Re: [ccp4bb] bruker smart and mosflm
Hi, That utility is available within the Bruker Suite. We have a Proteum system and it is available from the Bruker software, although there is a standalone version. A while back, I was able to convert some images so that they could be read by MOSFLM and XDS, but I was never successful in processing them with those programs. Cheers, Pedro. At 02:12 09-11-2010, Iain Kerr wrote: Hi Ed, Bruker used to supply a utility called FRM2FRM that would unwarp their images so that they were readable by Mosflm. You may want to consult them directly; Matt Benning (I believe he's still there) was most helpful when I was having problems with Bruker images a few years ago. HTH, Iain On 11/8/2010 12:01 PM, Ed Pozharski wrote: I am trying to read Bruker's Smart 6000 images with mosflm and it fails. Based on some limited googlearch I feel that NPIXELB:1 is a relevant information and when these files were processed in HKL (not by me), the relevant detector line says format ccd bruker smart6000 binned. I see from mosflm website that I might be in trouble here although it says that in recent version handling of bruker smart has been improved. In the mosflm crash file I get this From information in the image file, the detector has been recognized as: Bruker SMART If this is incorrect you must supply a DETECTOR keyword So my question is how do I figure out if this particular format is supported or not? Cheers, Ed. Industry and Medicine Applied Crystallography Macromolecular Crystallography Unit ___ Phones : (351-21) 446-9100 Ext. 1669 (351-21) 446-9669 (direct) Fax : (351-21) 441-1277 or 443-3644 email : mat...@itqb.unl.pt http://www.itqb.unl.pt/research/biological-chemistry/industry-and-medicine-applied-crystallography http://www.itqb.unl.pt/labs/macromolecular-crystallography-unit Mailing address : Instituto de Tecnologia Quimica e Biologica Apartado 127 2781-901 OEIRAS Portugal
Re: [ccp4bb] bruker smart and mosflm
By far the easiest way would be to use the programs (SAINT and SADABS) provided by Bruker. We get excellent data, e.g. for in-house S-SAD phasing, using these programs (either offline or as part of the Bruker GUI) for data collected on our SMART6000. For a detailed S-SAD example see Berhard's book page 424. Unlike MOSFLM, SAINT can integrate non-merohedral twins handling the reflection overlap properly and can process phi scans for which the oscillation axis is not perpendicular to the incident beam. George Prof. George M. Sheldrick FRS Dept. Structural Chemistry, University of Goettingen, Tammannstr. 4, D37077 Goettingen, Germany Tel. +49-551-39-3021 or -3068 Fax. +49-551-39-22582 On Mon, 8 Nov 2010, Ed Pozharski wrote: I am trying to read Bruker's Smart 6000 images with mosflm and it fails. Based on some limited googlearch I feel that NPIXELB:1 is a relevant information and when these files were processed in HKL (not by me), the relevant detector line says format ccd bruker smart6000 binned. I see from mosflm website that I might be in trouble here although it says that in recent version handling of bruker smart has been improved. In the mosflm crash file I get this From information in the image file, the detector has been recognized as: Bruker SMART If this is incorrect you must supply a DETECTOR keyword So my question is how do I figure out if this particular format is supported or not? Cheers, Ed. -- I'd jump in myself, if I weren't so good at whistling. Julian, King of Lemurs
Re: [ccp4bb] bruker smart and mosflm
Hi folks With respect to George, I don't think this is the easiest way. If learning to use a different program was the easiest way forward for any task, people would have dropped MS-Windows like a hot potato after the release of Vista and started using some other operating system that was better. I'm sure that many people here will have their own examples of other instances where they would prefer to carry on using a program they know well rather than learn something new, even if the new program offers advantages. I'd have to say, in general the easiest thing to do when confronted with Mosflm issues is to get in touch with the authors and ask them. We are all very friendly, approachable people who will do our best to help! On 9 Nov 2010, at 08:42, George M. Sheldrick wrote: By far the easiest way would be to use the programs (SAINT and SADABS) provided by Bruker. We get excellent data, e.g. for in-house S-SAD phasing, using these programs (either offline or as part of the Bruker GUI) for data collected on our SMART6000. For a detailed S-SAD example see Berhard's book page 424. Unlike MOSFLM, SAINT can integrate non-merohedral twins handling the reflection overlap properly and can process phi scans for which the oscillation axis is not perpendicular to the incident beam. George Prof. George M. Sheldrick FRS Dept. Structural Chemistry, University of Goettingen, Tammannstr. 4, D37077 Goettingen, Germany Tel. +49-551-39-3021 or -3068 Fax. +49-551-39-22582 On Mon, 8 Nov 2010, Ed Pozharski wrote: I am trying to read Bruker's Smart 6000 images with mosflm and it fails. Based on some limited googlearch I feel that NPIXELB:1 is a relevant information and when these files were processed in HKL (not by me), the relevant detector line says format ccd bruker smart6000 binned. I see from mosflm website that I might be in trouble here although it says that in recent version handling of bruker smart has been improved. In the mosflm crash file I get this From information in the image file, the detector has been recognized as: Bruker SMART If this is incorrect you must supply a DETECTOR keyword So my question is how do I figure out if this particular format is supported or not? Cheers, Ed. -- I'd jump in myself, if I weren't so good at whistling. Julian, King of Lemurs Harry -- Dr Harry Powell, MRC Laboratory of Molecular Biology, MRC Centre, Hills Road, Cambridge, CB2 0QH
[ccp4bb] AW: [ccp4bb] bruker smart and mosflm
I'd have to say, in general the easiest thing to do when confronted with Mosflm issues is to get in touch with the authors and ask them. We are all very friendly, approachable people who will do our best to help! I cannot agree more with this... Many thanks with all your help provided so far... (more needed surely soon :) ) Cheers Stefan
[ccp4bb] Free R with doubled cell edge
Dear BB, Thanks for all of your helpful and useful comments Whilst there was some agreement that simulated annealing should be enough to solve any problems, we have taken perhaps the cautious approach. We have produced a freeR set in the bigger unit cell using reindex as suggested by Eleanor: This is easy to do Reindex 2h,k,l then the cell will double; the FreeR will stay with the reflection, and you can use those FreeRs to append to your new data in the scala/truncate GUI. All the unset ones (2h+1,k,l) will be given new FreeRs and the old ones transferred. Eleanor Mostly for the reasons as outlines by Ethan: One problem with shaking things up as you describe is that if the original model was refined against higher resolution data than your new data set, you will probably never get back to the same model quality as you started with (see the ongoing discussion in another thread). And if the new data set is higher resolution, then you face the same problem in reverse. If you want to take your eventual new, higher resolution model back into the old cell you want subsequent refinement to have unbiased Rfree on that end also. Ethan as we now have higher resolution data (than we had for the small unit cell before) for both the small and doubled unit cell - the highest resolution data is for the doubled unit cell with 4 chains, but we would like to refine in the smaller cell as well at some point for completeness. As pointed out, there is a straight translation in the larger unit cell (doubled along a), h(odd) 0 0 reflections are weak, and Phenix Xtriage identifies the translation readily. However, Phaser has correctly positioned 4 chains and we are happily refining in Refmac, so I think that should not be a problem. Many thanks to all who commented on the BB and off line. Cheers Ed __ T.Edwards Ph.D. Garstang 8.53d Astbury Centre for Structural Molecular Biology University of Leeds, Leeds, LS2 9JT Telephone: 0113 343 3031 http://www.bmb.leeds.ac.uk/staff/tae/ People who know nothing about cheeses reel away from Camembert, Roquefort, and Stilton because the plebeian proboscis is not equipped to differentiate between the sordid and the sublime. Harvey Day (1971) Dear BB Sages, I have a problem where I think I could very easily do the wrong thing. And I don't really want to do that... We have solved a new structure using zinc SAD phases (1 zinc in 27kD, 2 Zn/AU - Shelx, RESOLVE, ARPwARP. Cool.). In p21 30 109 65 90 105 90 at 2.5A However, we have now collected 1.9A data. In p21... 60 109 65 90 107 90 4 chains per AU instead of 2 with a doubling of a. Self rotations with the new data suggest 2 two-folds, one quite near crystallographic. It seems that the doubling of the a edge is adding an NCS two-fold that is almost crystallographic. Now, having refined against the 2.5A data to R/Rfree of about 25/30 we would like to use that model to do MR against the new high res data (We didn't collect Zn peak data for the new crystal - didn't think we'd need it.). I have done that and found 4 mols with Phaser in about 60 seconds. Still cool. So, we would like to transfer Free R flags to the new data to avoid refining against what had been labelled as Free R. My problem is - how do I do that properly? I am worried that some of the working data in the bigger cell will be correlated with Free data via the near crystallographic NCS. I clearly don't want to just copy them from the old mtz file with a0 I recall some discussion about this from years ago on the BB but can't find the right threads. Can anybody point me to the correct way to do this please - I presumably want to label with Free R flags symmetry related Free R labelled reflections from the old data that are related by the new NCS 2-fold (that is close to crystallographic) in the new data. Right?? If I have worded that correctly... I am hoping that will make sense to somebody. I think that the solutions that were recently suggested for lower vs higher symmetry in the same unit cell do not apply here. One suggestion has been to do the MolRep, choose new free Rs, give it all a good hard shake with high temp simulated annealing and hope that any bias is gone. I'm not sure that I am comfortable with the word hope here... But, if the consensus of opinion of the wise folk at the BB is that this will pass muster at the point where the charming and delightful referees are commenting on the extremely high impact (obviously :-) manuscript, then I will quote you all! I await your wise words. Free R. Again. Sorry. Cheers Ed __ T.Edwards Ph.D. Garstang 8.53d Astbury Centre for Structural Molecular Biology University of Leeds, Leeds, LS2 9JT Telephone: 0113 343 3031 http://www.bmb.leeds.ac.uk/staff/tae/
Re: [ccp4bb] AW: [ccp4bb] bruker smart and mosflm
Tying customers to formats with unbreakable, softwares and secret tricks is seldom productive. Customers suspect that something really wrong with the machines is hiding behind that. It is not clear if it is legal. After all, academic customers pay money taken from public and transferred to granting agencies. It means that public support unbreakable format codings, softwares and secret tricks... The question is what for? - for unbreakable format codings, softwares and secret tricks? It puts a lot of noise into the system which is already noisy and people start to prefer open codes... There is another option: maybe these are still XENTRONIX formats that were about 18 or 8 altogether if elders remember properly? Dr Felix Frolow Professor of Structural Biology and Biotechnology Department of Molecular Microbiology and Biotechnology Tel Aviv University 69978, Israel Acta Crystallographica F, co-editor e-mail: mbfro...@post.tau.ac.il Tel: ++972-3640-8723 Fax: ++972-3640-9407 Cellular: 0547 459 608 On Nov 9, 2010, at 15:30 , Stefan Gerhardt wrote: I'd have to say, in general the easiest thing to do when confronted with Mosflm issues is to get in touch with the authors and ask them. We are all very friendly, approachable people who will do our best to help! I cannot agree more with this... Many thanks with all your help provided so far... (more needed surely soon :) ) Cheers Stefan
[ccp4bb] Postdoc position
We are seeking an enthusiastic and motivated researcher to join our group as a postdoctoral fellow at Institute of molecular and cell Biology (IMCB), Singapore. Our laboratory uses biochemical/biophysical, cellular and crystallographic techniques to understand the molecular mechanisms of translational control, eukaryotic mRNA decay, and the Hippo signaling pathway. Qualified candidates should have experience in either Protein Crystallography or Biochemistry and Molecular Biology, with prior publications. All enquires should be made directly to Dr. Haiwei Song via email hai...@imcb.a-star.edu.sgmailto:%20hai...@imcb.a-star.edu.sg. Further information is available at http://www.imcb.a-star.edu.sg/php/shw.php Note: This message may contain confidential information. If this Email/Fax has been sent to you by mistake, please notify the sender and delete it immediately. Thank you.
