Re: [ccp4bb] open mask with coot
Coot will read CNS maps. Is the CNS mask format different to the CNS map format? If so, convert your CNS mask to a CNS map first. (I presume CNS can do this - I've not used it.) Xiaowei Pan wrote: hello Crystallographers I have generated a solvent mask by CNS ,how can I open the .mask file with COOT? The mask file generated by CNS is different from CCP4. The mask fomat of CCP4 is mask.msk,and I can choose open map to open it in COOT. but I cann't open CNS format .mask with COOT, it did not recoganize the fomat. Thanks and regards! Xiaowei 2009-04-21 Xiaowei Pan
Re: [ccp4bb] My cysteines
Hello James, my first guess would be a second conformation. If the cysteine is part of a disulfide bridge, it could be a partially broken bridge due to radiation damage, and the extra atom would be the sulfhydryl group in VdW distance to the former partner cysteine. Best regards, Dirk. Am 21.04.2009 um 11:39 schrieb James Stroud: Hello All, I have a couple of cysteines with some extra density about 1 covalent bond's length away from the sulfur center. It looks to be one atom's worth of extra density. Because I could fit it in an icon sized graphic and I anticipate that someone will suggest I post a picture, I'm attaching a picture of the positive fofc density. Does anyone have any idea of the usual culprits here? I see no negative density in the region. James greencys.png *** Dirk Kostrewa Gene Center, A 5.07 Ludwig-Maximilians-University Feodor-Lynen-Str. 25 81377 Munich Germany Phone: +49-89-2180-76845 Fax:+49-89-2180-76999 E-mail: kostr...@lmb.uni-muenchen.de ***
Re: [ccp4bb] My cysteines
How about an oxidised cysteine? Sulfenic acid is a possibility (http://en.wikipedia.org/wiki/Sulfenic_acid), although it will generally oxidise further to sulfonic acid (http://en.wikipedia.org/wiki/Sulfonic_acid). I've seen them before in structures of old (4-5 year old) crystals (see figure 2 of Biochemistry, 2005, 44 (42), pp 13820–13836. DOI: 10.1021/bi0512849). Cheers, Stephen 2009/4/21 James Stroud xtald...@gmail.com: Hello All, I have a couple of cysteines with some extra density about 1 covalent bond's length away from the sulfur center. It looks to be one atom's worth of extra density. Because I could fit it in an icon sized graphic and I anticipate that someone will suggest I post a picture, I'm attaching a picture of the positive fofc density. Does anyone have any idea of the usual culprits here? I see no negative density in the region. James -- Dr Stephen Graham Division of Structural Biology Wellcome Trust Centre for Human Genetics Roosevelt Drive Oxford OX3 7BN United Kingdom Phone: +44 1865 287 549
Re: [ccp4bb] Low-level disable ccp4i database...?
Try $CCP4/ccp4i/etc/unix/configure.def Given your panic, am aiming for quick rather than complete answer ... (sorry, was too busy to answer at 3am). m On Tue, 2009-04-21 at 03:44 +0100, Frank Von Delft wrote: Yes, I was framed. Thanks for the quick response. Okay, question 2: There is no ~/.CCP4/unix/configure.def, because it's the first time ccp4i is run on this account. What do I do? And question 3: How can I set it up for all users? Somewhere in $CCP4? (Turns out home directories are local on every machine.) And question 4: Will this be multi-user in the upcoming release that will not need overriding (alla Ronan Keegan's email)? Oh please let it be, there are so few single-user labs... phx Winn, MD (Martyn) martyn.w...@stfc.ac.uk 21/04/09 0:15 Well, the guys may have distributed a phx-specific configure file, but otherwise, I think it is USE_DBCCP4I_ON_STARTUP in ~/.CCP4/unix/configure.def At least it worked for me after the briefest of tests of the Windows equivalent. Cheers Martyn -Original Message- From: CCP4 bulletin board on behalf of Frank Von Delft Sent: Mon 4/20/2009 11:04 PM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] Low-level disable ccp4i database...? Panic, I'm trying to configure ccp4i for a tutorial (i.e. multiple clueless students about to descend on the same user account), but the DB handler is somehow not responding, nor will it let me get to System Administration to turn it off. (I'm sorry Dave, I'm afraid I can't do that.) (Ref Ronan Keegan's reply on 18 March 09 on the BB.) What is the low-level way to turn it off? It must be either in the installation directory, or in ~/.CCP4 somewhere, but I couldn't find it. Hope someone's solved this before... phx -- *** * * * Dr. Martyn Winn * * * * STFC Daresbury Laboratory, Daresbury, Warrington, WA4 4AD, U.K. * * Tel: +44 1925 603455E-mail: martyn.w...@stfc.ac.uk* * Fax: +44 1925 603825Skype name: martyn.winn * * URL: http://www.ccp4.ac.uk/martyn/ * ***
[ccp4bb] My cysteines
Hello All, I have a couple of cysteines with some extra density about 1 covalent bond's length away from the sulfur center. It looks to be one atom's worth of extra density. Because I could fit it in an icon sized graphic and I anticipate that someone will suggest I post a picture, I'm attaching a picture of the positive fofc density. Does anyone have any idea of the usual culprits here? I see no negative density in the region. James inline: greencys.png
[ccp4bb] Postdoc - Structural Biology of Hsp90 Complexes
Postdoctoral Training Fellow - Structural Biology of Hsp90 Complexes Section of Structural Biology, ICR Chester Beatty Laboratories Chelsea, London, UK A Wellcome Trust-funded Postdoctoral position is available from 1st October 2009 in the laboratory of Professor Laurence Pearl FRS, in the Section of Structural Biology, to study the structural basis for regulation and activation of 'client' proteins by the Hsp90 molecular chaperone system. The Postdoc will be responsible for expression, purification, crystallization and structural analysis of protein complexes involving the Hsp90 molecular chaperone, its co-chaperones and client proteins that depend on Hsp90 for their biological function. The Institute of Cancer Research (a College of the University of London) is a world-class cancer research organization receiving the highest rating in the 2008 RAE. In partnership with The Royal Marsden NHS Foundation Trust, we form the largest comprehensive cancer centre in Europe, dedicated to research that extends from world leading basic science in epidemiology, genetics and structural and molecular biology, through drug discovery and development, to cancer diagnosis and patient treatment. The Section of Structural Biology at ICR is exceptionally well equipped for all aspects of modern structural biology, with state-of-the-art laboratories for molecular biology, recombinant expression in bacterial and eukaryotic systems, biochemistry, X-ray crystallography and electron microscopy. Excellent synchrotron access (~ 2 days/month) is available through rolling beam allocation programmes at Diamond and ESRF. Applicants must have a PhD, and experience in recombinant expression, protein purification, crystallisation and X-ray crystallography. Information on our previous work in this field can be found by searching PubMed and via the ICR Website http://www.icr.ac.uk/index.shtml The starting salary for the position will be in the range £26,966 to £35,518 p.a. inclusive (based on previous post-doctoral experience) and the post is offered initially on a fixed term contract of up to 2 years. Informal enquiries can be made to Professor Laurence Pearl (laurence.pe...@icr.ac.uk). Please note -- this address is for enquiries ONLY and CVs must be submitted in line with the instructions below. To apply, please send two copies of your CV, including the names and addresses of two referees to the HR Office, The Institute of Cancer Research, 123 Old Brompton Road, London SW7 3RP, quoting reference C 219 For a job description and person specification please visit our website at: www.icr.ac.uk/jobs.html. Alternatively, you may call our 24 hr recruitment line on 020 7153 5475. Closing date: 8 May 2009 -- - Laurence H. Pearl PhD FMedSci FRS Professor of Protein Crystallography and Section Chairman Section of Structural Biology, Institute of Cancer Research Chester Beatty Laboratories, 237 Fulham Road, London SW3 6JB Phone +44-(0)20 7153 5422 : Secretary 5443 : FAX 5457 - Live Simply and do Serious Things .. - Dorothy Crowfoot Hodgkin - The Institute of Cancer Research: Royal Cancer Hospital, a charitable Company Limited by Guarantee, Registered in England under Company No. 534147 with its Registered Office at 123 Old Brompton Road, London SW7 3RP. This e-mail message is confidential and for use by the addressee only. If the message is received by anyone other than the addressee, please return the message to the sender by replying to it and then delete the message from your computer and network.
Re: [ccp4bb] My cysteines
For other examples of oxidised cysteines you can look at our venerable series of reverse transcriptase structures... (Stuart, Stammers, Ren, Esnouf and others) residue 280 on the A chain, from memory. Regards, Robert -- Dr. Robert Esnouf, University Research Lecturer, Head of Bioinformatics and IT, The Division of Structural Biology and The Oxford Protein Production Facility, The Henry Wellcome Building for Genomic Medicine, Roosevelt Drive, Oxford OX3 7BN, UK Emails: rob...@strubi.ox.ac.uk Tel: (+44) - 1865 - 287783 and rob...@esnouf.comFax: (+44) - 1865 - 287547
[ccp4bb] Postdoctoral Associate Positions in Structural Biology
Postdoctoral Associate Positions in Structural Biology Two Postdoctoral Associate positions are immediately available in the Department of Biochemistry and Molecular Biology at Baylor College of Medicine. The first position is to focus on structural and functional studies of influenza virus. The second position is on structural and functional studies of complexes involved in epigenetic silencing. Both positions employ techniques such as biochemistry, molecular biology, tissue cell culture and X-ray crystallography, and will have the opportunity to expose to state-of-the-art computational techniques and drug discovery. The minimum requirement is a doctoral degree in biochemistry, protein chemistry or other related fields. Prior experience in structural biology is not required but is encouraged. The successful applicant must be self-motivated, enthusiastic and highly devoted. Competitive salary and fringe benefit will be provided. Baylor College of Medicine is located in the Texas Medical Center, Houston, TX. Houston is ranked the top #1 on Kiplinger's 2008 Best Cities. It is the fourth most populous city in the United States, and an international city that is a leader in the arts, education, and health care. Interested individuals should submit a CV, a cover letter, and names of three referees to: Qinghua Wang, Ph.D., Assistant Professor Department of Biochemistry and Molecular Biology Baylor College of Medicine One Baylor Plaza, BCM-125 Houston, TX 77030 Email: qingh...@bcm.tmc.edu
[ccp4bb] How small is a microbeam?
Just an interesting question of semantics that annoyingly comes up from time to time when people are comparing x-ray beam diameters. What counts as microbeam? Of course micro has the precise meaning in SI as being a factor of 10^-6. The problem is that the prefix micro just means extremely small in common usage. The term is used very confusingly everywhere. Take microwaves. Microwaves have wavelengths from 1 millimeter to 1 meter. Go figure. They're just extremely small radio waves. Now I believe that it is more widely accepted that nanofabrication is making objects that are measured in nanometers. So shouldn't microbeams rightly be x-ray beams with diameters measured in microns (i.e. 1 mm and = 1 micron). Of course this makes all crystallography beams microbeams and everything smaller than 1 micron a nanobeam. That won't be popular. I've always called anything smaller than 50 microns microbeam because that's about as small of an aperture-based collimator as we could make. So a user should ask for microbeam if regular collimator is too large. I was always puzzled at the APS habit of calling this minibeam, but it's starting to sound better all the time. But in practice, I think microbeam sometimes means smaller beam than yours. So microbeam used to be 30 microns, 10 or 5, now maybe 1 micron. Pretty soon no microbeam at all. I think maybe I'll stick with small, smaller than usual, and someday extremely small. I'd love to hear people's opinion on the topic. Richard Gillilan MacCHESS
Re: [ccp4bb] How small is a microbeam?
Hi Richard, Interesting topic raise you did... On a philosophical level, I would define a microbeam as a beam which matches in size with a microcrystal. Then question becomes what is a microcrystal? If we wanted to be purely scientific, though, we should not be measuring anything in mm or microns and everything should be in cm, shouldn't it? And don't get me even started about inches... But all the jokes aside, when standard beams used to be 200 microns or even larger, it was probably natural to call 50 micron beam a microbeam. However, many beamlines now have a standard beam which is on the order of 20-60 microns and therefore the meaning of microbeam is also evolving. APS should not be broadly blamed for introducing minibeam - it was just our beamlines (GM/CA-CAT) that did that. Reasons for discriminating 5-10 micron beams (minibeam) from ca 1 micron (microbeam) might have been not so much their size but what it involved to achieve these sizes. 5 micron and 1 micron beams, at least in our facility, required drastically different beamline optics, tolerances on the goniometer performance, hutch temperature stability, number of sleepless nights etc etc etc. Therefore, we wanted to internally discriminate between these two, very different efforts. Then the term leaked out in the community. Who wants to branch out into discussing the habit of using microbeam and microfocus interchangeably? Cheers, N. Ruslan Sanishvili (Nukri), Ph.D. GM/CA-CAT Biosciences Division, ANL 9700 S. Cass Ave. Argonne, IL 60439 Tel: (630)252-0665 Fax: (630)252-0667 rsanishv...@anl.gov -Original Message- From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On Behalf Of Richard Gillilan Sent: Tuesday, April 21, 2009 11:00 AM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] How small is a microbeam? Just an interesting question of semantics that annoyingly comes up from time to time when people are comparing x-ray beam diameters. What counts as microbeam? Of course micro has the precise meaning in SI as being a factor of 10^-6. The problem is that the prefix micro just means extremely small in common usage. The term is used very confusingly everywhere. Take microwaves. Microwaves have wavelengths from 1 millimeter to 1 meter. Go figure. They're just extremely small radio waves. Now I believe that it is more widely accepted that nanofabrication is making objects that are measured in nanometers. So shouldn't microbeams rightly be x-ray beams with diameters measured in microns (i.e. 1 mm and = 1 micron). Of course this makes all crystallography beams microbeams and everything smaller than 1 micron a nanobeam. That won't be popular. I've always called anything smaller than 50 microns microbeam because that's about as small of an aperture-based collimator as we could make. So a user should ask for microbeam if regular collimator is too large. I was always puzzled at the APS habit of calling this minibeam, but it's starting to sound better all the time. But in practice, I think microbeam sometimes means smaller beam than yours. So microbeam used to be 30 microns, 10 or 5, now maybe 1 micron. Pretty soon no microbeam at all. I think maybe I'll stick with small, smaller than usual, and someday extremely small. I'd love to hear people's opinion on the topic. Richard Gillilan MacCHESS
[ccp4bb] pI for protein-detergent complexes
Hi, Is there a way to estimate pI for protein-detergent complexes? Thanks. Joe
Re: [ccp4bb] How small is a microbeam?
Sanishvili, Ruslan wrote: .. Reasons for discriminating 5-10 micron beams (minibeam) from ca 1 micron (microbeam) might have been not so much their size but what it involved to achieve these sizes. Might I ask - do you really get data from 1 micron protein crystals? The reduction in scattering power (==crystal volume) from 5x5x5 microns to 1x1x1 is 125 and so it seems to present a grand challenge. I had understood there to be a more fundamental size limit, coming from radiation damage, which is still several microns for typical proteins. Do you suggest that ~1 micron sized crystals are no longer exclusively in the domain of powder diffraction? Millions of crystals working together to increase the signal does help a lot for such tiny ones :-) Going back to the original question, with 'nano' instead of 'micro', the FDA has defined [1] a 100 nm size-range limit of nanotechnology. Name suggetions for 100nm - 999 nm are most welcome. Are they submicron? Cheers, Jon [1] http://www.fda.gov/nanotechnology/regulation.html
Re: [ccp4bb] How small is a microbeam?
Hi Jon, You can indeed get data with 1 micron(ish) beam. See for example http://journals.iucr.org/d/issues/2008/02/00/wd5082/index.html Different question is whether there is any benefit in using micron size beam. It is subject of much work and discussion (e.g. http://www.nsls.bnl.gov/newsroom/events/workshops/2009/mx/) Regards, Nukri Ruslan Sanishvili (Nukri), Ph.D. GM/CA-CAT Biosciences Division, ANL 9700 S. Cass Ave. Argonne, IL 60439 Tel: (630)252-0665 Fax: (630)252-0667 rsanishv...@anl.gov -Original Message- From: Jon Wright [mailto:wri...@esrf.fr] Sent: Tuesday, April 21, 2009 3:36 PM To: Sanishvili, Ruslan Cc: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] How small is a microbeam? Sanishvili, Ruslan wrote: .. Reasons for discriminating 5-10 micron beams (minibeam) from ca 1 micron (microbeam) might have been not so much their size but what it involved to achieve these sizes. Might I ask - do you really get data from 1 micron protein crystals? The reduction in scattering power (==crystal volume) from 5x5x5 microns to 1x1x1 is 125 and so it seems to present a grand challenge. I had understood there to be a more fundamental size limit, coming from radiation damage, which is still several microns for typical proteins. Do you suggest that ~1 micron sized crystals are no longer exclusively in the domain of powder diffraction? Millions of crystals working together to increase the signal does help a lot for such tiny ones :-) Going back to the original question, with 'nano' instead of 'micro', the FDA has defined [1] a 100 nm size-range limit of nanotechnology. Name suggetions for 100nm - 999 nm are most welcome. Are they submicron? Cheers, Jon [1] http://www.fda.gov/nanotechnology/regulation.html
Re: [ccp4bb] How small is a microbeam?
Hi Yes good data with a micron size beam but, in this case, the path length was 20- 30 micron. I presume one would like a complete data set rather than a single or a few processable images. If the latter, then in principle anything is possible provided background is minimised and a low dose approach is taken - as for single particle cryo electron microscopy. I presume how to do all this will be one of the issues to be discussed at the workshop (which I am looking forward to). Regards Colin -Original Message- From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On Behalf Of Sanishvili, Ruslan Sent: 21 April 2009 22:21 To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] How small is a microbeam? Hi Jon, You can indeed get data with 1 micron(ish) beam. See for example http://journals.iucr.org/d/issues/2008/02/00/wd5082/index.html Different question is whether there is any benefit in using micron size beam. It is subject of much work and discussion (e.g. http://www.nsls.bnl.gov/newsroom/events/workshops/2009/mx/) Regards, Nukri Ruslan Sanishvili (Nukri), Ph.D. GM/CA-CAT Biosciences Division, ANL 9700 S. Cass Ave. Argonne, IL 60439 Tel: (630)252-0665 Fax: (630)252-0667 rsanishv...@anl.gov -Original Message- From: Jon Wright [mailto:wri...@esrf.fr] Sent: Tuesday, April 21, 2009 3:36 PM To: Sanishvili, Ruslan Cc: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] How small is a microbeam? Sanishvili, Ruslan wrote: .. Reasons for discriminating 5-10 micron beams (minibeam) from ca 1 micron (microbeam) might have been not so much their size but what it involved to achieve these sizes. Might I ask - do you really get data from 1 micron protein crystals? The reduction in scattering power (==crystal volume) from 5x5x5 microns to 1x1x1 is 125 and so it seems to present a grand challenge. I had understood there to be a more fundamental size limit, coming from radiation damage, which is still several microns for typical proteins. Do you suggest that ~1 micron sized crystals are no longer exclusively in the domain of powder diffraction? Millions of crystals working together to increase the signal does help a lot for such tiny ones :-) Going back to the original question, with 'nano' instead of 'micro', the FDA has defined [1] a 100 nm size-range limit of nanotechnology. Name suggetions for 100nm - 999 nm are most welcome. Are they submicron? Cheers, Jon [1] http://www.fda.gov/nanotechnology/regulation.html This e-mail 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 authorised 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 the e-mail. Any opinions expressed within this e-mail are those of the individual and not necessarily of Diamond Light Source Ltd. Diamond Light Source Ltd. cannot guarantee that this e-mail 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. Diamond Light Source Limited (company no. 4375679). Registered in England and Wales with its registered office at Diamond House, Harwell Science and Innovation Campus, Didcot, Oxfordshire, OX11 0DE, United Kingdom
Re: [ccp4bb] How small is a microbeam?
Yes Colin, of course you are right about the 20-30 micron flight path. I thought John's question was about micron-size beam, not the micron-size crystal. Reading it over, I saw my mistake. As for the micron-size crystals, manipulating those will be another fun task. Fortunately, tractor beams (which some call more prosaic name of optical tweezers) are now reality and they should help. Cheers, N. Ruslan Sanishvili (Nukri), Ph.D. GM/CA-CAT Biosciences Division, ANL 9700 S. Cass Ave. Argonne, IL 60439 Tel: (630)252-0665 Fax: (630)252-0667 rsanishv...@anl.gov -Original Message- From: Nave, C (Colin) [mailto:colin.n...@diamond.ac.uk] Sent: Tuesday, April 21, 2009 4:44 PM To: Sanishvili, Ruslan; CCP4BB@JISCMAIL.AC.UK Subject: RE: [ccp4bb] How small is a microbeam? Hi Yes good data with a micron size beam but, in this case, the path length was 20- 30 micron. I presume one would like a complete data set rather than a single or a few processable images. If the latter, then in principle anything is possible provided background is minimised and a low dose approach is taken - as for single particle cryo electron microscopy. I presume how to do all this will be one of the issues to be discussed at the workshop (which I am looking forward to). Regards Colin -Original Message- From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On Behalf Of Sanishvili, Ruslan Sent: 21 April 2009 22:21 To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] How small is a microbeam? Hi Jon, You can indeed get data with 1 micron(ish) beam. See for example http://journals.iucr.org/d/issues/2008/02/00/wd5082/index.html Different question is whether there is any benefit in using micron size beam. It is subject of much work and discussion (e.g. http://www.nsls.bnl.gov/newsroom/events/workshops/2009/mx/) Regards, Nukri Ruslan Sanishvili (Nukri), Ph.D. GM/CA-CAT Biosciences Division, ANL 9700 S. Cass Ave. Argonne, IL 60439 Tel: (630)252-0665 Fax: (630)252-0667 rsanishv...@anl.gov -Original Message- From: Jon Wright [mailto:wri...@esrf.fr] Sent: Tuesday, April 21, 2009 3:36 PM To: Sanishvili, Ruslan Cc: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] How small is a microbeam? Sanishvili, Ruslan wrote: .. Reasons for discriminating 5-10 micron beams (minibeam) from ca 1 micron (microbeam) might have been not so much their size but what it involved to achieve these sizes. Might I ask - do you really get data from 1 micron protein crystals? The reduction in scattering power (==crystal volume) from 5x5x5 microns to 1x1x1 is 125 and so it seems to present a grand challenge. I had understood there to be a more fundamental size limit, coming from radiation damage, which is still several microns for typical proteins. Do you suggest that ~1 micron sized crystals are no longer exclusively in the domain of powder diffraction? Millions of crystals working together to increase the signal does help a lot for such tiny ones :-) Going back to the original question, with 'nano' instead of 'micro', the FDA has defined [1] a 100 nm size-range limit of nanotechnology. Name suggetions for 100nm - 999 nm are most welcome. Are they submicron? Cheers, Jon [1] http://www.fda.gov/nanotechnology/regulation.html This e-mail 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 authorised 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 the e-mail. Any opinions expressed within this e-mail are those of the individual and not necessarily of Diamond Light Source Ltd. Diamond Light Source Ltd. cannot guarantee that this e-mail 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. Diamond Light Source Limited (company no. 4375679). Registered in England and Wales with its registered office at Diamond House, Harwell Science and Innovation Campus, Didcot, Oxfordshire, OX11 0DE, United Kingdom
Re: [ccp4bb] How small is a microbeam?
The other use for these ultra-small beams is to illuminate part of a larger xtal to find the best diffracting (or leat mosaic) regions and/or to raster out of the radiation damaged areas. This way even large xtals can benefit from this. Nukri should chime in on this point as well since GMCA-CAT is pioneering this approach. - Th Nave, C (Colin) wrote: Hi Yes good data with a micron size beam but, in this case, the path length was 20- 30 micron. I presume one would like a complete data set rather than a single or a few processable images. If the latter, then in principle anything is possible provided background is minimised and a low dose approach is taken - as for single particle cryo electron microscopy. I presume how to do all this will be one of the issues to be discussed at the workshop (which I am looking forward to). Regards Colin -Original Message- From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On Behalf Of Sanishvili, Ruslan Sent: 21 April 2009 22:21 To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] How small is a microbeam? Hi Jon, You can indeed get data with 1 micron(ish) beam. See for example http://journals.iucr.org/d/issues/2008/02/00/wd5082/index.html Different question is whether there is any benefit in using micron size beam. It is subject of much work and discussion (e.g. http://www.nsls.bnl.gov/newsroom/events/workshops/2009/mx/) Regards, Nukri Ruslan Sanishvili (Nukri), Ph.D. GM/CA-CAT Biosciences Division, ANL 9700 S. Cass Ave. Argonne, IL 60439 Tel: (630)252-0665 Fax: (630)252-0667 rsanishv...@anl.gov -Original Message- From: Jon Wright [mailto:wri...@esrf.fr] Sent: Tuesday, April 21, 2009 3:36 PM To: Sanishvili, Ruslan Cc: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] How small is a microbeam? Sanishvili, Ruslan wrote: .. Reasons for discriminating 5-10 micron beams (minibeam) from ca 1 micron (microbeam) might have been not so much their size but what it involved to achieve these sizes. Might I ask - do you really get data from 1 micron protein crystals? The reduction in scattering power (==crystal volume) from 5x5x5 microns to 1x1x1 is 125 and so it seems to present a grand challenge. I had understood there to be a more fundamental size limit, coming from radiation damage, which is still several microns for typical proteins. Do you suggest that ~1 micron sized crystals are no longer exclusively in the domain of powder diffraction? Millions of crystals working together to increase the signal does help a lot for such tiny ones :-) Going back to the original question, with 'nano' instead of 'micro', the FDA has defined [1] a 100 nm size-range limit of nanotechnology. Name suggetions for 100nm - 999 nm are most welcome. Are they submicron? Cheers, Jon [1] http://www.fda.gov/nanotechnology/regulation.html This e-mail 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 authorised 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 the e-mail. Any opinions expressed within this e-mail are those of the individual and not necessarily of Diamond Light Source Ltd. Diamond Light Source Ltd. cannot guarantee that this e-mail 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. Diamond Light Source Limited (company no. 4375679). Registered in England and Wales with its registered office at Diamond House, Harwell Science and Innovation Campus, Didcot, Oxfordshire, OX11 0DE, United Kingdom
