[ccp4bb] No diffraction
Dear crystallographers I have a protein of 90 kDa forming dimers. Crystals formed with microbatch and vapor diffusion method in 24 hours but no diffraction at home source. Dissolved crystals was confirmed to be the protein with mass spec. Any suggestions to improve diffraction would be welcome. Thanking you in advance. Theresa
Re: [ccp4bb] No diffraction
Might I suggest consulting the CCP4 user community wiki on the topic: http://strucbio.biologie.uni-konstanz.de/ccp4wiki/index.php/Improving_crystal_quality Good luck, Katherine On Thu, Jan 26, 2012 at 9:33 AM, Theresa H. Hsu theresah...@live.comwrote: Dear crystallographers I have a protein of 90 kDa forming dimers. Crystals formed with microbatch and vapor diffusion method in 24 hours but no diffraction at home source. Dissolved crystals was confirmed to be the protein with mass spec. Any suggestions to improve diffraction would be welcome. Thanking you in advance. Theresa
Re: [ccp4bb] No diffraction
But first of all: try to add a synchrotron to the crystals Poul On 26/01/2012, at 16.48, Katherine Sippel wrote: Might I suggest consulting the CCP4 user community wiki on the topic: http://strucbio.biologie.uni-konstanz.de/ccp4wiki/index.php/Improving_crystal_quality Good luck, Katherine On Thu, Jan 26, 2012 at 9:33 AM, Theresa H. Hsu theresah...@live.com wrote: Dear crystallographers I have a protein of 90 kDa forming dimers. Crystals formed with microbatch and vapor diffusion method in 24 hours but no diffraction at home source. Dissolved crystals was confirmed to be the protein with mass spec. Any suggestions to improve diffraction would be welcome. Thanking you in advance. Theresa
Re: [ccp4bb] Introducing an ELN
I think that all these points are interesting and valid. On Jan 25, 2012, at 10:37, Chris Morris wrote: Tassos reports: 1. None of the twenty test-users was satisfied with any of the two solutions - and each was annoyed for a different reason. This suggests that the choice of ELN is not the most difficult part of the adoption process. Maybe the test users at the NKI were annoyed by the idea of using an ELN at all. That would surely apply to some users. Some were actually very keen, and thats why they signed up for it. In my experience, the hardest part is ensuring that it provides benefits to the people who have to enter the data, and provides them early. The fact that it will make information retrieval easier in three years is not enough. I suggest focussing on electronic support for housekeeping: booking time on an instrument, finding the files the instrument created, ordering oligos, recording when you use the last of a reagent. Scientists work very independently in most respects, but they do have certain obligations that flow from sharing the lab space. You can make use of these to encourage compliance with the ELN. If you do, then most of the science will get recorded in passing. I think that this was exactly one of the problems. The ELNs we tested had no option for booking instruments, no way to find files from instruments let alone read them (it would support only TIF, JPEG, Doc, XLS, PDF), and would not do stock keeping: all these are thought to be out of the ELN scope. And that makes an ELN inherently less useful. Lack of instrument support is another issue: a machine that would allow us to import real chromatograms to ELN would be cool - alas, the solution that was suggested to us is to save as PDF or XLS and reload ...! (it took 3 weeks to come back with this great plan!) For the rest I have nothing much to say, I basically agree. A. I suggest also ensuring that it includes electronic tools that actually help. Two examples from PiMS are primer design, and automatically uploading and interpreting results from the Caliper GX instrument. It must allow round trips with spreadsheets, i.e. dump ELN data as a spreadsheet, edit it, upload it again. Despite their substantial disadvantages, some scientists will not give them up. It should also allow crossreferencing with paper note books. Some will continue to use a lab notebook. When they discover that the ELN serves as a searchable index to it, they will warm to the ELN. I suggest aiming for no paper at your lab progress meetings within say 12 months. When you reach that point, everything important is in the ELN. Before then, the ELN is not giving real value. You will need someone who is keen on the introduction of the ELN, to customise it, provide first line user support, and act as a single point of contact with the supplier. This might be a scientist or an IT person. I have also seen this done well by a technician, Delphine Chesnel when she was at the EMBL Hamburg. If you can't find such a champion, then introduction will not be successful. Some of the problem here is an own goal by the community: scientists are trained to use paper during their degrees, so ELNs are a controversial change of practice. One person who, unusually, began with an ELN told me how inconvenient it is now she works in a paper-based lab. PepTalk 2012 had a workshop on this topic. The recording and notes are here: http://www.structuralbiology.eu/support/forums/networks/pims/why-dont-scientists-use-limselns regards, Chris Chris Morris chris.mor...@stfc.ac.uk Tel: +44 (0)1925 603689 Fax: +44 (0)1925 603634 Mobile: 07921-717915 Skype: chrishgmorris http://pims.structuralbiology.eu/ http://www.citeulike.org/blog/chrishmorris Daresbury Lab, Daresbury, Warrington, UK, WA4 4AD P please don't print this e-mail unless you really need to Anastassis (Tassos) Perrakis, Principal Investigator / Staff Member Department of Biochemistry (B8) Netherlands Cancer Institute, Dept. B8, 1066 CX Amsterdam, The Netherlands Tel: +31 20 512 1951 Fax: +31 20 512 1954 Mobile / SMS: +31 6 28 597791
Re: [ccp4bb] No diffraction
Ditto to Poul's advice. I've had many many many cases where crystals diffract poorly (or not at all) on home sources only to show excellent diffraction at a synchrotron. (Whether or not a home source is properly calibrated is probably the biggest issue, but that's for another discussion). On Jan 26, 2012, at 8:33 AM, Theresa H. Hsu wrote: Dear crystallographers I have a protein of 90 kDa forming dimers. Crystals formed with microbatch and vapor diffusion method in 24 hours but no diffraction at home source. Dissolved crystals was confirmed to be the protein with mass spec. Any suggestions to improve diffraction would be welcome. Thanking you in advance. Theresa - Francis E. Reyes M.Sc. 215 UCB University of Colorado at Boulder
Re: [ccp4bb] No diffraction
It depends a lot on which home source and which synchrotron, there are enormous differences. Goettingen is uniquely well placed because we can reach four synchrotrons in a few (3-7) hours by high speed train and in theory at least five more with a longer train journey, trains are very convenient for transporting crystals. Two of these synchrotrons do not give a higher resolution than our home system, but at least they can vary the wavelength. However if we think we can see at least two reflections at home, of course we take the crystal to a (suitable) synchrotron. George On 01/26/2012 04:54 PM, Francis E Reyes wrote: Ditto to Poul's advice. I've had many many many cases where crystals diffract poorly (or not at all) on home sources only to show excellent diffraction at a synchrotron. (Whether or not a home source is properly calibrated is probably the biggest issue, but that's for another discussion). On Jan 26, 2012, at 8:33 AM, Theresa H. Hsu wrote: Dear crystallographers I have a protein of 90 kDa forming dimers. Crystals formed with microbatch and vapor diffusion method in 24 hours but no diffraction at home source. Dissolved crystals was confirmed to be the protein with mass spec. Any suggestions to improve diffraction would be welcome. Thanking you in advance. Theresa - Francis E. Reyes M.Sc. 215 UCB University of Colorado at Boulder
Re: [ccp4bb] No diffraction
As other have/surely will suggest, by all means try RT collection to establish if your crystals really diffract OK, or if your cryo conditions are killing them. We have lots of experience in our lab getting "beamstop" diffraction with certain samples when subjected to cryoprotection. Depending on the intensity of your home source (and its life-cycle age), small crystals may not be large enough to produce usable or visible diffraction. With our home source, we really need 0.3 mm crystals (larger if thin plates) to get usable diffraction. Cheers, ___ Roger S. Rowlett Gordon Dorothy Kline Professor Department of Chemistry Colgate University 13 Oak Drive Hamilton, NY 13346 tel: (315)-228-7245 ofc: (315)-228-7395 fax: (315)-228-7935 email: rrowl...@colgate.edu On 1/26/2012 10:33 AM, Theresa H. Hsu wrote: Dear crystallographers I have a protein of 90 kDa forming dimers. Crystals formed with microbatch and vapor diffusion method in 24 hours but no diffraction at home source. Dissolved crystals was confirmed to be the protein with mass spec. Any suggestions to improve diffraction would be welcome. Thanking you in advance. Theresa
Re: [ccp4bb] No diffraction
Theresa You should also try microseeding into *random screens *by making a seed stock with the crystals that you have, to use with both microbatch and vapor diffusion experiments. You will often pick up new and better conditions and you're more likely to get well-formed crystals right out of the screens. I hope it works Patrick _ Refs: Allan D’Arcy, Frederic Villarda, May Marsh. An automated microseed matrix-screening method for protein crystallization. Acta Crystallographica section D 63 (2007), 550–554. Galina Obmolova,* Thomas J. Malia, Alexey Teplyakov, Raymond Sweet and Gary L. Gilliland. 'Promoting crystallization of antibody–antigen complexes via microseed matrix screening.' Acta Crystallographica Section D 66 (2010) 927–933. Open-access at http://journals.iucr.org/d/issues/2010/08/00/bw5361/bw5361.pdf A. G. Villaseñor, A. Wong, A. Shao, A. Garg, A. Kuglstatter and S. F. Harris. 'Acoustic matrix microseeding: improving protein crystal growth with minimal chemical bias.' Acta Crystallographica Section D 66 (2010) 568-576. Gregory Ireton and Barry Stoddard. 'Microseed matrix screening to improve crystals of yeast cytosine deaminase'. Acta Crystallographica section D60 (2004) 601–605. Patrick D. Shaw Stewart, Stefan A. Kolek, Richard A. Briggs, Naomi E. Chayen and Peter F.M. Baldock. 'Random Microseeding: A Theoretical and Practical Exploration of Seed Stability and Seeding Techniques for Successful Protein Crystallization'. Cryst. Growth Des., 2011, 11 (8), pp 3432–3441. On-line at http://pubs.acs.org/doi/abs/10.1021/cg2001442. * If you don't have a subscription to Crystal Growth and Design, click **here*http://www.douglas.co.uk/mms.htm#CGDFreeCopy * to obtain a free copy (we're limited to 50 downloads in the first year).* On 26 January 2012 15:33, Theresa H. Hsu theresah...@live.com wrote: Dear crystallographers I have a protein of 90 kDa forming dimers. Crystals formed with microbatch and vapor diffusion method in 24 hours but no diffraction at home source. Dissolved crystals was confirmed to be the protein with mass spec. Any suggestions to improve diffraction would be welcome. Thanking you in advance. Theresa -- patr...@douglas.co.ukDouglas Instruments Ltd. Douglas House, East Garston, Hungerford, Berkshire, RG17 7HD, UK Directors: Peter Baldock, Patrick Shaw Stewart http://www.douglas.co.uk Tel: 44 (0) 148-864-9090US toll-free 1-877-225-2034 Regd. England 2177994, VAT Reg. GB 480 7371 36
Re: [ccp4bb] Introducing an ELN
As the proud owner of a carefully organized, highly annotated VMS backup tape (reel-to-reel, of course), my main concern is that paper is the only format that we'll be able to count on reading a decade (or more) from now. = Phoebe A. Rice Dept. of Biochemistry Molecular Biology The University of Chicago phone 773 834 1723 http://bmb.bsd.uchicago.edu/Faculty_and_Research/01_Faculty/01_Faculty_Alphabetically.php?faculty_id=123 http://www.rsc.org/shop/books/2008/9780854042722.asp Original message Date: Thu, 26 Jan 2012 16:50:04 +0100 From: CCP4 bulletin board CCP4BB@JISCMAIL.AC.UK (on behalf of Anastassis Perrakis a.perra...@nki.nl) Subject: Re: [ccp4bb] Introducing an ELN To: CCP4BB@JISCMAIL.AC.UK I think that all these points are interesting and valid. On Jan 25, 2012, at 10:37, Chris Morris wrote: Tassos reports: 1. None of the twenty test-users was satisfied with any of the two solutions - and each was annoyed for a different reason. This suggests that the choice of ELN is not the most difficult part of the adoption process. Maybe the test users at the NKI were annoyed by the idea of using an ELN at all. That would surely apply to some users. Some were actually very keen, and thats why they signed up for it. In my experience, the hardest part is ensuring that it provides benefits to the people who have to enter the data, and provides them early. The fact that it will make information retrieval easier in three years is not enough. I suggest focussing on electronic support for housekeeping: booking time on an instrument, finding the files the instrument created, ordering oligos, recording when you use the last of a reagent. Scientists work very independently in most respects, but they do have certain obligations that flow from sharing the lab space. You can make use of these to encourage compliance with the ELN. If you do, then most of the science will get recorded in passing. I think that this was exactly one of the problems. The ELNs we tested had no option for booking instruments, no way to find files from instruments let alone read them (it would support only TIF, JPEG, Doc, XLS, PDF), and would not do stock keeping: all these are thought to be out of the ELN scope. And that makes an ELN inherently less useful. Lack of instrument support is another issue: a machine that would allow us to import real chromatograms to ELN would be cool - alas, the solution that was suggested to us is to save as PDF or XLS and reload ...! (it took 3 weeks to come back with this great plan!) For the rest I have nothing much to say, I basically agree. A. I suggest also ensuring that it includes electronic tools that actually help. Two examples from PiMS are primer design, and automatically uploading and interpreting results from the Caliper GX instrument. It must allow round trips with spreadsheets, i.e. dump ELN data as a spreadsheet, edit it, upload it again. Despite their substantial disadvantages, some scientists will not give them up. It should also allow crossreferencing with paper note books. Some will continue to use a lab notebook. When they discover that the ELN serves as a searchable index to it, they will warm to the ELN. I suggest aiming for no paper at your lab progress meetings within say 12 months. When you reach that point, everything important is in the ELN. Before then, the ELN is not giving real value. You will need someone who is keen on the introduction of the ELN, to customise it, provide first line user support, and act as a single point of contact with the supplier. This might be a scientist or an IT person. I have also seen this done well by a technician, Delphine Chesnel when she was at the EMBL Hamburg. If you can't find such a champion, then introduction will not be successful. Some of the problem here is an own goal by the community: scientists are trained to use paper during their degrees, so ELNs are a controversial change of practice. One person who, unusually, began with an ELN told me how inconvenient it is now she works in a paper-based lab. PepTalk 2012 had a workshop on this topic. The recording and notes are here: http://www.structuralbiology.eu/support/forums/networks/pims/why-dont-scientists-use-limselns regards, Chris Chris Morris chris.mor...@stfc.ac.uk Tel: +44 (0)1925 603689 Fax: +44 (0)1925 603634 Mobile: 07921-717915 Skype: chrishgmorris http://pims.structuralbiology.eu/ http://www.citeulike.org/blog/chrishmorris Daresbury Lab,
Re: [ccp4bb] No diffraction
For crystallization: Your xtal may come out a little bit fast. If the condition contain alcohol, such as IPA, you may have to modify it. If you let people know the condition, it may be more helpful. Also, please check the purity of your protein. Kevin On Thu, Jan 26, 2012 at 7:33 AM, Theresa H. Hsu theresah...@live.com wrote: Dear crystallographers I have a protein of 90 kDa forming dimers. Crystals formed with microbatch and vapor diffusion method in 24 hours but no diffraction at home source. Dissolved crystals was confirmed to be the protein with mass spec. Any suggestions to improve diffraction would be welcome. Thanking you in advance. Theresa
Re: [ccp4bb] No diffraction
Maybe, you can adjust the ion strength of your condition. On Thu, Jan 26, 2012 at 8:32 AM, Kevin Jin kevin...@gmail.com wrote: For crystallization: Your xtal may come out a little bit fast. If the condition contain alcohol, such as IPA, you may have to modify it. If you let people know the condition, it may be more helpful. Also, please check the purity of your protein. Kevin On Thu, Jan 26, 2012 at 7:33 AM, Theresa H. Hsu theresah...@live.com wrote: Dear crystallographers I have a protein of 90 kDa forming dimers. Crystals formed with microbatch and vapor diffusion method in 24 hours but no diffraction at home source. Dissolved crystals was confirmed to be the protein with mass spec. Any suggestions to improve diffraction would be welcome. Thanking you in advance. Theresa
[ccp4bb] Coot on an SGI
Hi there we are trying to install Coot onto one of our old SGIs and so we installed Coot 0.0.33 (IRIX). However when starting Coot, such as in the Coot (install) directory, we get an error message stating thatlib libgcc_s.so is required but can not be found. We have the sgi freeware gcc_lib installed (the link on the Coot page to sgi.freeware, is dead ) but can only find libgcc_a in our gcc_lib. Can someone tell us how we can get hold of the right library? Thanks so much for any help Gina NOTICE: This email message is for the sole use of the intended recipient(s) and may contain confidential and privileged information. Any unauthorized review, use, disclosure or distribution is prohibited. If you are not the intended recipient, please contact the sender by reply email and destroy all copies of the original message.
Re: [ccp4bb] Introducing an ELN
Unless you have written on the paper using cursive script. Many schools in the US have stopped teaching longhand reading/writing so in a generation or two many paper records will be undecipherable to all but historians. My wife has some handwritten letters from ancestors written in German around 1920 that even Germans have great trouble reading today. The paper is holding up quite well though. ;-) Dale Tronrud On 01/26/12 08:30, Phoebe Rice wrote: As the proud owner of a carefully organized, highly annotated VMS backup tape (reel-to-reel, of course), my main concern is that paper is the only format that we'll be able to count on reading a decade (or more) from now. = Phoebe A. Rice Dept. of Biochemistry Molecular Biology The University of Chicago phone 773 834 1723 http://bmb.bsd.uchicago.edu/Faculty_and_Research/01_Faculty/01_Faculty_Alphabetically.php?faculty_id=123 http://www.rsc.org/shop/books/2008/9780854042722.asp Original message Date: Thu, 26 Jan 2012 16:50:04 +0100 From: CCP4 bulletin board CCP4BB@JISCMAIL.AC.UK (on behalf of Anastassis Perrakis a.perra...@nki.nl) Subject: Re: [ccp4bb] Introducing an ELN To: CCP4BB@JISCMAIL.AC.UK I think that all these points are interesting and valid. On Jan 25, 2012, at 10:37, Chris Morris wrote: Tassos reports: 1. None of the twenty test-users was satisfied with any of the two solutions - and each was annoyed for a different reason. This suggests that the choice of ELN is not the most difficult part of the adoption process. Maybe the test users at the NKI were annoyed by the idea of using an ELN at all. That would surely apply to some users. Some were actually very keen, and thats why they signed up for it. In my experience, the hardest part is ensuring that it provides benefits to the people who have to enter the data, and provides them early. The fact that it will make information retrieval easier in three years is not enough. I suggest focussing on electronic support for housekeeping: booking time on an instrument, finding the files the instrument created, ordering oligos, recording when you use the last of a reagent. Scientists work very independently in most respects, but they do have certain obligations that flow from sharing the lab space. You can make use of these to encourage compliance with the ELN. If you do, then most of the science will get recorded in passing. I think that this was exactly one of the problems. The ELNs we tested had no option for booking instruments, no way to find files from instruments let alone read them (it would support only TIF, JPEG, Doc, XLS, PDF), and would not do stock keeping: all these are thought to be out of the ELN scope. And that makes an ELN inherently less useful. Lack of instrument support is another issue: a machine that would allow us to import real chromatograms to ELN would be cool - alas, the solution that was suggested to us is to save as PDF or XLS and reload ...! (it took 3 weeks to come back with this great plan!) For the rest I have nothing much to say, I basically agree. A. I suggest also ensuring that it includes electronic tools that actually help. Two examples from PiMS are primer design, and automatically uploading and interpreting results from the Caliper GX instrument. It must allow round trips with spreadsheets, i.e. dump ELN data as a spreadsheet, edit it, upload it again. Despite their substantial disadvantages, some scientists will not give them up. It should also allow crossreferencing with paper note books. Some will continue to use a lab notebook. When they discover that the ELN serves as a searchable index to it, they will warm to the ELN. I suggest aiming for no paper at your lab progress meetings within say 12 months. When you reach that point, everything important is in the ELN. Before then, the ELN is not giving real value. You will need someone who is keen on the introduction of the ELN, to customise it, provide first line user support, and act as a single point of contact with the supplier. This might be a scientist or an IT person. I have also seen this done well by a technician, Delphine Chesnel when she was at the EMBL Hamburg. If you can't find such a champion, then introduction will not be successful. Some of the problem here is an own goal by the community: scientists are trained to use paper during their degrees, so ELNs are a controversial change of practice. One person who, unusually, began with an ELN told me how inconvenient it is now she works in a paper-based lab. PepTalk 2012 had a workshop on this topic. The
Re: [ccp4bb] Introducing an ELN
Can't you get a plug-in for that? JPK On Thu, Jan 26, 2012 at 11:35 AM, Dale Tronrud det...@uoxray.uoregon.edu wrote: Unless you have written on the paper using cursive script. Many schools in the US have stopped teaching longhand reading/writing so in a generation or two many paper records will be undecipherable to all but historians. My wife has some handwritten letters from ancestors written in German around 1920 that even Germans have great trouble reading today. The paper is holding up quite well though. ;-) Dale Tronrud On 01/26/12 08:30, Phoebe Rice wrote: As the proud owner of a carefully organized, highly annotated VMS backup tape (reel-to-reel, of course), my main concern is that paper is the only format that we'll be able to count on reading a decade (or more) from now. = Phoebe A. Rice Dept. of Biochemistry Molecular Biology The University of Chicago phone 773 834 1723 http://bmb.bsd.uchicago.edu/Faculty_and_Research/01_Faculty/01_Faculty_Alphabetically.php?faculty_id=123 http://www.rsc.org/shop/books/2008/9780854042722.asp Original message Date: Thu, 26 Jan 2012 16:50:04 +0100 From: CCP4 bulletin board CCP4BB@JISCMAIL.AC.UK (on behalf of Anastassis Perrakis a.perra...@nki.nl) Subject: Re: [ccp4bb] Introducing an ELN To: CCP4BB@JISCMAIL.AC.UK I think that all these points are interesting and valid. On Jan 25, 2012, at 10:37, Chris Morris wrote: Tassos reports: 1. None of the twenty test-users was satisfied with any of the two solutions - and each was annoyed for a different reason. This suggests that the choice of ELN is not the most difficult part of the adoption process. Maybe the test users at the NKI were annoyed by the idea of using an ELN at all. That would surely apply to some users. Some were actually very keen, and thats why they signed up for it. In my experience, the hardest part is ensuring that it provides benefits to the people who have to enter the data, and provides them early. The fact that it will make information retrieval easier in three years is not enough. I suggest focussing on electronic support for housekeeping: booking time on an instrument, finding the files the instrument created, ordering oligos, recording when you use the last of a reagent. Scientists work very independently in most respects, but they do have certain obligations that flow from sharing the lab space. You can make use of these to encourage compliance with the ELN. If you do, then most of the science will get recorded in passing. I think that this was exactly one of the problems. The ELNs we tested had no option for booking instruments, no way to find files from instruments let alone read them (it would support only TIF, JPEG, Doc, XLS, PDF), and would not do stock keeping: all these are thought to be out of the ELN scope. And that makes an ELN inherently less useful. Lack of instrument support is another issue: a machine that would allow us to import real chromatograms to ELN would be cool - alas, the solution that was suggested to us is to save as PDF or XLS and reload ...! (it took 3 weeks to come back with this great plan!) For the rest I have nothing much to say, I basically agree. A. I suggest also ensuring that it includes electronic tools that actually help. Two examples from PiMS are primer design, and automatically uploading and interpreting results from the Caliper GX instrument. It must allow round trips with spreadsheets, i.e. dump ELN data as a spreadsheet, edit it, upload it again. Despite their substantial disadvantages, some scientists will not give them up. It should also allow crossreferencing with paper note books. Some will continue to use a lab notebook. When they discover that the ELN serves as a searchable index to it, they will warm to the ELN. I suggest aiming for no paper at your lab progress meetings within say 12 months. When you reach that point, everything important is in the ELN. Before then, the ELN is not giving real value. You will need someone who is keen on the introduction of the ELN, to customise it, provide first line user support, and act as a single point of contact with the supplier. This might be a scientist or an IT person. I have also seen this done well by a technician, Delphine Chesnel when she was at the EMBL Hamburg. If you can't find such a champion, then introduction will not be successful. Some of the problem here is an own goal by the community: scientists are trained to use paper during their degrees, so ELNs are a controversial change of practice. One person who, unusually, began with an ELN told
Re: [ccp4bb] Problem with getting Rfree and Rf down
Merging in radiation damaged data can indeed raise R/Rfree because the structure factors no longer correspond to the native structure. Rather, they are an intensity-average of the native and damaged structures, and that can be hard to fit to a coordinate model! How much damage is too much? I'd say its when the change in the data or error due to damage becomes comparable with the lowest error you could hope to get when fitting a model to the native data: ~20-30% (R/Rfree). This generally happens after about 20-30 MGy (Banumathi et al. 2006; Owen et al, 2006; Kmetko et al. 2006). However, redundancy and radiation damage are not the same thing. Contrary to popular belief, it IS possible to take many many exposures from the same crystal without doing any more damage than the usual ~100 exposures. How? What manner of trickery is this? Simple! You use a shorter exposure time. Personally, I always think about redundancy or multiplicity in the context of a fixed crystal lifedose (http://dx.doi.org/10.1107/S0909049509004361). That is, you only get so many seconds of shutter-open time before the crystal is dead. So, to me, strategy is nothing more than deciding how to divide up those shutter-open seconds, and the only way to increase redundancy/multiplicity is to shorten the exposure time. Which, by the way, is almost always a good idea. -James Holton MAD Scientist On 1/24/2012 11:52 AM, Miguel Ortiz Lombardia wrote: El 24/01/12 18:56, Greg Costakes escribió: Whoops, I misspoke... I meant Rsym and Rmerge increase with higher redundancies. But then suppose that one merges data from a crystal that is degrading while exposed, sp the data gets degraded. This is not at all unusual. In the absence of a deep understanding of refinement, intuition suggests that degraded data should produce degraded models. If Rwork and Rfree are measuring anything useful they should go up redundancy in those not-so-unusual cases. Or intuition is misguiding me again. -- Miguel --- Greg Costakes PhD Candidate Department of Structural Biology Purdue University Hockmeyer Hall, Room 320 240 S. Martin Jischke Drive, West Lafayette, IN 47907 ** Hard work often pays of in time, but Procrastination always pays off now ** *From: *Dale Tronruddet...@uoxray.uoregon.edu *To: *Greg Costakesgcost...@purdue.edu *Cc: *CCP4BB@JISCMAIL.AC.UK *Sent: *Tuesday, January 24, 2012 12:43:43 PM *Subject: *Re: [ccp4bb] Problem with getting Rfree and Rf down Is this observation about redundancies a general rule that I missed? It seems rather surprising to me. What have results have others seen? Dale Tronrud On 01/24/12 07:23, Greg Costakes wrote: snip... Higher redundancies (7 or so) do tend to increase overall R/Rfree. snip... --- Greg Costakes PhD Candidate Department of Structural Biology Purdue University Hockmeyer Hall, Room 320 240 S. Martin Jischke Drive, West Lafayette, IN 47907 ** Hard work often pays of in time, but Procrastination always pays off now ** *From: *Sam Arnostimeisam.nosr...@gmail.com *To: *CCP4BB@JISCMAIL.AC.UK *Sent: *Monday, January 23, 2012 4:48:50 PM *Subject: *[ccp4bb] Problem with getting Rfree and Rf down Hi every one I have some crystals in the space group P3121. I collect 180 frames of data. My crystals do not diffract better than at most 2.0 angstrom, but the Rf barely goes below 23%, and Rfree also remains somewhere between 28-33%. I have tried to refine my data as much as I can. I do not know whether the problem is because of the bad diffraction or collecting extra frames. The structure factors are also high but they get better as the crystals diffract better. Thanks Sam
[ccp4bb] Job Posting on Behalf of Albert Einstein College of Medicine
*POST-DOCTORAL POSITION* Three post-doctoral positions are available to join a multi-disciplinary research group investigating the regulation of biological motors activity from the cellular to the molecular level. The group is formed by the laboratories of Gary Gerfen, Ao Ma, David Sharp and Hernando Sosa in the Department of Physiology and Biophysics of the Albert Einstein College of Medicine. For these positions the ideal candidates would have experience in the general areas of cell biology, structural biology, molecular simulation and statistical mechanics. Expertise with one or more of the following techniques will be required: protein expression and purification, cell imaging, electron paramagnetic resonance (EPR), electron microscopy and molecular dynamics simulations. For this project we have state of the art facilities present in each of the participating laboratories and at the core facilities of the Albert College of Medicine. These capabilities include EPR (PELDOR, high frequency, HYSCORE), several modalities of fluorescence microscopy (con-focal, epi, tirf, single-molecule polarization etc), cryo-electron microscopy and state-of-the-art Linux clusters for molecular simulations. All four laboratories in the group are located in the Albert Einstein College of Medicine in New York City, which offers excellent opportunities for stimulating and highly inter-disciplinary scientific interactions within the group, between theory/simulation and experiments, with the rest of the college and with many other scientific institutions in the New York area. Interested candidates please send an email letter, CV and reference names to either: Gary Gerfen (gary.ger...@einstein.yu.edu), Ao Ma (ao...@einstein.yu.edu), David Sharp (david.sh...@einstein.yu.edu), Hernando Sosa ( hernando.s...@einstein.yu.eduhttp://oneclick.jobtarget.com/Users/hsosa/AppData/Local/Microsoft/Windows/Temporary%20Internet%20Files/Content.Outlook/Q7O3XC8L/hernando.s...@einstein.yu.edu ). Yeshiva University is an equal opportunity employer committed to workforce diversity.
[ccp4bb] CCP4 win dev
Dear ccp4 win developers: I would like to compile Ian's EDSTAT program using my windows7/64 ifort compiler. I have a few questions re library linking and win-compliable source distribution - wonder who I may kindly harass off-board. Best regards, BR - Bernhard Rupp 001 (925) 209-7429 +43 (676) 571-0536 b...@ruppweb.org b...@hofkristallamt.org http://www.ruppweb.org/ - No animals were hurt or killed during the production of this email. -
Re: [ccp4bb] Coot on an SGI
Dear Gina: I think Coot 0.0.33 originated sometime early in the Nixon administration, and I finally parted with my SGIs a few years ago, so am not in a good position to advise. I seem vaguely to remember some non-canonical naming of the files. What happens if you make a symbolic link from the one you have to the one that is required? As I recall, coot on an SGI (at least on my R1, which I think has a processor almost as fast as that in my generation A iPod touch) was impossibly slow. By contrast, I can run the very latest svn revision of coot in stereo on a $270 Zalman monitor attached to a $600 mac mini. I'm sorry this doesn't answer your question, but I think an ancient version of coot on an ancient computer will just be a world of hurt. -- Bill William G. Scott Professor Department of Chemistry and Biochemistry and The Center for the Molecular Biology of RNA 228 Sinsheimer Laboratories University of California at Santa Cruz Santa Cruz, California 95064 USA On Jan 26, 2012, at 8:59 AM, Clayton, Gina wrote: Hi there we are trying to install Coot onto one of our old SGIs and so we installed Coot 0.0.33 (IRIX). However when starting Coot, such as in the Coot (install) directory, we get an error message stating thatlib libgcc_s.so is required but can not be found. We have the sgi freeware gcc_lib installed (the link on the Coot page to sgi.freeware, is dead ) but can only find libgcc_a in our gcc_lib. Can someone tell us how we can get hold of the right library? Thanks so much for any help Gina NOTICE: This email message is for the sole use of the intended recipient(s) and may contain confidential and privileged information. Any unauthorized review, use, disclosure or distribution is prohibited. If you are not the intended recipient, please contact the sender by reply email and destroy all copies of the original message.
[ccp4bb] Iphone app to display protein models
Dear All, I was wondering if there is any IOS5 based app to display protein models, which are not in public database, on Iphone. There is an app called Molecules for displaying models but that utilizes coordinates from RCSB and pubchem. Thanks, Shiva
Re: [ccp4bb] Iphone app to display protein models
On 01/27/2012 04:00 PM, Shiva Bhowmik wrote: Dear All, I was wondering if there is any IOS5 based app to display protein models, which are not in public database, on Iphone. Better than this: Jolecule from Dr. Bosco Ho. Jolecule works in HTML5 browsers such as Chrome and Safari, mostly in Firefox, and even on the iPad http://jolecule.appspot.com/ However, if you intend to keep your PDB secret, I'm not sure it is wise to use any webservice. Regards, Francois. There is an app called Molecules for displaying models but that utilizes coordinates from RCSB and pubchem. Thanks, Shiva
