Re: [ccp4bb] Bruker Smart and Mosflm
Dear George, You said: 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. Is there any advantage in having a phi-axis non-perpendicular to the beam? I would imagine the Lorentz factor increases for a large portion of the reflections, so in the end the majority has to be rejected anyway. The limit would be to have the phi-axis parallel to the beam. I suppose both SAINT and MOSFLM would have problems processing images collected that way. Is there an advantage in making more than one phi-scan? It does not give you extra information, just more of the same. I would think that one phi scan and additional omega scans at different settings of chi/kappa would be the most efficient way of getting complete data,. Best wishes, Bram _ Bram Schierbeek Rigaku Europe E: bram.schierb...@rigaku.com W: http://www.rigaku.com/
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
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] bruker smart and mosflm
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 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.
