iCritical.
[ccp4bb] CeBEM/CCP4 South American School in Macromolecular Crystallography - Final week for applications
Dear Colleagues, This is a reminder about the second CeBEM/CCP4 South American School in Macromolecular Crystallography. The closing date for applications is Monday the 10th of February. This year's school will take place at Sao Carlos University in Brazil. Full details including the program and application information can be found at the school website: http://www.ifsc.usp.br/mx2014 Title: Macromolecular Crystallography School 2014: From data processing to structure refinement and beyond Dates: April 8th to 16th 2014 Purpose of the course and intended audience: The course is intended mainly for graduate students, postdoctoral researchers and young scientists in the area of structural biology. The school is not meant as an introductory level course to protein crystallography. It is designed more for applicants with reasonable expertise in crystallography and experience with the CCP4 suite. The purpose of the school is to address specific problems that the applicants face while processing diffraction data and while solving and refining novel structures. Applicants with diffraction data (solved, partially solved or unsolved) will be given strong consideration, although these are not mandatory requirements. The workshop will cover many popular programs used for data processing and structure solution with the software developers available to help throughout the week. Programs covered will include: Mosflm, Aimless, XDS, Refmac, ARP/wARP, Phaser, Crank, ARCIMBOLDO, Coot, SHELXC/D/E, Balbes, MrBUMP, Buccaneer and many more. Grants will be available for traveling students needing assistance with funding. Best wishes, Eduardo, Garib, Richard and Ronan -- Scanned by iCritical.
Re: [ccp4bb] MrBUMP not running after update
Dear Jie, Thanks for spotting this problem. I've made a fix for MrBUMP that should address the problem. It will be included in the next CCP4 update which will go out tomorrow (Tuesday 17th of December) all being well. Best wishes, Ronan On 10/12/13 01:34, jie liu wrote: Dear All I just installed CCP4-6.4 and all the subsequent updates. Now MrBump failed with the following error message: The program run with command: /usr/local/ccp4-6.4.0/bin/ccp4-python -u /usr/local/ccp4-6.4.0/bin/mrbump HKLIN /home/jie/Structures/local/se-p26c8newn6/ccp4_6.3/high_x4c.mtz SEQIN /home/jie/Structures/local/se-p26c8newn6/ccp4_6.3/seq.seq HKLOUT /home/jie/Structures/local/se-p26c8newn6/ccp4_6.3/high_x4c_mrbump_soln1.mtz XYZOUT /home/jie/Structures/local/se-p26c8newn6/ccp4_6.3/high_x4c_mrbump_soln1.pdb has failed with error message Traceback (most recent call last): File /usr/local/ccp4-6.4.0/bin/mrbump, line 107, in module queue = master.fast_search_MR(init, target_info, mstat) File /usr/local/ccp4-6.4.0/share/mrbump/include/initialisation/MRBUMP_master.py, line 482, in fast_search_MR ps.get_top_hit(mstat.sorted_MR_list, init, mstat) File /usr/local/ccp4-6.4.0/share/mrbump/include/structures/Matches.py, line 1431, in get_top_hit CHAIN=mstat.chain_list[chain] KeyError: '1e6j_p2' It was running fine with CCP4-6.3. Could someone help please? Thanks! Jie -- Scanned by iCritical.
Re: [ccp4bb] MRBUMP - PHASER ?
Hi Douglas, Have you applied all of the automatic updates to your installed version of CCP4? There was a bug relating to this that I fixed at one point and it was pushed out using our update system. However, if you've installed from source code you won't have this option. Best wishes, Ronan On 10/09/13 15:44, Bailey, Douglas (NIH/NCI) [E] wrote: Hello Everyone, PHASER is returning the following error Input Error: No Mode Set when called from MRBUMP. CCP4-6.3.0 running on Centos5-x64. Any help , ideas, comment would be greatly appreciated. Thanks, Doug # ### CCP4 PROGRAM SUITE: Phaser 2.5.1 ### # User: jacek Run time: Tue Sep 10 10:02:53 2013 Version: 2.5.1 OS type: linux Release Date: Fri Jul 6 07:21:42 2012 (svn ) If you use this software please cite: $TEXT:Reference1: $$ $$ Phaser Crystallographic Software A.J. McCoy, R.W. Grosse-Kunstleve, P.D. Adams, M.D. Winn, L.C. Storoni R.J. Read J. Appl. Cryst. (2007). 40, 658-674 $$ * *** Phaser Module: PREPROCESSOR 2.5.1 *** * END BFONT COLOR=#FF8800 $TEXT:Warning: $$ Baubles Markup $$ - INPUT ERROR: No MODE set - $$ Douglas Bailey NCI-Frederick 1050 Boyles Street Frederick, Maryland 21702 301-846-5328 -- Scanned by iCritical.
Re: [ccp4bb] remove job posting
Dear Jilliu, If you contact us here at the ccp4 help desk (c...@ccp4.ac.ukmailto:c...@ccp4.ac.uk) we can remove the advert from the CCP4 vacancies website. However, we can't remove it from the various archives of the mailing list that exist around the web. Let me know which advert you want removed. Best wishes, Ronan From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of jlliu liu Sent: 15 February 2013 04:09 To: ccp4bb Subject: [ccp4bb] remove job posting Can anyone tell me how to remove the job posting on CCP4BB? Thanks! -- Scanned by iCritical.
Re: [ccp4bb] Thx...
Hi Eugene, Yes we should do this post-haste. First day that we are all present in RAL next week. Ronan -Original Message- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of eugene.krissi...@stfc.ac.uk Sent: 01 February 2013 09:42 To: ccp4bb Subject: Re: [ccp4bb] Thx... Thank you very much Bernhard. Feedbacks like yours have enormous encouraging effect on developers. Eugene. On 1 Feb 2013, at 00:02, Bernhard Rupp (Hofkristallrat a.D.) wrote: Hi Fellows from the programming department(s), I just had the pleasure to work with the new update mechanism and Win CCP4 6.3 GUI. That you can get from the summary page directly to Coot (which also automatically updates) and that everything works as advertised is very impressive and I perhaps even necessary for CCP4 to keep its market share with the push-button crowd. I think it is awesome progress and thanks to all the friendly coders for their efforts. The collective time savings are enormous. Best regards, BR - Bernhard Rupp 001 (925) 209-7429 +43 (676) 571-0536 b...@ruppweb.org hofkristall...@gmail.com http://www.ruppweb.org/ --- The road to scientific serfdom is paved with Nature papers --- -- Scanned by iCritical. -- Scanned by iCritical.
Re: [ccp4bb] Ample, shelxe-beta and F to I conversion confusion
Hi Huw, Well spotted! We originally gave structure factors to SHELXE in our testing as for most of our test cases we only had F/SIGF available. We were advised to change to intensities but somehow in the released version the -f flag remained. I'll make the change and put it in a CCP4 update. Ideally we should be using the original intensities rather than converting the structure factors so we'll look to adding that as an input option. Thanks again for spotting this. Best wishes, Ronan -Original Message- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Huw Jenkins Sent: 28 January 2013 10:14 To: ccp4bb Subject: [ccp4bb] Ample, shelxe-beta and F to I conversion confusion Hi, I've been running Ample and I'm a bit confused about the input for the shelxe-beta auto-tracing. The input mtz for Ample has F, SIGF and FreeR and it appears that Ample converts the structure factor amplitudes to intensities using mtz2various with the FSQUARED keyword as the log file contains the following: Data line--- LABIN FP=F SIGFP=SIGF FREE=FreeR_flag Data line--- OUTPUT SHELX Data line--- FSQUARED Fs are squared on output - better to use original Is from TRUNCATE output Data line--- END However then shelxe is run with the command: shelxe shelxe-input.pda -a15 -q -s0.4779 -o -f -n -t3 I thought that the -f flag tells shelxe that the input hkl file contains Fs not Is so this should not be present? When I run shelxe with the phaser/molrep solutions and a hkl file generated either from the merged intensities with mtz2hkl or unmerged intensities with xdsconv I get much lower CCs for the autotracing which makes sense as all of the solutions so far are rubbish! The Ample logs contain CCs 30 for all solutions which doesn't seem correct. Any information would be greatly appreciated! Thanks, Huw -- Scanned by iCritical.
[ccp4bb] CCP4 Update 016
Dear CCP4 Users A CCP4 update has just been released, consisting of the following changes. * Qtrview: Now uses runwincoot.bat script to start Wincoot on Windows * MrBUMP: Assumes intensities rather than structure factor amplitudes when calling SHELXE * Pdb_merge: Execution permissions added to binary (Mac OSX and Linux) * Pdbcur: Execution permissions added to binary (Mac OSX and Linux) * Pisa: Execution permissions added to binary (Mac OSX and Linux) * INDEX.html: CCP4 documentation index updated to have link to Aimless program documentation If you do not currently receive updates, consider re-installing your CCP4 setup using the latest binary packages, which now have the CCP4 Update Manager (ccp4um) integrated. Note that auto-updates will work correctly only with CCP4 release 6.3.0, therefore upgrade if necessary. Please report any bugs to c...@stfc.ac.ukmailto:c...@stfc.ac.uk Many thanks for using CCP4. Ronan Keegan -- Scanned by iCritical.
[ccp4bb] Postdoctoral Position in Structural Biology of Immune Receptors
Dear All, I repost this message on behalf of Dr. Jia-huai Wang, as this position needs to be filled as soon as possible. For inquiries please contact Dr. Wang directly at jw...@red.dfci.harvard.edu Postdoctoral Position in Structural Biology of Immune Receptors: There is an immediate opening for a postdoctoral position in protein crystallography at the Dana-Farber Cancer Institute, Harvard Medical School. The research project is focused on the structural and functional investigation of leukocyte integrins, which are cell surface receptors that play a key role in immunity. The successful candidate should have a Ph.D. in structural biology. In addition to a knowledge of X-ray crystallography, the applicant should also have experience in molecular biology, and protein biochemistry. This includes cloning, protein expression and purification, particularly in eukaryotic systems such as baculavirus. Interested candidates should email a CV and three contacts for reference to Dr. Jia-huai Wang at jw...@red.dfci.harvard.edu. For more information regarding the Wang Laboratory, please see the website:http://wang.dfci.harvard.edu Sincerely, lorenzo Lorenzo Ihsan FInci, Ph.D. Postdoctoral Scientist, Wang Laboratory Harvard Medical School Dana-Farber Cancer Institute Boston, MA Peking University The College of Life Sciences Beijing, China -- Scanned by iCritical.
Re: [ccp4bb] Bug of GUI of ACORN?
Dear Jiawei, Thanks for spotting this and bringing it to our attention. It is a serious bug in the interface when using the default protocol for Acorn. When running Acorn to determine heavy atoms the default is to truncate the resolution to 3.5 Angstroms. However this default is there for all modes of operation and as it uses the same keyword for general resolution truncation it causes this issue. I'll send you a fix for it in a later email but we'll also provide this as an update in the next ccp4 auto update which will hopefully be the end of this week or early next week. (Note: to install the ccp4 auto updater please visit http://www.ccp4.ac.uk/download/update_manual.html). Best wishes, Ronan -Original Message- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of jwwang Sent: 05 December 2012 01:34 To: ccp4bb Subject: [ccp4bb] Bug of GUI of ACORN? Hi, In the GUI of ACORN, I use all the default setting, which should mean all observed reflections in the mtz file will be used for ab initio phasing. However, the command file output by GUI includes the keyword RESO 50 3.5. It's ridiculous that GUI has cut off the resolution to 3.5 A, which makes the ACORN running failed. If I set the full resolution in GUI with Use data from resolution range 50 1.2, the command file will include two RESO keyword --- RESO 50 1.2 RESO 50 3.5, which means resolution was still cut to the 3.5 A. Is it a bug in the GUI of ACORN? BTW, if you use the script to run ACORN, everything is fine. Best, Jiawei Wang -- Scanned by iCritical.
[ccp4bb] CCP4 Study Weekend 2013
Dear All, A quick reminder that these next few days are the last chance to register for next month's CCP4 Study Weekend. Registration will close next Monday the 10th of December. The meeting will take place at the East Midlands Conference Centre in Nottingham, UK from the 3rd to the 5th of January and is entitled Molecular Replacements, focusing on the presentation and discussion of advanced methods and techniques in this important field. For more information about the meeting and to register please visit the Study Weekend website at: http://www.cse.scitech.ac.uk/events/CCP4_2013/ We look forward to seeing you in Nottingham. Best wishes, Ronan -- Scanned by iCritical.
[ccp4bb] CCP4 6.3.0 update 009
Dear CCP4 Users, A CCP4 update has just been released, consisting of the following changes: * Refmac 5.7.0032: some minor bug fixes * Gesamt: PDB file names are now included in the PDB screening option output The easiest way to obtain the update is to install the CCP4 update client, if you have not done so already. Details on how to install the CCP4 Update Manager are available from: http://www.ccp4.ac.uk/download/update_manual.html Note that auto-updates will work correctly only with CCP4 release 6.3.0, therefore upgrade if necessary. Please report any bugs to c...@stfc.ac.uk. Many thanks for using CCP4, -- Ronan Keegan -- Scanned by iCritical.
[ccp4bb] CCP4 Study Weekend 2013
Dear All, A quick reminder to you all about this coming January's CCP4 Study Weekend entitled Molecular Replacements (January 3rd-5th 2010). As the title suggests, the meeting will be all about the latest developments in molecular replacement with many leading crystallographers and software developers giving presentations on the subject. The deadline for the first round of registrations will be the 23rd of November after which the registration price will increase from £210 to £260. So please get your registration in before then. After a few years in Warwick, the meeting will be returning to the East Midlands Conference Centre at Nottingham University in the UK. For more details and to register please see the Study Weekend website at: http://www.cse.scitech.ac.uk/events/CCP4_2013/ We hope to see you there. Best wishes, Ronan -- Scanned by iCritical.
Re: [ccp4bb] CCP4 Study Weekend 2013
Dear All again, DoH! Minor typo in my previous email. The dates are January 3rd-5th 2013! (not 2010). Best wishes, Ronan -Original Message- From: Keegan, Ronan (STFC,RAL,SC) Sent: 08 November 2012 18:06 To: ccp4bb Cc: Miller, Shirley (STFC,DL,SC) Subject: CCP4 Study Weekend 2013 Dear All, A quick reminder to you all about this coming January's CCP4 Study Weekend entitled Molecular Replacements (January 3rd-5th 2010). As the title suggests, the meeting will be all about the latest developments in molecular replacement with many leading crystallographers and software developers giving presentations on the subject. The deadline for the first round of registrations will be the 23rd of November after which the registration price will increase from £210 to £260. So please get your registration in before then. After a few years in Warwick, the meeting will be returning to the East Midlands Conference Centre at Nottingham University in the UK. For more details and to register please see the Study Weekend website at: http://www.cse.scitech.ac.uk/events/CCP4_2013/ We hope to see you there. Best wishes, Ronan -- Scanned by iCritical.
[ccp4bb] CCP4 update 6.3.0 006
Dear CCP4 Users, A CCP4 update has just been released, consisting of the following changes: * MrBUMP: model building options added * PISA: new QT interface * AMPLE: bug fixes and expanded interface (Linux and MAC only) * tlsextract: correction of output format which broke parsing of output * DiffractionImage: corrections to reading of pilatus mini-cbf * ccp4i: New AMPLE (Linux and Mac) and MrBUMP interfaces, QT-PISA launcher and bug fixes * crank: bug fix (Windows only) The easiest way to obtain the update is to install the CCP4 update client, if you have not done so already. Note that auto-updates will work correctly only with CCP4 release 6.3.0, therefore upgrade if necessary. Report bugs to c...@stfc.ac.uk. Many thanks for using CCP4, -- Ronan Keegan -- Scanned by iCritical.
Re: [ccp4bb] Mr. Bump and adding FASTA to CCP4 6.3 installation?
Hi Nate, The fasta licencing doesn't allow us to distribute it with the suite so it needs to be downloaded separately. For MrBUMP to find it you should have it somewhere in your system PATH. The easiest thing to do is to put the fasta3? .exe executable into your $CCP4/bin directory. However, to avoid having to do this every time you install a new version of CCP4 you should add the path to where you've installed the fasta executables to your system PATH environment variable. On windows this can be done by right mouse clicking on My Computer, select Properties , select Advanced tab and then select Environment Variables. Here you can edit the PATH variable and add the fasta bin directory location. In your case I guess that this will be C:\CCP4\fasta\bin. You'll need to restart your ccp4i for the new settings to take effect. If you need any more help with installation or running MrBUMP please let me know. Best wishes, Ronan From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Nathan Pollock Sent: 16 August 2012 05:47 To: ccp4bb Subject: [ccp4bb] Mr. Bump and adding FASTA to CCP4 6.3 installation? Hello, Mr. Bump requires Fasta to be installed. Could someone tell me what needs to be done to install Fasta so that it is seen and used by CCP4 6.3 programs? Installers for previous versions, 6.1 and 6.2, also installed Fasta, for 6.3 we are supposed to download and install manually. OK, I downloaded and unpacked into C:\CCP4\fasta\ - now what? The download site, http://fasta.bioch.virginia.edu/fasta_www2/fasta_down.shtml , says not a word about installation in Windows, nor it is mentioned in the Readme file. Thanks! - Nate -- Scanned by iCritical.
Re: [ccp4bb] Aimless on MS Windows?
Dear Jan, There will be a Windows version of Aimless in the upcoming 6.3.0 release of CCP4 which is due very soon. We'll announce it on the bb when it's ready. Best wishes, Ronan -Original Message- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Jan Gebauer Sent: 14 June 2012 14:11 To: ccp4bb Subject: [ccp4bb] Aimless on MS Windows? Hi, I'm wondering, whether it's possible to run AIMLESS on Windows. Is there a binary version or instruction on how to compile if for windows? Would it work under windows anyhow? From time to time, I do crystallographic work under Windows (even more since phenix is ported). Regards, Jan -- Dr. Jan Gebauer AG Prof. Baumann Institut für Biochemie / Uni-Köln Otto-Fischer-Str. 12-14 / 50674 Köln Fon: +49 (221) 470 3212 Fax: +49 (221) 470 5066
[ccp4bb] CCP4 Study Weekend 2012
Dear All, This a final reminder about next month's CCP4 Study Weekend taking place at Warwick University in the UK from January 4th to 6th. The topic of this meeting will be Data collection and processing. There are still a few registration places remaining but the registration deadline is this coming Friday 9th of December. For more information and to register for the meeting please see the study weekend website: http://www.cse.scitech.ac.uk/events/CCP4_2012/index.html http://www.cse.scitech.ac.uk/events/CCP4_2012/index.htmlKind regards, Katherine, Johan and the CCP4 team
[ccp4bb] CCP4 Study Weekend 2012
Dear all, There's just one week remaining to register at the reduced rate for the upcoming CCP4 Study Weekend in January entitled Data Collection and Processing. The meeting is taking place at the University of Warwick, UK, from the 4th-6th of January 2012. For more details about the meeting including the programme and registration details please see the 2012 Study Weekend website: http://www.cse.scitech.ac.uk/events/CCP4_2012/ We look forward to seeing you in Warwick. Katherine, Johan and the CCP4 team
[ccp4bb] CCP4 Study Weekend 2012 - Data Collection and Processing
Dear All, This is a reminder about this coming January's CCP4 Study Weekend taking place from the 4th - 6th of January at Warwick University in the UK. The topic for the 2012 meeting will be Data Collection and Processing and a provisional programme is now available. The meeting will cover all aspects of data collection and processing with presentations from eminent researchers in the field from all around the world. To view the programme and for registration details please visit the CCP4 Study Weekend 2012 website: http://www.cse.scitech.ac.uk/events/CCP4_2012/ As always, we have bursaries available to students to help with costs. However, numbers are limited so please get your registration in early if you wish to take advantage of our support. We look forward to seeing you in Warwick. Kind regards, Katherine, Johan and all of us here in CCP4
[ccp4bb] CCP4 6.2.0 Released
Dear All, We're very pleased to announce the release of the latest version of the CCP4 software suite. Version 6.2.0 (Giggleswick) is now available from the CCP4 download website: http://www.ccp4.ac.uk/download.php The release is available for Linux, Mac OSX and Windows platforms. Updates include the latest versions of Refmac (version 5.6.0117), Phaser (2.3.0), Molrep (11.0.0), Pointless (1.5.22), iMosflm (1.0.5)/Mosflm (7.0.7), Xia2 (0.3.3.1) and Crank (1.4) along with many more. This version of the suite also includes several new programs including Cprodrg for generating ligand restraints, Jligand, a graphical interface for generating ligands and linking ligands, Csloop for loop building and Multicomb for multivariate phase combination. More information is available from: http://www.ccp4.ac.uk/html/CHANGESinV6_2.html We'd like to thank all of the developers who have contributed to CCP4 6.2.0 and all of those who have helped in testing it. See you in Madrid! Kind regards, Ronan Ronan Keegan CCP4 Group
[ccp4bb] CCP4 SW Web Broadcast
Dear All, For those of you hoping to view the CCP4 Study Weekend online, we're experiencing some technical difficulties with the webcast equipment. Unfortunately the live stream won't be available for the first part of the meeting. We're hoping to fix it as soon as possible and we'll send an update as soon as it's available. Our apologies for the inconvenience. Best wishes, Ronan Ronan Keegan CCP4 Group
Re: [ccp4bb] CCP4 SW Web Broadcast
Dear all, The web stream is now working and can be accessed from: http://extrplay.dl.ac.uk/ There will be full coverage tomorrow (Friday). Apologies again for the delay. Best wishes, Ronan -Original Message- From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On Behalf Of ronan.kee...@stfc.ac.uk Sent: 06 January 2011 08:50 To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] CCP4 SW Web Broadcast Dear All, For those of you hoping to view the CCP4 Study Weekend online, we're experiencing some technical difficulties with the webcast equipment. Unfortunately the live stream won't be available for the first part of the meeting. We're hoping to fix it as soon as possible and we'll send an update as soon as it's available. Our apologies for the inconvenience. Best wishes, Ronan Ronan Keegan CCP4 Group
[ccp4bb] CCP4 Study Weekend 2011 - Final week for registration
Dear All, A final reminder about next month's CCP4 Study Weekend entitled Model Building and Refinement and Validation. The meeting will run from the 5th to the 7th of January and will be held at the University of Warwick in the UK. We have a limited number of places left and the deadline for registration is this coming Friday the 10th of December. Details about the programme, registration and all other aspects of the meeting are available from: http://www.cse.scitech.ac.uk/events/CCP4_2011/ We look forward to seeing you in Warwick. Best wishes, Roberto, Bernhard and the CCP4 team.
[ccp4bb] CCP4 Study Weekend - January 5th-7th 2011
Dear All, A quick reminder to you all about this coming January's CCP4 Study Weekend entitled Model Building Refinement Validation (January 5th-7th 2011). The deadline for the first round of registrations is Monday the 22nd of November after which the registration price will increase from £210 to £260. So please get your registration in before then. This time the meeting will be held at Warwick University in the UK. For more details and to register please see the Study Weekend website at: http://www.cse.scitech.ac.uk/events/CCP4_2011/ We hope to see you there. Best wishes, Ronan Ronan Keegan CCP4 Group
[ccp4bb] Protein Biochemist/Crystallographer Position available at Genentech in San Francisco
For more than 30 years, Genentech has been at the forefront of the biotechnology industry, using human genetic information to develop novel medicines for serious and life-threatening diseases. Today, Genentech is among the world's leading biotech companies, with multiple therapies on the market for cancer and other serious medical conditions. Please take this opportunity to learn about Genentech, where we believe that our employees are our most important asset. The following opportunity exists in our South San Francisco, CA, headquarters: Scientist - Protein Biochemist/Crystallographer Responsibilities: The position will play a key role in exploring the structure and functional properties of proteins of therapeutic interest and their interactions with ligands. He/she will purify, characterize, crystallize and determine the structure of proteins and protein-ligand complexes, with a focus on developing and implementing automated higher-throughput methods while contributing to small molecule discovery programs, basic research projects and participating in multi-disciplinary drug discovery teams. In this position, the candidate will work within a group that encompasses protein expression, purification, crystallography and NMR spectroscopy. He/she will collaborate with scientists throughout the Research organization. Requirements: A PhD in Structural Biology, Biophysics, Biochemistry or a related discipline is required, in addition to relevant postdoctoral experience. The candidate will show evidence of sustained productivity and independent contributions in science, as demonstrated by a strong publication record. He/she should be a technical expert in protein purification, characterization and crystallization with demonstrated expertise in handling challenging proteins for structural studies. Strong analytical, organizational and communication skills are essential, as well as the ability to work independently and in a collaborative team-oriented setting. Experience in solving X-ray crystal structures of proteins and protein complexes and familiarity with techniques such as ITC, surface plasmon resonance, ELISAs and/or immunoprecipitation to characterize proteins in support of structural biology is highly desired. Genentech is dedicated to fostering an environment that is inclusive and encourages diversity of thought, style, skills and perspective. To learn more about our current opportunities, please visit: http://careers.gene.com and reference Req. #130878. Please use Web - CCP4 when a source is requested. Genentech is an equal opportunity employer. -- Scanned by iCritical.
[ccp4bb] CCP4 Study Weekend Januay 6th-8th 2010
Dear All, A quick reminder to you all about this coming January's CCP4 Study Weekend entitled From Crystal to Structure with CCP4 (January 6th-8th 2010). The deadline for the first round of registrations will be the 21st of November after which the registration price will increase from £210 to £260. So please get your registration in before then. After the success of this year's event, the meeting will be held again at the East Midlands Conference Centre in Nottingham University in the UK. For more details and to register please see the Study Weekend website at: http://www.cse.scitech.ac.uk/events/CCP4_2010/ We hope to see you there. Best wishes, Ronan Ronan Keegan CCP4 Group -- Scanned by iCritical.
Re: [ccp4bb] MrBUMP
Hi Riya, You'll need to install at least one of these programs for it to work. What kind of operating system have you got? Clustalw/2 is about the easiest to install and is available from here: ftp://ftp.ebi.ac.uk/pub/software/clustalw2/2.0.11/ Let me know if you need any further help with it. Best wishes, Ronan Ronan Keegan CCP4 Group riya doreen wrote: Hi everyone, I am trying to run MrBUMP through the CCP4 6.1.1 but the program is complaining that no multiple alignment programs like mafft, clustalw, clustalw2, probcons, or t_coffee were found on the system. Will I need to install all these programs and will they need to be in the CCP4 directory ? Thanks
Re: [ccp4bb] CCP4 6.1.0 Balbes error
Dear Victor, Are you using python 3 by any chance? Balbes makes use of the popen2 function for running the underlying CCP4 programs but this is replaced by the subprocess function in python 3. We'll be updating Balbes to reflect this change but in the mean time you should try installing an older python such as python 2.6. Kind regards, Ronan Ronan Keegan CCP4 Group Victor Alves wrote: Dear BB Balbes (run from within CCP4i) gave me one MR solution but stopped with this error. I am now using the Balbes WWW server, but could some of you knowledgeable guys have some ideas of might be going on? Thanks Victor Alves Some info from log file: BALBES Version is 0.0.1.Mar_31_2008 JOB STARTS AT Mon Jun 8 18:02:06 2009 * Information from CCP4Interface script *** The program run with command: /usr/local/xtal/ccp4/ccp4-6.1.1/share/balbes/BALBES_0.0.1/bin_py/balbes OUT_ROOTDIR /home/victor/xtalwork/OlpA-M10/2_balbes NAME_ROOT 2_balbes HKLIN /home/victor/xtalwork/OlpA-M10/olpa_m10_scala_I4122.mtz SEQIN /home/victor/xtalwork/OlpA-M10/olpa_m10_info/OlpA_M10.seq XYZOUT /home/victor/xtalwork/OlpA-M10/olpa_m10_balbes_out1.pdb HKLOUT /home/victor/xtalwork/OlpA-M10/olpa_m10_balbes_out1.mtz has failed with error message /usr/local/xtal/ccp4/ccp4-6.1.1/share/balbes/BALBES_0.0.1/bin_py/balbes:22: DeprecationWarning: The popen2 module is deprecated. Use the subprocess module. import popen2, select, fcntl *** #CCP4I TERMINATION STATUS 0 /usr/local/xtal/ccp4/ccp4-6.1.1/share/balbes/BALBES_0.0.1/bin_py/balbes:22: DeprecationWarning: The popen2 module is deprecated. Use the subprocess module. import popen2, select, fcntl #CCP4I TERMINATION TIME 08 Jun 2009 18:23:47 #CCP4I MESSAGE Task failed
Re: [ccp4bb] SCALEPACK2MTZ failed
Dear Raja, This is a known bug in version 6.1.1. There is a fix for it available from the CCP4 problems pages. See item no. 7 in the following page: http://www.ccp4.ac.uk/problems.php#6.1.1-ccp4i You'll need to download import_scaled.script and replace the version that you have in: /sw/share/xtal/ccp4-6.1.1/ccp4i/scripts/ Hope this helps. Kind regards, Ronan Raja Dey wrote: Dear Friends, I got the following error while running SCALEPACK2MTZ in the latest version of CCP4 Program Suite 6.1.1 CCP4Interface 2.0.4 running on a macbook with intel core 2 duo. I also tried to run earlier SCALEPACK2MTZ job which was successfully finished before, but now failed with the same error message. Is there any clue or remedy? SCALEPACK2MTZ: Normal termination Times: User: 0.1s System:0.0s Elapsed: 0:00 /pre /html #CCP4I TERMINATION STATUS 0 Error from script /sw/share/xtal/ccp4-6.1.1/ccp4i/scripts/import_scaled.script: can't read dataset_name: no such variable #CCP4I TERMINATION TIME 22 May 2009 09:38:45 #CCP4I MESSAGE Task failed Thanks... Raja Explore and discover exciting holidays and getaways with Yahoo! India Travel Click here! http://in.rd.yahoo.com/tagline_Travel_1/*http://in.travel.yahoo.com/
Re: [ccp4bb] Problem with multiple users running ccp4i on one machine
Dear Jun Dong, This is a problem with the new mechanism used in CCP4 to store project and job data (the CCP4 DBhandler). The quick fix for now is to turn it off and use the old mechanism for storing the project data. To do this in the CCP4i interface go to System Administration, select Database Configuration and un-check the radio button that sets the option to connect to the database server on start up. Then have all your users restart CCP4i. Kind regards, Ronan Keegan CCP4 Group Jun Dong wrote: Dear CCP4 developers, I just wonder if there will be a fix for this problem. Basically when the first user is running ccp4i on a linux server and then when the second user tries to run ccp4i on the same linux server, the second user will only see the fist user's DirectoriesProjectDir. Best regards, Jun Dong Division of Structural Biology The Wellcome Trust Centre for Human Genetics Oxford University Roosevelt Drive Oxford OX3 7BN Tel: 01865 287558
Re: [ccp4bb] problem with ccp4 6.1.0 installation
Dear Witek, On some systems we have found that there can be a problem with the CCP4 distributed version of Graphviz which is used to display the graphical view of the project. This is caused by a missing font package. It looks as if this has caused the error you see. To fix it we suggest that you install the official Graphviz distribution available from: http://www.graphviz.org/ This includes the missing fonts and should work for you. Make sure that the new executables for Graphviz precede the CCP4 versions in your PATH. Let me know if this works for you. Kind regards, Ronan Keegan CCP4 Scientific Programmer Witek Kwiatkowski wrote: Hello, After installation I tried Graphical View of Project and I got: dotgraph_render: error: graph 1.000 5.861 0.528 node Job1 0.472 0.264 0.945 0.500 1: autoSHARP\nautoSHARP filled box black #9DD05B node Job2 1.667 0.264 0.945 0.500 2: autoSHARP\nautoSHARP filled box black #9DD05B node Job3 3.194 0.264 1.611 0.511 3: refmac5\nRestrained refinement using\nisotropic B factors filled box black #9DD05B node Job4 5.056 0.264 1.611 0.511 4: refmac5\nRestrained refinement using\nisotropic B factors filled box black #9DD05B stop Error: Could not find/open font Error: Could not find/open font Error: Could not find/open font Error: Could not find/open font Error: Could not find/open font Error: Could not find/open font Error: Could not find/open font Error: Could not find/open font Error: Could not find/open font Error: Could not find/open font --- Anyone had simmilar problem? What and where the font should be? Thanks, Witek
Re: [ccp4bb] imosflm and ccp4 v6.1 on linux
Hi Stephen,
Have you a project set up in CCP4i? Make sure that your CCP4i project
directory is set before you try to start Imosflm. When run through
CCP4i, Imosflm uses this directory to write it's output files.
You can set the project directory by clicking on the
DirectoriesProjectsDir button in the interface.
Hope this helps.
Kind regards,
Ronan
Carr, SB (Stephen) wrote:
Dear all,
I have just installed ccp4 v6.1 on a linux box running centos 5.1. Most things
seem to be working fine, but when I attempt to launch imosflm from the gui I
get the following message:
Error in startup script: can't create directory : no such file or directory
while executing
file mkdir $env(MOSDIR)
invoked from within
if { ! [file exists $env(MOSDIR)] } {
file mkdir $env(MOSDIR)
} {
if { ! [file isdirectory $env(MOSDIR)] } {
puts stop here; the directory f...
(file /home/applications/CCP4-6.1/ccp4-6.1.0/ccp4i/imosflm/imosflm.tcl
line 51)
and cannot figure out how to solve it although I am sure that it should be
fairly trivial to solve.
Any help would be greatly appreciated
best regards
Steve Carr
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[ccp4bb] Medical Research Council Position in Dundee
*MRC PROTEIN PHOSPHORYLATION UNIT* *COLLEGE OF LIFE SCIENCES* *UNIVERSITY OF DUNDEE, SCOTLAND* *PROGRAMME LEADER * The Unit invites applications for the above position from scientists with exciting research programmes aimed at understanding the role of protein phosphorylation in cell regulation and human disease. We invite applications from established scientists wishing to relocate their laboratory to the Unit, younger investigators aiming to start their own laboratory or cell biologists with X-ray crystallographic experience. The appointment will be made on the Medical Research Council’s Programme Leader Band 2 scale (£43,147-no upper limit) or Programme Leader-Track Band 3 scale (£34,933-£42,754 per annum), with initial placement depending on achievements and experience. The MRC Protein Phosphorylation Unit is a major international centre for cell signalling and its innovative collaboration with the pharmaceutical industry (The Division of Signal Transduction Therapy) received a Queen’s Anniversary Award in 2006. To view the Unit’s current programmes please consult our website (_www.dundee.ac.uk/lifesciences/mrcppu/ http://www.dundee.ac.uk/lifesciences/mrcppu/_). Applications in the form of a CV, outline statement of current research and future plans, and providing the names and contact numbers of three referees should be e.mailed to Sir Philip Cohen FRS FRSE, Director, MRC Protein Phosphorylation Unit, College of Life Sciences, University of Dundee (email [EMAIL PROTECTED] mailto:[EMAIL PROTECTED]_) by October 31^st 2008. Informal enquiries should also be sent to the Director. /The MRC is an Equal Opportunities Employer/
Re: [ccp4bb] MrBump Installation ccp4
Hi Daniel, Sorry to hear about your problem with mrbump. You say that you put the Fasta35 executable in the ccp4i bin directory(note the i). This directory is probably not in your system PATH. I would recommend that you put it into the $CCP4/bin which should be in your system path provided that CCP4 is set up correctly. Kind regards, Ronan Daniel Wohlwend wrote: Hi all, We' ve just encountered a problem concerning the installation of MrBump on our Linux machine. MrBump needs Fasta35 for operation, but during installation does not recognise the already installed Fasta35, even if Fasta35 is placed in the ccp4i bin. Under the same location the recognition of ClustalW did not oppose a problem. Can anybody help us? Where do we have to put Fasta35 in order to continue the installation of MrBump? Or is something possibly wrong with the permissions (global or local)? If anyone has an idea, please let us know! Thanks a lot in advance! Daniel Daniel Wohlwend GZMB Abt. für molekulare Strukturbiologie Georg-August-Universitaet Goettingen Justus-von-Liebig-Weg 11 37077 Goettingen phone: 0551-39-14074 e-mail: [EMAIL PROTECTED]
Re: [ccp4bb] protein-protein docking programs
Hi Jerry, I've not got a whole lot of experience with docking programs but I have used 3D-dock (http://www.sbg.bio.ic.ac.uk/docking/) to do docking trials between two proteins and found it to be easy to set up and use. It uses an algorithm that mainly looks at surface complimentarity between the two proteins but it helps a lot if you use some biological information to restrain the results. Hope this helps, Ronan Jerry McCully wrote: Hi, All: Recently we solved a complex structure between two proteins, which indicated the interaction was kind of rigid. Therefore we want to test the binding mode of the receptor with another homologous ligand(very similar structure, RMSD 2.4 angstrom). Can somebody recommend a sophisticated docking program to do this? Thanks a lot. Jerry McCully With Windows Live for mobile, your contacts travel with you. Connect on the go. http://www.windowslive.com/mobile/overview.html?ocid=TXT_TAGLM_WL_Refresh_mobile_052008
[ccp4bb] PostDoctoral Position at SOLEIL
Dear Colleagues, Within the framework of the SAXIER European Contract, we are developing at SOLEIL, and in collaboration with an NMR team of the ICSN at Gif sur Yvette (CNRS), a piece of software to refine protein 3D structures against NMR Residual Dipole Couplings and solution SAXS experimental data. We are looking for a post-doctoral fellow to further improve the first version of the software. Please see the link below for more details. http://www.synchrotron-soleil.fr/portal/page/portal/Soleil/OffresEmplois/POST-DOC-BIO-SAXS Thank you very much, Javier Pérez Javier Pérez SWING - Synchrotron SOLEIL L'Orme des Merisiers BP 48 Saint-Aubin 91192 Gif sur Yvette Cedex France Tel +33 (0)1 69 35 96 19 Fax +33(0)1 69 35 94 56 [EMAIL PROTECTED]
[ccp4bb] [Fwd: [ccp4]: iso - anisotropic B factor refinement on Refmac5]
---BeginMessage--- Hi, I had a very curious result when doing a round of isotropic B factor refinement on Refmac5. After iso B my R is 19.2 and Rf 24.3. My resolution is 1.95, what does not justify anisotropic b-factor refinement. However I did it by mistake and it dropped my R to 17.8 and Rf to 23.5. More curiously, I next did a B iso refinement round and my R dropped to 16.1 and Rf to 21.8! Would you have any insights why my second round of iso B refinement dropped my Rs considerably after the aniso B refinement? Thank you very much, Rafael. ---End Message---
Re: [ccp4bb] sleeping refmac
Hi Harry, Might not be the problem but does this machine have its ccp4 scratch space ($CCP4_SCR) mounted from another machine by nfs across a network? Refmac writes a lot of temporary files to CCP4_SCR and if this is across a busy network it can really slow Refmac's progress. Ronan Harry M. Greenblatt wrote: BSD Dear All, One our our linux boxes (kernel 2.4.20) has begun recently to run refmac at worse than snail's pace. This is a 3.2 GHz Xeon dual CPU Dell machine from 4 years ago. All other things seem fine, including other CCP programs. But refmac jobs (for various proteins) that take a minute or two on other machines can sit for many tens of minutes making very slow progress (but yes, they are getting somewhere). Using top, one can see that the machine is completely idle, and the refmac job has used up a few seconds of CPU time, even after ten minutes, although its priority is normal. In top, under the status column, it has a status of D, which, according to the documentation, is uninterruptible sleep. Running refmac on another computer, I see that is does enter the D state a few times during the run, but never stays that way very long. Any ideas? Thanks Harry - Harry M. Greenblatt Staff Scientist Dept of Structural Biology [EMAIL PROTECTED] mailto:[EMAIL PROTECTED] Weizmann Institute of SciencePhone: 972-8-934-3625 Rehovot, 76100 Facsimile: 972-8-934-4159 Israel
[ccp4bb] MrBUMP version 0.4.0 release
Dear All, We're pleased to announce the latest release of MrBUMP. Pre-release version 0.4.0 is now available from the MrBUMP website: http://www.ccp4.ac.uk/MrBUMP The new features include: - The inclusion of the new CCP4i DBviewer, a graphical interface for viewing CCP4i jobs. This will form part of the upcoming 6.1 release of CCP4. We are grateful to Wanjuan (Wendy)Yang and Peter Briggs for letting us include it in MrBUMP. - Support for installing the scripts on Windows. - Removed the requirement for inputting an MTZ file when running in Model generation only mode. Sequence file is all that is required now. Kind regards, Ronan and Martyn
