Re: [ccp4bb] Off-topic - Crystallisation in anaerobic glove box
Thanks for all of the responses, there seems to be no real consensus, but I have discovered: 1 There are several small incubators supplied by - Molecular Dimensions, Revsci, Centeo 2 Good air conditioning may negate the need for an incubator. 3 A Glove box may not even be necessary depending on the samples sensitivity to oxygen. Certainly plenty for me to think about before I commit to buying a glove box. Yet again the bulletin board proves to be a great source of information for all things crystallographic! Best wishes, Steve Dr Stephen Carr Research Complex at Harwell (RCaH) Rutherford Appleton Laboratory Harwell Oxford Didcot Oxon OX11 0FA United Kingdom Email stephen.c...@rc-harwell.ac.uk tel 01235 567717 From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Stephen Carr [stephen.c...@rc-harwell.ac.uk] Sent: 11 March 2015 10:17 To: ccp4bb Subject: [ccp4bb] Off-topic - Crystallisation in anaerobic glove box Dear CCP4BBer's Apologies for the off-topic post, but the CCP4BB seems to be the best place to ask about crystallisation. I am looking to set up crystallisation in an anaerobic glove box and wondered how other people did this, specifically the crystallisation stage. My initial thoughts were to place a small crystallisation incubator inside the box, however the smallest I have come across so far (~27L) is still rather large. Has anyone come across smaller incubators? Alternatively are incubators even neccessary if the glove box is placed in a room with good air conditioning and stable temperature control? Any recommendations would be very helpful. Thanks in advance, Steve Carr Dr Stephen Carr Research Complex at Harwell (RCaH) Rutherford Appleton Laboratory Harwell Oxford Didcot Oxon OX11 0FA United Kingdom Email stephen.c...@rc-harwell.ac.uk tel 01235 567717 This email and any attachments may contain confidential, copyright and or privileged material, and are for the use of the intended addressee only. If you are not the intended addressee or an authorized recipient of the addressee, please notify us of receipt by returning the e-mail and do not use, copy, retain, distribute or disclose the information in or attached to this email. Any views or opinions presented are solely those of the author and do not necessarily represent those of the Research Complex at Harwell. There is no guarantee that this email or any attachments are free from viruses and we cannot accept liability for any damage which you may sustain as a result of software viruses which may be transmitted in or with the message. We use an electronic filing system. Please send electronic versions of documents, unless paper is specifically requested. This email may have a protective marking, for an explanation, please see: http://www.mrc.ac.uk/About/informationandstandards/documentmarking/index.htm.
[ccp4bb] Off-topic - Crystallisation in anaerobic glove box
Dear CCP4BBer's Apologies for the off-topic post, but the CCP4BB seems to be the best place to ask about crystallisation. I am looking to set up crystallisation in an anaerobic glove box and wondered how other people did this, specifically the crystallisation stage. My initial thoughts were to place a small crystallisation incubator inside the box, however the smallest I have come across so far (~27L) is still rather large. Has anyone come across smaller incubators? Alternatively are incubators even neccessary if the glove box is placed in a room with good air conditioning and stable temperature control? Any recommendations would be very helpful. Thanks in advance, Steve Carr Dr Stephen Carr Research Complex at Harwell (RCaH) Rutherford Appleton Laboratory Harwell Oxford Didcot Oxon OX11 0FA United Kingdom Email stephen.c...@rc-harwell.ac.uk tel 01235 567717 This email and any attachments may contain confidential, copyright and or privileged material, and are for the use of the intended addressee only. If you are not the intended addressee or an authorized recipient of the addressee, please notify us of receipt by returning the e-mail and do not use, copy, retain, distribute or disclose the information in or attached to this email. Any views or opinions presented are solely those of the author and do not necessarily represent those of the Research Complex at Harwell. There is no guarantee that this email or any attachments are free from viruses and we cannot accept liability for any damage which you may sustain as a result of software viruses which may be transmitted in or with the message. We use an electronic filing system. Please send electronic versions of documents, unless paper is specifically requested. This email may have a protective marking, for an explanation, please see: http://www.mrc.ac.uk/About/informationandstandards/documentmarking/index.htm.
Re: [ccp4bb] Refinement of Iron-sulphur clusters
Dear Matthew, Robbie Hans and Oliver, Thanks for the advice, it seems that it is simply the geometry definitions in the dictionaries distributed with CCP4 6.4 are different to those calculated from the atomic coordinates. For example, the chiral volume definitions in the for the 4Fe4S cluster are the opposite sign to those in my protein. So swapping the atom names has sorted that, I am still working on the other clusters, but progress is being made. Since I solved the structure by MR using coordinates downloaded from the pdb, I assumed the atom names would agree with the geometry definitions in Refmac (since the search model was also refined with refmac). Have the cif dictionaries been modified/updated recently? thanks again, Steve Dr Stephen Carr Research Complex at Harwell (RCaH) Rutherford Appleton Laboratory Harwell Oxford Didcot Oxon OX11 0FA United Kingdom Email stephen.c...@rc-harwell.ac.uk tel 01235 567717 From: Oliver Smart [osm...@smartsci.uk] Sent: 13 October 2014 12:09 To: ccp4bb Subject: Re: [ccp4bb] Refinement of Iron-sulphur clusters Stephen, Robbie advice is 100% correct. Be careful about the naming of the sulphur atoms (is S1 opposite S4 or next to it). I recall that the distributed CCP4 dictionaries have different atom naming than the PDB chemical components dictionary. If this is the problem is that the naming is different this should result in large restraint violations that should be appear in the REFMAC output (others can tell you where). In general diffraction from Fe S clusters is so strong that the atom positions are pretty much determined from the electron density. But in case it helps I did some work data mining restraints for Fe2S2 and Fe4S4 from CSD structures (this has to be done manually). Please find attached the resulting FES.cif and SF4.cif restraint dictionaries (distributed with BUSTER). Good luck, Oliver --- Dr Oliver Smart Director SmartSci Limited http://www.smartsci.uk/ Consultant Global Phasing Ltd http://www.globalphasing.com/ on 10/10/14 5:33 PM, Robbie Joosten robbie_joos...@hotmail.com wrote: Dear Stephen, The dictionary is very specific about atom names. If you have them swapped (as many PDB entries do). The angle and chiral volume restraints will wreck your cluster. You also need to make sure to provide LINK records to attach the cluster to the surrounding cysteines. HTH, Robbie Sent from my Windows Phone Van: Stephen Carr Verzonden: 10-10-2014 18:07 Aan: CCP4BB@JISCMAIL.AC.UK Onderwerp: [ccp4bb] Refinement of Iron-sulphur clusters Dear CCP4 BBers, I am currently refining a model of a protein containing three iron sulphur clusters using Refmac (v5.8.0078) and am getting some unusual results. One of the clusters (3fe 4s) seems to behave resonably and the refined electron density looks very nice. The atoms in the others clusters (4Fe4S and 4Fe3S), however, migrate towards the centre of the cluster producing Fo-Fc difference maps with strong negative density at the centre surrounded by blobs of positive density where the atoms should be. I have checkedthe refmac dictionaries and there are entries for each of the clusters, so I shouldn't have to explicitly include a cif file for the clusters as an input right? In fact, when I did try to include a dictionary file for one of the clusters refmac gave a warning message in the log about duplicate monomers dictionaries and it made no difference to the refinement/maps anyway. On checking the refmac log file there is no specific mention that there are hetero-groups in the pdb file and no explicit mention that it is using any dictionaries during the refinement. How can I tell if refmac is reading/using the dictionaries? Also bonds within the clusters are flagged up as outliers and deviating by more than 10 sigma from ideal suggesting that they are not getting read? I realise that something chemically odd could be going on at the centres, but if I omit them from the model and calculate maps very strong density comes back around where the atoms sat before refinement, so I am pretty confident that they are in the right place to start with. Any help with this problem would be greatly appreciated, I'm sure there is something obvious that I am missing but can't see what that is at the moment. It is particularly confusing since one cluster apparently behaves while the others do not. I could, of course, try phenix or buster, but I would like to get to the bottom of the problem with refmac if possible. Thanks very much in advance, Steve Dr Stephen Carr Research Complex at Harwell (RCaH) Rutherford Appleton Laboratory Harwell Oxford Didcot Oxon OX11 0FA United Kingdom Email stephen.c...@rc-harwell.ac.uk tel 01235 567717 This email and any attachments may contain confidential, copyright and or privileged material, and are for the use
[ccp4bb] Refinement of Iron-sulphur clusters
Dear CCP4 BBers, I am currently refining a model of a protein containing three iron sulphur clusters using Refmac (v5.8.0078) and am getting some unusual results. One of the clusters (3fe 4s) seems to behave resonably and the refined electron density looks very nice. The atoms in the others clusters (4Fe4S and 4Fe3S), however, migrate towards the centre of the cluster producing Fo-Fc difference maps with strong negative density at the centre surrounded by blobs of positive density where the atoms should be. I have checkedthe refmac dictionaries and there are entries for each of the clusters, so I shouldn't have to explicitly include a cif file for the clusters as an input right? In fact, when I did try to include a dictionary file for one of the clusters refmac gave a warning message in the log about duplicate monomers dictionaries and it made no difference to the refinement/maps anyway. On checking the refmac log file there is no specific mention that there are hetero-groups in the pdb file and no explicit mention that it is using any dictionaries during the refinement. How can I tell if refmac is reading/using the dictionaries? Also bonds within the clusters are flagged up as outliers and deviating by more than 10 sigma from ideal suggesting that they are not getting read? I realise that something chemically odd could be going on at the centres, but if I omit them from the model and calculate maps very strong density comes back around where the atoms sat before refinement, so I am pretty confident that they are in the right place to start with. Any help with this problem would be greatly appreciated, I'm sure there is something obvious that I am missing but can't see what that is at the moment. It is particularly confusing since one cluster apparently behaves while the others do not. I could, of course, try phenix or buster, but I would like to get to the bottom of the problem with refmac if possible. Thanks very much in advance, Steve Dr Stephen Carr Research Complex at Harwell (RCaH) Rutherford Appleton Laboratory Harwell Oxford Didcot Oxon OX11 0FA United Kingdom Email stephen.c...@rc-harwell.ac.uk tel 01235 567717 This email and any attachments may contain confidential, copyright and or privileged material, and are for the use of the intended addressee only. If you are not the intended addressee or an authorized recipient of the addressee, please notify us of receipt by returning the e-mail and do not use, copy, retain, distribute or disclose the information in or attached to this email. Any views or opinions presented are solely those of the author and do not necessarily represent those of the Research Complex at Harwell. There is no guarantee that this email or any attachments are free from viruses and we cannot accept liability for any damage which you may sustain as a result of software viruses which may be transmitted in or with the message. We use an electronic filing system. Please send electronic versions of documents, unless paper is specifically requested. This email may have a protective marking, for an explanation, please see: http://www.mrc.ac.uk/About/informationandstandards/documentmarking/index.htm.
[ccp4bb] Job opportunity - Research Complex at Harwell
Dear BB, We have a opening for a post-doctoral scientist at the Research Complex at Harwell. IRC157933: Post-Doctoral Research Scientist (Fixed Term until 28/02/2016) Salary: £27,084 - £32,324 per annum Research Complex at Harwell We are looking for an individual who can help us with the delivery of high quality original research on the structure and function of proteins and protein-DNA complexes involved in the resolution of Holliday junctions and other branched DNA structures. The sucessful candidate would be expected to: * Perform high quality research on the structural biology of Holliday junction resolution, including production and purification of proteins and DNA, crystallisation and crystal structure determination of protein-DNA complexes and the use of other biophysical techniques such as small angle X-ray and neutron scattering, electron microscopy etc. as required. * Be an active member of the Holliday junction research group and contribute to group meetings, formulation of research strategies etc. * Write and publishing research papers on the results of the work and also presenting the results of the work at conferences. The appointment is based at the Research Complex at Harwell (RCaH), a state-of-the-art multidisciplinary laboratory that provides facilities for researchers to undertake new and cutting edge scientific research in both life and physical sciences and the interface between them. More information is available at www.rc-harwell.ac.ukhttp://www.rc-harwell.ac.uk/ To join us you will need: * A PhD in Biochemistry, a biological or physical science subject or equivalent. * Laboratory experience carrying out original research in structural and / or molecular biology. * PhD or post-doctoral experience in protein purification, crystallisation or structure determination. * Excellent interpersonal and communication skills (both oral and written). * Ability to communicate research results, including presentations at conferences and publication of original papers. * Familiarity with software packages for protein structure analysis and molecular graphics. * The ability to generate ideas, analyse options, prioritise and make effective decisions. We are looking for a flexible individual who can adapt to need and circumstance and is ready for a challenge. Benefits include generous holiday entitlement and an excellent contributory final salary pension scheme. For an informal discussion about the role please contact stephen.c...@rc-harwell.ac.uk. Applications are handled by the UK Shared Business Services; to apply please visit our job board at www.topcareer.jobshttp://www.topcareer.jobs, and upload your CV along with a Cover Letter (when saving your documents quote IRC157933 in the filename). Applicants who would like to receive this advert in an alternative format (e.g. large print, Braille, audio or hard copy), or who are unable to apply online should contact us by telephone on 01793 867000 and quote reference number IRC157933 when calling. Closing date: 28th September 2014 The MRC is an Equal Opportunities Employer Final appointments will be subject to a pre employment screening Dr Stephen Carr Research Complex at Harwell (RCaH) Rutherford Appleton Laboratory Harwell Oxford Didcot Oxon OX11 0FA United Kingdom Email stephen.c...@rc-harwell.ac.uk tel 01235 567717 This email and any attachments may contain confidential, copyright and or privileged material, and are for the use of the intended addressee only. If you are not the intended addressee or an authorized recipient of the addressee, please notify us of receipt by returning the e-mail and do not use, copy, retain, distribute or disclose the information in or attached to this email. Any views or opinions presented are solely those of the author and do not necessarily represent those of the Research Complex at Harwell. There is no guarantee that this email or any attachments are free from viruses and we cannot accept liability for any damage which you may sustain as a result of software viruses which may be transmitted in or with the message. We use an electronic filing system. Please send electronic versions of documents, unless paper is specifically requested. This email may have a protective marking, for an explanation, please see: http://www.mrc.ac.uk/About/informationandstandards/documentmarking/index.htm.
Re: [ccp4bb] ctruncate error
Thanks for the help, the old version of truncate did the trick. Interestingly running the old version of truncate in either of the data reduction pipelines (with aimless or scala) produced mtz files containing no F's but the stand alone version produced an mtz with all the f's prsent. cheers, Steve Dr Stephen Carr Research Complex at Harwell (RCaH) Rutherford Appleton Laboratory Harwell Oxford Didcot Oxon OX11 0FA United Kingdom Email stephen.c...@rc-harwell.ac.uk tel 01235 567717 From: Parthasarathy Sampathkumar [spart...@gmail.com] Sent: 19 June 2014 19:55 To: ccp4bb Subject: Re: [ccp4bb] ctruncate error Yes.., I too had similar problem with Ctruncate, and used older truncate to overcome the issue. Best Wishes, Partha On Thu, Jun 19, 2014 at 2:38 PM, jie liu jl1...@njms.rutgers.edumailto:jl1...@njms.rutgers.edu wrote: Hi I also encountered the same problem after recent updates (not the most recent one, but a couple of updates back). Choosing to run old-truncate will get it around. Best wishes Jie - Original Message - From: Stephen Carr stephen.c...@rc-harwell.ac.ukmailto:stephen.c...@rc-harwell.ac.uk To: CCP4BB@JISCMAIL.AC.UKmailto:CCP4BB@JISCMAIL.AC.UK Sent: Thursday, June 19, 2014 1:11 PM Subject: [ccp4bb] ctruncate error Dear CCP4bb, I am experiencing an unusual error when running truncate. The program appears to be converting I's to F's, but then failing to output them in the resulting mtz file, see mtzdump output below: Col SortMinMaxNum % Mean Mean Resolution Type Column num order Missing complete abs. LowHigh label 1 ASC 0 26 0 100.00 12.6 12.6 79.95 3.00 H H 2 NONE 0 15 0 100.00 4.3 4.3 79.95 3.00 H K 3 NONE -42 42 0 100.00 0.7 16.0 79.95 3.00 H L 4 NONE0.019.0 0 100.00 9.56 9.56 79.95 3.00 I FreeR_flag 5 BOTH ? ? 129680.00 ?? -999.00 0.00 F F_delta16 6 BOTH ? ? 129680.00 ?? -999.00 0.00 Q SIGF_delta16 7 BOTH0.0 0.025 99.81 0.00 0.00 42.22 3.00 D DANO_delta16 8 BOTH0.0 0.0 11253 13.22 0.00 0.00 42.22 3.00 Q SIGDANO_delta16 9 BOTH ? ? 129680.00 ?? -999.00 0.00 G F_delta16(+) 10 BOTH ? ? 129680.00 ?? -999.00 0.00 L SIGF_delta16(+) 11 BOTH ? ? 129680.00 ?? -999.00 0.00 G F_delta16(-) 12 BOTH ? ? 129680.00 ?? -999.00 0.00 L SIGF_delta16(-) 13 BOTH 0 0 25 99.81 0.0 0.0 42.22 3.00 Y ISYM_delta16 14 NONE -8.9 72479.225 99.81 198.34 198.44 42.22 3.00 J IMEAN_delta16 15 NONE0.6 3135.725 99.81 5.25 5.25 42.22 3.00 Q SIGIMEAN_delta16 16 NONE -10.8 72479.225 99.81 198.18 198.37 42.22 3.00 K I_delta16(+) 17 NONE0.0 3135.725 99.81 6.79 6.79 42.22 3.00 M SIGI_delta16(+) 18 NONE -9.5 72479.225 99.81 198.30 198.47 42.22 3.00 K I_delta16(-) 19 NONE0.0 3135.725 99.81 6.70 6.70 42.22 3.00 M SIGI_delta16(-) No. of reflections used in FILE STATISTICS12968 The truncate log file shows no obvious errors apart from the cumulative intensity plot which indicates no reflections, all other diagnostic indicators for data quality seem to suggest everything is ok. I get the error with both ctruncate and truncate and also automatically as part of the scaling/merging pipelines. The data were processed with imosflm, scaled with aimless with neither flagging any errors with the data. I am running CCP4 6.4.0 on a linux box (Centos 6) and have installed the latest updates. Any suggestions as to what the fault might be and how to get around it would be greatly appreciated. best wishes, Steve Dr Stephen Carr Research Complex at Harwell (RCaH) Rutherford Appleton Laboratory Harwell Oxford Didcot Oxon OX11 0FA United Kingdom Email stephen.c...@rc-harwell.ac.ukmailto:stephen.c...@rc-harwell.ac.uk tel 01235 567717 This email and any attachments may contain confidential, copyright and or privileged material, and are for the use of the intended addressee only. If you are not the intended addressee or an authorized recipient of the addressee, please notify us of receipt by returning the e-mail and do not use, copy, retain, distribute or disclose the information in or attached to this email. Any views or opinions presented are solely those of the author and do not necessarily represent those of the Research Complex at Harwell. There is no guarantee that this email or any attachments are free from viruses and we cannot accept liability for any damage which you may sustain as a result of software viruses which may be transmitted
[ccp4bb] ctruncate error
Dear CCP4bb, I am experiencing an unusual error when running truncate. The program appears to be converting I's to F's, but then failing to output them in the resulting mtz file, see mtzdump output below: Col SortMinMaxNum % Mean Mean Resolution Type Column num order Missing complete abs. LowHigh label 1 ASC 0 26 0 100.00 12.6 12.6 79.95 3.00 H H 2 NONE 0 15 0 100.00 4.3 4.3 79.95 3.00 H K 3 NONE -42 42 0 100.00 0.7 16.0 79.95 3.00 H L 4 NONE0.019.0 0 100.00 9.56 9.56 79.95 3.00 I FreeR_flag 5 BOTH ? ? 129680.00 ?? -999.00 0.00 F F_delta16 6 BOTH ? ? 129680.00 ?? -999.00 0.00 Q SIGF_delta16 7 BOTH0.0 0.025 99.81 0.00 0.00 42.22 3.00 D DANO_delta16 8 BOTH0.0 0.0 11253 13.22 0.00 0.00 42.22 3.00 Q SIGDANO_delta16 9 BOTH ? ? 129680.00 ?? -999.00 0.00 G F_delta16(+) 10 BOTH ? ? 129680.00 ?? -999.00 0.00 L SIGF_delta16(+) 11 BOTH ? ? 129680.00 ?? -999.00 0.00 G F_delta16(-) 12 BOTH ? ? 129680.00 ?? -999.00 0.00 L SIGF_delta16(-) 13 BOTH 0 0 25 99.81 0.0 0.0 42.22 3.00 Y ISYM_delta16 14 NONE -8.9 72479.225 99.81 198.34 198.44 42.22 3.00 J IMEAN_delta16 15 NONE0.6 3135.725 99.81 5.25 5.25 42.22 3.00 Q SIGIMEAN_delta16 16 NONE -10.8 72479.225 99.81 198.18 198.37 42.22 3.00 K I_delta16(+) 17 NONE0.0 3135.725 99.81 6.79 6.79 42.22 3.00 M SIGI_delta16(+) 18 NONE -9.5 72479.225 99.81 198.30 198.47 42.22 3.00 K I_delta16(-) 19 NONE0.0 3135.725 99.81 6.70 6.70 42.22 3.00 M SIGI_delta16(-) No. of reflections used in FILE STATISTICS12968 The truncate log file shows no obvious errors apart from the cumulative intensity plot which indicates no reflections, all other diagnostic indicators for data quality seem to suggest everything is ok. I get the error with both ctruncate and truncate and also automatically as part of the scaling/merging pipelines. The data were processed with imosflm, scaled with aimless with neither flagging any errors with the data. I am running CCP4 6.4.0 on a linux box (Centos 6) and have installed the latest updates. Any suggestions as to what the fault might be and how to get around it would be greatly appreciated. best wishes, Steve Dr Stephen Carr Research Complex at Harwell (RCaH) Rutherford Appleton Laboratory Harwell Oxford Didcot Oxon OX11 0FA United Kingdom Email stephen.c...@rc-harwell.ac.uk tel 01235 567717 This email and any attachments may contain confidential, copyright and or privileged material, and are for the use of the intended addressee only. If you are not the intended addressee or an authorized recipient of the addressee, please notify us of receipt by returning the e-mail and do not use, copy, retain, distribute or disclose the information in or attached to this email. Any views or opinions presented are solely those of the author and do not necessarily represent those of the Research Complex at Harwell. There is no guarantee that this email or any attachments are free from viruses and we cannot accept liability for any damage which you may sustain as a result of software viruses which may be transmitted in or with the message. We use an electronic filing system. Please send electronic versions of documents, unless paper is specifically requested. This email may have a protective marking, for an explanation, please see: http://www.mrc.ac.uk/About/informationandstandards/documentmarking/index.htm.
Re: [ccp4bb] Phaser Fatal runtime error.
Dear all, Thanks for the many of responses, the data from Crysalis is scaled, but unmerged so needed to be fed through scala/truncate before running Phaser. Phaser is now running with no problems and I am looking at some nice maps. Bestr wishes and thanks again for your help, Steve Dr Stephen Carr Research Complex at Harwell (RCaH) Rutherford Appleton Laboratory Harwell Oxford Didcot Oxon OX11 0FA United Kingdom Email stephen.c...@rc-harwell.ac.uk tel 01235 567717 From: Roger Rowlett [rrowl...@colgate.edu] Sent: 27 June 2012 13:07 To: Carr, Stephen (MRC,RAL,RCAH) Cc: ccp4bb Subject: Re: [ccp4bb] Phaser Fatal runtime error. We have an in-house Agilent (Oxford) system and routinely use data with CCP4. You will need to run sortmtz, scala (w/constant scale), and truncate to prep the data properly. This can be done via batch file or GUI.You may also have to reset/reassign the space group for some space groups due to an apparent bug in the CrysalisPro MTZ conversion routine. You can find details at capsicum.colgate.edu/chwikihttp://capsicum.colgate.edu/chwiki in our crystallography pages. Roger Rowlett On Jun 26, 2012 1:34 PM, lt;Stephen Carrgt; stephen.c...@rc-harwell.ac.ukmailto:stephen.c...@rc-harwell.ac.uk wrote: Dear CCP4bb I have collected a data-set using the supernova x-ray generator from Agilent and taken the mtz file generated by the data processing software in crysalis pro forward for structure solution. The data collection was straight forward and the software seemingly processed the data successfully - space-group P2221, overall Rmerge 9%, I/sigmaI 11, redundancy 4.5 etc. Truncate converted the intensities to structure factors with no problems, but when I tried to use the data for molecular replacement with Phaser it produced the following error: FATAL RUNTIME ERROR: Reflections are not a unique set by symmetry I'm not sure how to proceed from here as other programs in the suite do not seem to detect this problem. Also when this error has been mentioned in the past on the bb it was with a data set collected on a Bruker home source and the data processed with Denzo/scalepack, and the suggested solution was to use the Bruker software to process the data. I am currently attempting to reprocess the data with mosflm, but that is likely to be the subject of another post! Any suggestions will be gratefully received. Best wishes, Steve Dr Stephen Carr Research Complex at Harwell (RCaH) Rutherford Appleton Laboratory Harwell Oxford Didcot Oxon OX11 0FA United Kingdom Email stephen.c...@rc-harwell.ac.ukmailto:stephen.c...@rc-harwell.ac.uk tel 01235 567717
[ccp4bb] Phaser Fatal runtime error.
Dear CCP4bb I have collected a data-set using the supernova x-ray generator from Agilent and taken the mtz file generated by the data processing software in crysalis pro forward for structure solution. The data collection was straight forward and the software seemingly processed the data successfully - space-group P2221, overall Rmerge 9%, I/sigmaI 11, redundancy 4.5 etc. Truncate converted the intensities to structure factors with no problems, but when I tried to use the data for molecular replacement with Phaser it produced the following error: FATAL RUNTIME ERROR: Reflections are not a unique set by symmetry I'm not sure how to proceed from here as other programs in the suite do not seem to detect this problem. Also when this error has been mentioned in the past on the bb it was with a data set collected on a Bruker home source and the data processed with Denzo/scalepack, and the suggested solution was to use the Bruker software to process the data. I am currently attempting to reprocess the data with mosflm, but that is likely to be the subject of another post! Any suggestions will be gratefully received. Best wishes, Steve Dr Stephen Carr Research Complex at Harwell (RCaH) Rutherford Appleton Laboratory Harwell Oxford Didcot Oxon OX11 0FA United Kingdom Email stephen.c...@rc-harwell.ac.uk tel 01235 567717
[ccp4bb] xia2 error
Dear all, I have come across an error when trying to run xia2 (version 0.3.3.1) via the ccp4 gui see below, #CCP4I TERMINATION STATUS 0 Error from script /home/applications/CCP4-6.2.0/ccp4-6.2.0/ccp4i/scripts/xia2.script: no files matched glob pattern *.log #CCP4I TERMINATION TIME 17 Feb 2012 12:49:21 #CCP4I TERMINATION OUTPUT_FILES /home/tfr35668/Diamond_I02_17012011/Steve/process/xia2_21 #CCP4I MESSAGE Task failed The error occurs before the program tries to read any image files and it seems to be complaining about a lack of log files before it has had a chance to write them. Any thoughts as to how to fix this would be greatly appreciated. I am running version 6.2.0 and performed a standard installation. best wishes, Steve Dr Stephen Carr Research Complex at Harwell (RCaH) Rutherford Appleton Laboratory Harwell Oxford Didcot Oxon OX11 0FA United Kingdom Email stephen.c...@rc-harwell.ac.uk tel 01235 567717
[ccp4bb] cTruncate failure after data scaling
Dear CCP4, I have encountered the following error message when scaling a recently collected data set. The program run with command: /home/applications/CCP4-6.1.13/ccp4-6.1.13/bin/ctruncate -hklin /tmp/tfr35668/Diamond270211_21_2_mtz.tmp -hklout /tmp/tfr35668/Diamond270211_21_4_mtz_S-SAD1_P43212.tmp -colin /*/*/\[IMEAN,SIGIMEAN\] -colano /*/*/\[I(+),SIGI(+),I(-),SIGI(-)\] -colout S-SAD1_P43212 has failed with error message CCP4MTZfile - internal error terminate called after throwing an instance of 'clipper::Message_fatal' The data have been integrated in imosflm with no apparent problems and Scala scales the data. The problem seems to be that ctruncate then falls over when trying to output the data (I specified the ctruncate run from within the scala window in the CCP4i gui). Searching for this error message doesn't bring up anything useful so could anyone suggest what might be going wrong? Thanks very much, Steve Dr Stephen Carr Research Complex at Harwell (RCaH) Rutherford Appleton Laboratory Harwell Oxford Didcot Oxon OX11 0FA United Kingdom Email stephen.c...@rc-harwell.ac.uk tel 01235 567717
[ccp4bb] Problems launching imosflm from ccp4i
2010-03-05
Thread
Stephen Carr Please Unsubscribe stephen.c...@diamond.ac.uk As This Address Is No Longer Active
Dear CCP4BB, I have installed the latest version of the ccp4 suite on a linux box (Centos 5.4) and mostly this has gone according to plan, however, when I try and run imosflm I get the error message cannot execute ccp4iwish:no such file or directory. A quick google search revealed that this was a problem on the pre-release of the OSX version of the suite so i tried the workaround suggested, but with no luck. Any thoughts on how to proceed would be gratefully received. Best regards, Steve Dr Stephen Carr Research Complex at Harwell Rutherford Appleton Laboratory Harwell Science and Innovation Campus Didcot Oxon OX11 0FA tel: 01235 567717 fax: 01235 567799 email: stephen.c...@rc-harwell.ac.uk www.rc-harwell.ac.uk
