Re: [ccp4bb] X-ray photon correlation length
Hi Both transverse and longitudinal coherence length need to be considered in this. These parameters are detemined by monochromators, focusing optics and the position of the specimen along the path not just the undulator (or x-ray generator). Matching to the specimen is not necessarily as simple as the dimensions of the mosaic blocks in the specimen. It is the optical path length which is important. One would have to consider the variation in refractive index between mosaic blocks and the surroundings. Cheers Colin -Original Message- From: CCP4 bulletin board on behalf of Ethan Merritt Sent: Thu 29/01/2009 19:24 To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] X-ray photon correlation length On Thursday 29 January 2009 10:59:23 Bernhard Rupp wrote: Ok, following seems to be correct: a) interaction length = mean free path : relevant for absorption b) correlation length = time correlation between photons : relevant for multi-photon scattering c) coherence length = longitudinal coherence length : relevant for single photon scattering. It follows from Heisenberg for a Lorentzian source (anode) with natural emisson line width per formula on p 5007 of Colin's ref Lc=(2/pi)lambda**2/delLambda Using 8084 eV and 2.1 eV respectively for Cu, I obtain ~3800 A coherence length for a Cu (anode) X-ray photon The pre-factor is different for other source types like synchrotron. The coherence length for an undulator source is the relativistically contracted length of the undulator. Ref: http://xdb.lbl.gov/Section2/Sec_2-1.html In any case I would accept the vague term of 'a few 1000 A' or 'several 1000 A' as a general statement for coherence length in materials where the interaction length is larger (practically always). Does this sound reasonable? My impression is that the coherence length from synchrotron sources is generally larger than the x-ray path through a protein crystal. But I have not gone through the exercise of plugging in specific storage ring energies and undulator parameters to confirm this impression. Perhaps James Holton will chime in again? Ethan From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On Behalf Of Nave, C (Colin) Sent: Thursday, January 29, 2009 10:14 AM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] X-ray photon correlation length Bernard I guess this came from Aren't detwinning methods appropriate only in the case of true twin domains which are larger than the X-ray photon correlation length in order for the assumption to be valid that |F|^2 from each domain can be summed? This wouldn't give rise to the apparent 'diffuse scatter' phenomenon. I think this is normally called coherence length. Probably best not to think of photons at all but waves (though there is an equivalent quantum mechanical treatment based, as V Nagarajan says, on the uncertainty principle). I don't think the domains have to be larger then the correlation (sorry coherence) length of the incident x-rays in any case. They have to be large enough to give an intensity which can be integrated. If smaller domains are present, the intensity just spread out a bit more.When the domains are very large, the size of the spots would be determined by the incident beam properties. The article cited some years ago on CCP4BB gives a primer on all this J. Phys.: Condens. Matter 16 (2004) 5003-5030 PII: S0953-8984(04)75896-8. Coherent x-ray scattering Friso van der Veen1,2 and Franz Pfeiffer1 http://www.iop.org/EJ/article/0953-8984/16/28/020/cm4_28_020.pdf?request-id= 8848d3f0-5a4b-4ffe-8ea4-c1eabfaf1657 Cheers Colin _ From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On Behalf Of Bernhard Rupp Sent: 29 January 2009 17:51 To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] X-ray photon correlation length I always wondered - how is the X-ray photon correlation length defined and where do I find it? This is not the interaction length, I assume. So, to the physicists: How large is the 'X-ray photon correlation length' for a given wavelength in a given material? I had the impression that the term photon correlation refers to the time correlation of the scattering such as in photon correlation spectroscopy. Best regards, BR 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
Re: [ccp4bb] X-ray photon correlation length
Bernhard Yes I stand corrected, 'coherence length' it is. I think I did mean 'coherence' and not 'correlation', it's just that I had 'correlation' on my mind from something else I was doing. What I need is a 'concept checker' in addition to a spelling grammar checker! -- Ian -Original Message- From: owner-ccp...@jiscmail.ac.uk [mailto:owner-ccp...@jiscmail.ac.uk] On Behalf Of Bernhard Rupp Sent: 29 January 2009 18:59 To: 'Nave, C (Colin)'; CCP4BB@JISCMAIL.AC.UK Subject: RE: [ccp4bb] X-ray photon correlation length Ok, following seems to be correct: a) interaction length = mean free path : relevant for absorption b) correlation length = time correlation between photons : relevant for multi-photon scattering c) coherence length = longitudinal coherence length : relevant for single photon scattering. It follows from Heisenberg for a Lorentzian source (anode) with natural emisson line width per formula on p 5007 of Colin's ref Lc=(2/pi)lambda**2/delLambda Using 8084 eV and 2.1 eV respectively for Cu, I obtain ~3800 A coherence length for a Cu (anode) X-ray photon The pre-factor is different for other source types like synchrotron. In any case I would accept the vague term of 'a few 1000 A' or 'several 1000 A' as a general statement for coherence length in materials where the interaction length is larger (practically always). Does this sound reasonable? BR From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On Behalf Of Nave, C (Colin) Sent: Thursday, January 29, 2009 10:14 AM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] X-ray photon correlation length Bernard I guess this came from Aren't detwinning methods appropriate only in the case of true twin domains which are larger than the X-ray photon correlation length in order for the assumption to be valid that |F|^2 from each domain can be summed? This wouldn't give rise to the apparent 'diffuse scatter' phenomenon. I think this is normally called coherence length. Probably best not to think of photons at all but waves (though there is an equivalent quantum mechanical treatment based, as V Nagarajan says, on the uncertainty principle). I don't think the domains have to be larger then the correlation (sorry coherence) length of the incident x-rays in any case. They have to be large enough to give an intensity which can be integrated. If smaller domains are present, the intensity just spread out a bit more.When the domains are very large, the size of the spots would be determined by the incident beam properties. The article cited some years ago on CCP4BB gives a primer on all this J. Phys.: Condens. Matter 16 (2004) 5003-5030 PII: S0953-8984(04)75896-8. Coherent x-ray scattering Friso van der Veen1,2 and Franz Pfeiffer1 http://www.iop.org/EJ/article/0953-8984/16/28/020/cm4_28_020.p df?request-id=8848d3f0-5a4b-4ffe-8ea4-c1eabfaf1657 Cheers Colin From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On Behalf Of Bernhard Rupp Sent: 29 January 2009 17:51 To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] X-ray photon correlation length I always wondered - how is the X-ray photon correlation length defined and where do I find it? This is not the interaction length, I assume. So, to the physicists: How large is the 'X-ray photon correlation length' for a given wavelength in a given material? I had the impression that the term photon correlation refers to the time correlation of the scattering such as in photon correlation spectroscopy... Best regards, BR 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 Scanned by iCritical. Disclaimer This communication is confidential and may contain privileged information intended solely for the named
Re: [ccp4bb] difficult MAD dataset
Hi Alison, You wrote: We recently collected a complete 2.5A MAD dataset. However, finding a solution has not been as straightfoward for reasons unclear to us. Is there radiation damage in one or more of the later sets? Did you try 1 or 1.5 wavelength? (See Dauter, /Acta Cryst./ (2002). D*58*, 1958) Best wishes, Bram *Bram Schierbeek* Application Scientist Structural Biology Bruker AXS B.V. Oostsingel 209, P.O.Box 811 2600 AV Delft, the Netherlands Tel.: +31 (15) 2152508 Fax:+31 (15)2152599 bram.schierb...@bruker-axs.nl _www.bruker-axs.com_ www.bruker-axs.de
Re: [ccp4bb] OT: VectorNTI alternatives
On Jan 28, 2009, at 3:47 AM, Darren Hart wrote: ps anyone using VNTI might consider a backup of their work by exporting files to .gb format. I don't know if a locked up (expired) version permits this and you will have no notice that it is about to expire. My license recently expired. I had been running VectorNTI on my Mac through a Windows virtual machine. When the license ran out, I was unable to export any of the sequences that I had created. Now, if there was only a way to turn back time so that my computer thought it was still 2008 ... ehm ... ;) Jeff
Re: [ccp4bb] OT: VectorNTI alternatives
Hello, I spoke to Invitrogen (France) today and they said that, if asked, they would provide a 2 month free license so that people could do exactly this and recover their files. The also said they would send me details on a simple procedure to extract the data from a locked version which I will post on the bb. They told me they have 100,000 users - so hardly a minor specialist application! At €650-€4000 per license, that looks quite fruitful for them. An earlier poster made the point that it is a good thing to pay for good software. I agree and don't want to seem like a moaner, but I object to the strategy employed here on this occasion. Hence my original post to find out what the alternatives are. Darren 2009/1/30 Jeffrey Wilson wil...@ucmail.uc.edu On Jan 28, 2009, at 3:47 AM, Darren Hart wrote: ps anyone using VNTI might consider a backup of their work by exporting files to .gb format. I don't know if a locked up (expired) version permits this and you will have no notice that it is about to expire. My license recently expired. I had been running VectorNTI on my Mac through a Windows virtual machine. When the license ran out, I was unable to export any of the sequences that I had created. Now, if there was only a way to turn back time so that my computer thought it was still 2008 ... ehm ... ;) Jeff -- ** Dr. Darren Hart, Team Leader High Throughput Protein Lab Grenoble Outstation European Molecular Biology Laboratory (EMBL) ** EMBL webpages: http://tinyurl.com/6xdltl http://tinyurl.com/667jrp Email: h...@embl.fr Tel: +33 4 76 20 77 68 Fax: +33 4 76 20 71 99 Skype: hartdarren Postal address: EMBL, 6 rue Jules Horowitz, BP181, 38042 Grenoble, Cedex 9, France **
Re: [ccp4bb] Nvidia 3D
Warren, If we are buying a system from scratch, can I get the GeForce 2 card and 3D bundle and have it work for winCoot? Scott On Tue, Jan 27, 2009 at 2:58 PM, Warren DeLano war...@delsci.com wrote: https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind0901L=CCP4BBT=0F=S =P=192056https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind0901L=CCP4BBT=0F=S=P=192056 https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind0901L=CCP4BBT=0F=; S=P=192056https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind0901L=CCP4BBT=0F=S=P=192056 -Original Message- From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On Behalf Of Chris Waddling Sent: Tuesday, January 27, 2009 12:56 PM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] Nvidia 3D Has anyone taken the plunge and tried this setup with Coot or PyMol? Seems interesting: http://www.nvidia.com/object/GeForce_3D_Vision_Main.html Chris -- Dr. Christopher A. Waddling, Ph.D. University of California at San Francisco MC 2140 S126C 600 16th St., San Francisco, CA 94158-2517 (415) 476-8288 (office) (415) 502-7779 (lab) (415) 514-4142 (fax) (415) 810-7556 (cell) waddl...@msg.ucsf.edu AIM duckie2k1 Skype chriswaddling -- Scott D. Pegan, Ph.D. Senior Research Specialist Center for Pharmaceutical Biotechnology University of Illinois at Chicago
Re: [ccp4bb] Nvidia 3D
If we are buying a system from scratch, can I get the GeForce 2 card and 3D bundle and have it work for winCoot? I very much doubt it. If I understand it correctly this systems only works with DirectX applications. Since (Win)Coot uses OpenGL rather than DirectX it is unlikely to work (although there seem to be some emulators around, but who knows what they do). Furthermore the 3D bundle requires the application to run in full screen mode, which is currently not available for (Win)Coot. So I guess we need to wait a bit longer and hope that Nvidia (or whoever else) comes up with a proper quad-buffered, OpenGL solution for LCD 3D viewing. Bernhard On Tue, Jan 27, 2009 at 2:58 PM, Warren DeLano war...@delsci.com mailto:war...@delsci.com wrote: https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind0901L=CCP4BBT=0F=S =P=192056 https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind0901L=CCP4BBT=0F=S=P=192056 https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind0901L=CCP4BBT=0F=; S=P=192056 https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind0901L=CCP4BBT=0F=S=P=192056 -Original Message- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Chris Waddling Sent: Tuesday, January 27, 2009 12:56 PM To: CCP4BB@JISCMAIL.AC.UK mailto:CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] Nvidia 3D Has anyone taken the plunge and tried this setup with Coot or PyMol? Seems interesting: http://www.nvidia.com/object/GeForce_3D_Vision_Main.html Chris -- Dr. Christopher A. Waddling, Ph.D. University of California at San Francisco MC 2140 S126C 600 16th St., San Francisco, CA 94158-2517 (415) 476-8288 (office) (415) 502-7779 (lab) (415) 514-4142 (fax) (415) 810-7556 (cell) waddl...@msg.ucsf.edu mailto:waddl...@msg.ucsf.edu AIM duckie2k1 Skype chriswaddling -- Scott D. Pegan, Ph.D. Senior Research Specialist Center for Pharmaceutical Biotechnology University of Illinois at Chicago
Re: [ccp4bb] temperature after 30 minutes using microscopes ?
On Jan 21, 2009, at 6:35 PM, matthew.frank...@imclone.com wrote: My light source is halogen, but it's coupled to the microscope through a fiber optic light pipe. I know from experience that the older model scopes with the bulb right in the base get quite warm after they've been on for a while. I'm pretty sure my fiber optic setup can be retrofitted to most microscopes... We have a Olympus microscope with fiber optic light source. We intentionally purchased this because of past experiences with standard bases heating up. So far, our experience is similar to Matt's in that the base rarely heats up to any significant degree. Jeff Jeffrey Wilson, Ph.D. University of Cincinnati College of Medicine Molecular Genetics Department 231 Albert Sabin Way MSB 3109A Cincinnati, OH 45267-0524 (513) 558-1360
Re: [ccp4bb] difficult MAD dataset
Alison, Given: There is a pseudo-translation with 55 % peak at a fractional coordinate of 0.5, 0.5, 0.48. I don't think you can be certain about: Systematic absences along a and b axis were observed thus the dataset was scaled in P21212 space group. Try testing all eight possible Ortho. sp. grps, and also be prepared to consider P2 or P21. The pseudo-centring you see in the self-Patterson would seem to be consistent w/ I222 (or very unlikely, I212121), or perhaps (C222 or C2221) with NCS? From Berhnard's Matthews Coeff. calc. (http://www.ruppweb.org/Mattprob/): +--- --+ | N(mol) Prob(N) Prob(N)Vm Vs Mw | | for resolution overall A**3/Da % solvent Da | +--- --+ | 1 0.0021 0.0027 10.77 88.58 9900.00 | | 2 0.0033 0.00535.38 77.1519800.00 | | 3 0.0662 0.09203.59 65.7329700.00 | | 4 0.4170 0.45502.69 54.3139600.00 | | 5 0.4861 0.42672.15 42.8849500.00 | | 6 0.0233 0.01561.79 31.4659400.00 | | 7 0.0021 0.00271.54 20.0469300.00 | +--- --+ It looks like you have a higher symmetry (centered) space group, or you have NCS. Is your heavy atom search space group agnostic? Dave David Borhani, Ph.D. D. E. Shaw Research, LLC 120 West Forty-Fifth Street, 39th Floor New York, NY 10036 david.borh...@deshawresearch.com 212-478-0698 http://www.deshawresearch.com
Re: [ccp4bb] OT: VectorNTI alternatives
I'm not sure if it was already mentioned, but for those who use Vector NTI's ContigExpress to assemble and analyze sequencing data, the Staden package (http://staden.sourceforge.net/) is a great alternative. Cheers, Thomas
Re: [ccp4bb] difficult MAD dataset
Dear Alison, Christian Dumas of our institute has recently developed and published a program for HA detection. Being extremely powerful, and easy to use (http://www.cbs.cnrs.fr/SP/crystal/SUPERFLIP/), it has produced very precise HA positions for datasets that no other program could treat previously. Even space group issues may be overcome by simply working in P1. It's frankly quite an astonishing piece of software. Good luck Stefan == Stefan T. Arold, PhD Centre de Biochimie Structurale CNRS UMR 5048 - UM 1 - INSERM UMR 554 29 rue de Navacelles 34090 MONTPELLIER Cedex - France email: stefan.ar...@cbs.cnrs.fr Phone: +33 (0)4.67.41.77.02 Fax: +33 (0)4.67.41.79.13 == - Original Message - From: Alison Li alis...@sfu.ca To: CCP4BB@JISCMAIL.AC.UK Sent: Thursday, January 29, 2009 10:37 PM Subject: [ccp4bb] difficult MAD dataset We recently collected a complete 2.5A MAD dataset. However, finding a solution has not been as straightfoward for reasons unclear to us. We would be grateful for any helpful advice or suggestions. The thin plate shaped crystal was grown from a relatively small protein (90 residues). The crystal diffracted well with visible and defined reflections up to ~2.8A range. With both HKL2000 and mosflm, initial indexing indicated orthorhombic unit cell with dimension of 52 x 82 x 100. Systematic absences along a and b axis were observed thus the dataset was scaled in P21212 space group. The unit cell dimension and space group suggested 4 protein chains per ASU. There is a pseudo-translation with 55 % peak at a fractional coordinate of 0.5, 0.5, 0.48. There are 7 methionines per chain. Thus we expect 28 Se per ASU. Mass spectroscopy and fluoresence scan both confirmed successful incorporation of Se-methionine in the crystal. According to xtriage, anomalous signal extended to 3.0A at least in the peak dataset (The table of measurability as a function of resolution is shown below). unused: - 43.0868 [ 0/5 ] bin 1: 43.0868 - 5.3953 [2751/2902] 0.5838 bin 2: 5.3953 - 4.2836 [2893/2905] 0.4575 bin 3: 4.2836 - 3.7425 [2891/2899] 0.2820 bin 4: 3.7425 - 3.4005 [2888/2896] 0.1898 bin 5: 3.4005 - 3.1568 [2864/2898] 0.1222 bin 6: 3.1568 - 2.9708 [2835/2898] 0.0653 bin 7: 2.9708 - 2.8220 [2777/2906] 0.0458 bin 8: 2.8220 - 2.6992 [2714/2902] 0.0226 bin 9: 2.6992 - 2.5953 [2550/2865] 0.0168 bin 10: 2.5953 - 2.5057 [2307/2914] 0.0071 unused: 2.5057 - [ 0/0 ] However, HA search using hkl2map, Autosol, and Autosharp resulted in only 3~4 HA sites. When hkl2map was used, most HA sites had poor CC and Patterson FOM and did not clearly stand out as they normally should. Structural homologs suggest that the protein has a compact single core domain comprised of 4 a-helices. The positions of most HAs are unlikely to be located in the flexible region. If any abnormalies are seen with the dataset, it's during scaling step in HKL2000. Chi2 is unusually high at lower resolution (Chi2 is 3 from 3.5A as shown below) and there is a relatively high percentage of rejections (1.5 %). Shell Lower Upper Average Average Norm. Linear Square limitAngstrom I error stat. Chi**2 R-fac R-fac 50.00 5.38 4299.077.349.0 7.886 0.076 0.085 5.38 4.27 2938.752.735.0 5.843 0.083 0.090 4.27 3.73 2314.245.933.5 3.935 0.082 0.084 3.73 3.39 1245.334.428.9 2.838 0.101 0.094 3.39 3.15 658.628.125.9 1.957 0.132 0.127 3.15 2.96 451.927.125.7 1.322 0.157 0.138 2.96 2.82 307.227.126.3 1.001 0.201 0.169 2.82 2.69 253.128.828.1 0.866 0.225 0.193 2.69 2.59 199.331.531.0 0.801 0.262 0.233 2.59 2.50 159.534.734.4 0.688 0.292 0.261 All reflections 1312.939.031.9 2.748 0.100 0.089 Xtriage also complains that there are abnormal intensities at some resolution ranges. Finally, the crystallization requires CdSO4, so we suspect that cadmium ions are incorporated in the crystal. If so, we suspect there may be weak anomalous signal contribution from Cd as well. In summary, we appear to have a complete dataset that shows strong anomalous signal. However it appears that we have overlooked something or there is an unusual crystallographic issue that we are not aware of. Any suggestions will be very much appreciated. Alison Li Graudate student, Dr. Mark Paetzel's group Simon Fraser University, BC, Canada
[ccp4bb] Job opportunity: Systems Specialist II - Automation, Protein Crystallography
For more than 30 years, Genentech has been at the forefront of the biotechnology industry, using human genetic information to develop novel medicines for serious and life-threatening diseases. Today, Genentech is among the world's leading biotech companies, with multiple therapies on the market for cancer and other serious medical conditions. Please take this opportunity to learn about Genentech, where we believe that our employees are our most important asset. The following opportunity exists in our South San Francisco, CA, headquarters: Systems Specialist II - Automation, Protein Crystallography Responsibilities: We are seeking a highly collaborative and mechanically adept individual to join the Genentech protein crystallography group, consisting of approximately 20 scientists, research associates, and postdoctoral fellows engaged in structure determination of proteins and protein-ligand complexes of therapeutic interest. The successful candidate will have primary responsibility for maintaining and improving our in-house X-ray crystallography facility, which currently consists of X-ray generators and detectors, automated crystal imaging systems, and robotic crystallization equipment. The individual will be the primary contact for vendor-assisted troubleshooting and will perform daily and preventative maintenance. The individual will have the opportunity to collaborate on diverse projects by assisting with in-house data collection. Requirements: This position requires a Bachelor's degree in Engineering, Physics, or a relevant discipline and three years of experience in an industrial or crystallography/automation environment. Practical mechanical aptitude and attention to detail are required. Experience in troubleshooting robotic equipment and/or X-ray equipment is preferred. Experience in computer programming and X-ray software is a plus. Strong teamwork, collaboration and communication skills are essential. Genentech is dedicated to fostering an environment that is inclusive and encourages diversity of thought, style, skills and perspective. Do not reply to this e-mail. To learn more about our current opportunities, please visit: http://careers.gene.com and reference Req. #126110. Please use Web - CCP4 when a source is requested. Again, please do not reply to this e-mail. Genentech is an Equal Opportunity Employer.
Re: [ccp4bb] Transfer Rfree flag
Can someone tell me if there is a relatively straightforward way of transferring Free R flags between two CNS format reflection files ? DATAMAN - http://xray.bmc.uu.se/usf/dataman_man.html#S63 --dvd ** Gerard J. Kleywegt Dept. of Cell Molecular Biology University of Uppsala Biomedical Centre Box 596 SE-751 24 Uppsala SWEDEN http://xray.bmc.uu.se/gerard/ mailto:ger...@xray.bmc.uu.se ** The opinions in this message are fictional. Any similarity to actual opinions, living or dead, is purely coincidental. **
Re: [ccp4bb] sparse matrix screen design
Are there any good free programs for the design of one's own sparse matrix screens? I am looking for something in the lines of a set of mixtures of what gives you the best coverage of, say, seven variables with five states each in 96 experiments. If memory serves, both Stefan Knight (stefan.kni...@molbio.slu.se) and Charles Carter The Younger (car...@med.unc.edu) have written programs to do this. --dvd ** Gerard J. Kleywegt Dept. of Cell Molecular Biology University of Uppsala Biomedical Centre Box 596 SE-751 24 Uppsala SWEDEN http://xray.bmc.uu.se/gerard/ mailto:ger...@xray.bmc.uu.se ** The opinions in this message are fictional. Any similarity to actual opinions, living or dead, is purely coincidental. **
Re: [ccp4bb] X-ray photon correlation length
Ethan Merritt wrote: My impression is that the coherence length from synchrotron sources is generally larger than the x-ray path through a protein crystal. But I have not gone through the exercise of plugging in specific storage ring energies and undulator parameters to confirm this impression. Perhaps James Holton will chime in again? Hmm. I think I should point out that (contrary to popular belief) I am not a physicist. I am a biologist. Yup. BS and PhD both in biology. However, since I work at a synchrotron I do have a lot of physicists and engineers around to talk to. Guess some of it has rubbed off. I passed Bernhard's question along to Howard Padmore (who is definitely a physicist) here at ALS and he gave me a very good description of the longitudinal coherence length, similar to that provided by Colin's posted reference: coherence_length = lambda^2/delta-lambda This made a lot of sense to me until I started to consider what happens if lambda ranges from 1 to 3 A, like it does in Laue diffraction. One might expect from this formula that the coherence length would be very small, smaller than a typical protein unit cell, and then you would predict that none of the scattering from any of the unit cells interferes with each other and that you should see the molecular transform in the diffraction pattern. But the oldest observation in crystallography is that Laue patterns have sharp spots. You don't see the molecular transform, despite how nice that would be (no more phase problem!). I think the coherence length is related to how TWO different photons can interfere with each other, and this is a rare event indeed. It has nothing to do with x-ray diffraction as we know it. No matter how low your flux is, even one photon per second, you will eventually build up the same diffraction pattern you get at 10^13 photons/s. Colin is right that photons should be considered as waves and on the length scale of unit cells, it is a very good approximation to consider the electromagnetic wave front coming from the x-ray source to be a flat plane, as Bragg did in his famous construction. So, I think perhaps Bernhard asked the wrong question? I think the question should have been how far apart can two unit cells be before they stop interfering with each other? The answer to this one is: quite a bit. Consider a silicon crystal (like the ones in my monochromator). These things are about 10 cm across, but every atom is in perfect alignment with every other. It is one single mosaic domain that you can hold in your hand. And as soon as you shine an x-ray beam on a large perfect crystal, lots of weird stuff happens. Unlike protein crystals the scattering of the x-rays is so strong that the scattered wave not only depletes the incoming beam (it penetrates less than 1 mm and is nearly 100% reflected), but this now very strong diffracted ray can reflect again on its way out of the crystal (off of the same HKL index, but different unit cells). Then some of that secondarily-diffracted ray will be in the same direction as the main beam, and interfere with it (extinction). Accounting for all of this is what Ewald did in his so-called dynamical theory of diffraction. The important thing to remember about perfect crystals is that a SINGLE PHOTON interacting with my 10 cm wide silicon crystal will experience all these dynamical effects. It doesn't matter what the coherence length is. Now, if a perfect crystal is really really small (much smaller than the interaction length of scattering), then there is no opportunity for the re-scattering and extinction and all that weird stuff to happen. In this limiting case, the scattered intensity is simply proportional to the number of unit cells in the beam and also to |F|^2. This is the basic intensity formula that Ewald showed how to integrate over all the depleting beams and re-scattering stuff to explain a large perfect crystal. As I understand it, the fact that there were large, macroscopic single crystals that were found to still obey the formula for a microscopic crystal came as something of a shock in the time of Darwin and Ewald. They explained this observation by supposing that these crystals were ideally imperfect and actually made up of lots of little perfect crystals that were mis-oriented with respect to one another enough so that the diffracted ray from one would be very unlikely to re-reflect off of another mosaic domain before it left the crystal. Protein crystals are a very good example of ideally imperfect crystals. I'm not sure where this rumor got started that the intensity reflected from a mosaic block or otherwise perfect lattice is proportional to the square of the number of unit cells. This is never the case. The reason is explained in Chapter 6 of M. M. Woolfson's excellent textbook, but the long and short of it is: yes the instantaneous intensity
[ccp4bb] Refmac5.scripts error -
All: I'm trying to get the latest version of Refmac up and running - the one bundled into ccp4 6.1.0 - and have come across an error I've never seen before: #CCP4I TERMINATION STATUS 0 Error from script /usr/local/ccp4-6.1.0/ccp4-6.1.0/ccp4i/scripts/refmac5.script: can't read space_group: no such variable #CCP4I TERMINATION TIME 29 Jan 2009 18:23:02 #CCP4I TERMINATION OUTPUT_FILES /home/caruthej/bo3/ccp4/bo3A_71_Unspecified.refmac.cif bo3A #CCP4I MESSAGE Task failed I found that this error is mentioned on the problems page for ccp4 version 5.0 - 5.0.2 and the suggested fix is to apply the following patch: ftp://ftp.ccp4.ac.uk/ccp4/5.0.2/patches/CCP4_utils-25Aug2004.tcl.diff to the scripts directory. Does anyone know if the same patch can be used to fix this error for the latest version of Refmac5 that's bundled into ccp4 6.1.0 as well as the version that was available in 2004 when the patch was created? Sorry for the simplistic question, but I don't have permission to install or modify programs on the system I'm using so I can't readily perform the experiment and the IT guy wants to know if anybody has any experience using this patch with the latest version of Refmac5 before he starts monkeying around with it. thanks, Jon Caruthers Stowell Lab University of Colorado
Re: [ccp4bb] mapping sequence conservation metrics on the B factor column ...
Hi Tassos, I very much like Homolmapper: http://www.mcb.ucdavis.edu/faculty-labs/lagarias/homolmapper_home/homolmapper%20web%20page.htm You can map several conserved properties onto your structures, not just plain sequence. Best, Miguel Le 29 janv. 09 à 22:25, Anastassis Perrakis a écrit : Dear all, I was wondering what is the state of the art for this old dark art ... are there any good servers / programs that allow to easily upload your own sequence alignments or create a 'transparent' alignment (I want to see the alignment first and not a total black box) and then allow you to write out sequence conservation based either on identity or in e.g a Dayhoff matrix on the B factor column for displaying it later in eg Pymol? To be clear I do not want a structural alignment, but mapping sequence alignment of eg a family to a single structure of a family member. Thanks in advance, Tassos -- This message has been scanned for viruses and dangerous content by MailScanner, and is believed to be clean. -- Miguel Ortiz Lombardía Architecture et Fonction des Macromolécules Biologiques UMR6098 ( CNRS, U. de Provence, U. de la Méditerranée ) Case 932 163 Avenue de Luminy 13288 Marseille cedex 9 France Tel : +33(0) 491 82 55 93 Fax: +33(0) 491 26 67 20 e-mail: miguel.ortiz-lombar...@afmb.univ-mrs.fr Web: http://www.pangea.org/mol/spip.php?rubrique2 -- This message has been scanned for viruses and dangerous content by MailScanner, and is believed to be clean.
