Re: [ccp4bb] combine Se-SAD phase with Model-phase
This is only a suggestion but sometimes it helps. First idea - try as hard as you can to extend the native data - at 3.6A resolution all model building is extremely hard! To work with what you have I would do this - others may have different ideas. Combine both data sets into one mtz file, and include your SHARP phasing PHIB FOM HLA etc (not solvent flattened yet) run DM with averaging for the homodimer, using the native F to 3.6A and the SHARP phases - this will extend your phases to 3.6A You will have to be a bit clever to only average over the homo-dimer and not the second component. You will need a mask covering one molecule (A say) and the transformation matrix which converts A to B. There is documentation to explain this With luck that should improve the map. Then I would refine your existing model, with the phase restraints HLADM etc using REFMAC. This will give you combined output phases and the resultant maps SHOULD improve.. But as I said - at 3.6A you will not get a very clear ma and it will be tricky to build extra residues. The Se markers should help.. Eleanor Raja Dey wrote: Hi, It would be of great help if you can give some suggestion on the following problem. I have two data sets of a complex molecule. One is native (3.6A) and the other is Se-der (4.5A). In one complex molecule I have one homo-dimer in complex with DNA( 2 times 90 aa + 2 times 15 na = ~MW 28000, call it as component 1) plus a second long helical protein(130 aa, call it as component 2). I have two such complex molecule in the AU (space gr. P65). I got a very good solution by PHASER(using native data) for the component 1, but component 2 has some ambiguity. I used the solution of component 1 and Se-der data to create Ano-diff Fourier map from model phase. I got clear peaks at 3.5 sigma exactly at the Met-S positions. I pulled out 11 Se sites, 9 of which are precisely exists at the right positions looked upon the model component 1). Other 2 are expecting on the two copy of component 2. What I did next? 1. I used CNS to create both SAD phase from Se and Model phase from component 1 and then combined them. Used the combine HL co-eff to run density modification and create 2Fo-Fc map. Very poor quality, but you can see some features. 2. Used only SAD phase from Se sites and run density modification followed by 2Fo-Fc map generation. Useless map. 3. Run SHARP/AutoSHARP with Se sites upto DM. Then run solvent flattening with model component 1. No good map. Do you know any other way to go from here? Running rigid.inp, anneal.inp, minimize.inp and bgroup.inp sequentially with the component 1 I reached R/R(free) 40%/45%. Any suggestion is well appreciated. Regards... Raja From Chandigarh to Chennai - find friends all over India. Go to http://in.promos.yahoo.com/groups/citygroups/
Re: [ccp4bb] combine Se-SAD phase with Model-phase
On Thu, May 08, 2008 at 07:26:40AM +0530, Raja Dey wrote: 3. Run SHARP/AutoSHARP with Se Just run autoSHARP in SIRAS mode: you have a native and a derivative (Se). autoSHARP is clever enough to then assign those special Se-S atoms to you derivative, see the explanation at http://www.globalphasing.com/sharp/manual/chapter2.html#MADnative which is for MAD and SHARP, but you'll get the idea also for autoSHARP. This way you get the anomalous and 'isomorphous' differences as signal. sites upto DM. Then run solvent flattening with model component 1. What do you mean with model component 1? Did you include your curent model into the density modification step (good idea)? For how many cycles - and what was the initial CC for the model here? If your anomalous signal of the Se is very weak and borderline you could try and use the model phases as a restraint in SHARP during refinement and LLG map calculation (not for the phasing step!). There are tools in SHARP for that as well. Another trick I use quite often is to estimate the anisotropic B-factor of your data (reference dataset in SHARP jargon): this would take out any anisotropy that you have, leading to more isotropic maps going into density modification - and that could make a lot of difference, since most real-space modificaitons in density modifcation assume some normal shape for electron density (or at least could be thrown off by severe anisotropy). But you have to be careful when dealing with low-resolution data and/or incomplete data (wedges missing etc). Let me know if you need additional info ... Cheers Clemens -- *** * Clemens Vonrhein, Ph.D. vonrhein AT GlobalPhasing DOT com * * Global Phasing Ltd. * Sheraton House, Castle Park * Cambridge CB3 0AX, UK *-- * BUSTER Development Group (http://www.globalphasing.com) ***
[ccp4bb] Ferritin crystallisation
Dear all, scanning the literature, it seems that horse spleen Ferritin has so far been crystallised only in presence of Cadmium ions. Is this correct? Does anybody know of conditions lacking Cd? Clemens
[ccp4bb] Post-Doctoral Opportunity in Oulu, Finland
Post-Doctoral Opportunity in Oulu, Finland A post-doctoral opportunity, funded by the Sigrid Juselius Foundation, exists in our group for an initial period of approximately 1 year, with possible extension. The work will involve structural studies on proteins important for the function of the human nervous system, mainly proteins from the myelin sheath. The successful candidate will have extensive hands-on experience on at least some of the following: large-scale expression and purification of recombinant proteins, membrane protein purification and characterisation, protein crystallisation, X-ray crystallography, small-angle X-ray scattering. Any further relevant experience will also be considered an asset. A large number of ready-to-use expression clones for the target proteins exists in the lab. The University of Oulu is the largest university in Northern Finland. The Department of Biochemistry is fully equipped for protein structural biology work, and we have frequent access to European synchrotrons for data collection. To apply, please send me an email with a full CV (including list of publications) plus the contact details of at least two scientists for references. More information can be found at www.biochem.oulu.fi/kursula. Informal queries by email are also welcome. Best regards, Petri --- Petri Kursula, Ph.D. Academy Research Fellow Docent of Neurobiochemistry Department of Biochemistry University of Oulu Oulu, Finland [EMAIL PROTECTED] cc.oulu.fi/~pkursula www.biochem.oulu.fi/kursula ---
[ccp4bb] stereo with Nvidia Quadro
Good day, I have been trying to enable stereo mode on a PC (SuSE10.1) with an NVIDIA NV37GL [Quadro FX 330/Quadro NVS280] graphics card (according to Xorg.0.log). (--) PCI:*(5:0:0) nVidia Corporation NV37GL [Quadro FX 330/Quadro NVS280] rev 162, Mem @ 0xdd00/24, 0xc000/28, 0xde00/24, BIOS @ 0xdfc0/17 (II) NVIDIA(0): NVIDIA GPU Quadro NVS 280 PCI-E at PCI:5:0:0 (GPU-0) Accroding to some web page about O, the options are set to (**) NVIDIA(0): Option Stereo 3 (**) NVIDIA(0): Option NvAGP 1 (**) NVIDIA(0): Option IgnoreEDID false (**) NVIDIA(0): Option UseEdidFreqs true Yet, the log file says (WW) NVIDIA(0): Stereo is only available on Quadro cards (II) NVIDIA(0): Disabling stereo. I was wondering whether anyone could explain what is so un-Quadro about this card? (Currently, the display is an LCD, but the same messages came up when the display was a CRT) Thank you for your help, Tim -- Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A
Re: [ccp4bb] stereo with Nvidia Quadro
The nVidia cards used for stereo are the Quadro FX series. The Quadro NVS series are for running multiple monitors, but not fancy 3D graphics. You can explore the manufacturer's web site for details. - === With the single exception of Cornell, there is not a college in the United States where truth has ever been a welcome guest - R.G. Ingersoll === David J. Schuller modern man in a post-modern world MacCHESS, Cornell University [EMAIL PROTECTED] On Thu, 2008-05-08 at 15:01 +0200, Tim Gruene wrote: Good day, I have been trying to enable stereo mode on a PC (SuSE10.1) with an NVIDIA NV37GL [Quadro FX 330/Quadro NVS280] graphics card (according to Xorg.0.log). (--) PCI:*(5:0:0) nVidia Corporation NV37GL [Quadro FX 330/Quadro NVS280] rev 162, Mem @ 0xdd00/24, 0xc000/28, 0xde00/24, BIOS @ 0xdfc0/17 (II) NVIDIA(0): NVIDIA GPU Quadro NVS 280 PCI-E at PCI:5:0:0 (GPU-0) Accroding to some web page about O, the options are set to (**) NVIDIA(0): Option Stereo 3 (**) NVIDIA(0): Option NvAGP 1 (**) NVIDIA(0): Option IgnoreEDID false (**) NVIDIA(0): Option UseEdidFreqs true Yet, the log file says (WW) NVIDIA(0): Stereo is only available on Quadro cards (II) NVIDIA(0): Disabling stereo. I was wondering whether anyone could explain what is so un-Quadro about this card? (Currently, the display is an LCD, but the same messages came up when the display was a CRT) Thank you for your help, Tim -- Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A
Re: [ccp4bb] stereo with Nvidia Quadro
Dear David, thank you for your answer. Do you (or anyone on the list) know if any FX-card would work with NuVision 60GX (like FX370, FX570), or only the dear ones (FX1400 and above)? Tim -- Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A On Thu, 8 May 2008, David J. Schuller wrote: The nVidia cards used for stereo are the Quadro FX series. The Quadro NVS series are for running multiple monitors, but not fancy 3D graphics. You can explore the manufacturer's web site for details. - === With the single exception of Cornell, there is not a college in the United States where truth has ever been a welcome guest - R.G. Ingersoll === David J. Schuller modern man in a post-modern world MacCHESS, Cornell University [EMAIL PROTECTED] On Thu, 2008-05-08 at 15:01 +0200, Tim Gruene wrote: Good day, I have been trying to enable stereo mode on a PC (SuSE10.1) with an NVIDIA NV37GL [Quadro FX 330/Quadro NVS280] graphics card (according to Xorg.0.log). (--) PCI:*(5:0:0) nVidia Corporation NV37GL [Quadro FX 330/Quadro NVS280] rev 162, Mem @ 0xdd00/24, 0xc000/28, 0xde00/24, BIOS @ 0xdfc0/17 (II) NVIDIA(0): NVIDIA GPU Quadro NVS 280 PCI-E at PCI:5:0:0 (GPU-0) Accroding to some web page about O, the options are set to (**) NVIDIA(0): Option Stereo 3 (**) NVIDIA(0): Option NvAGP 1 (**) NVIDIA(0): Option IgnoreEDID false (**) NVIDIA(0): Option UseEdidFreqs true Yet, the log file says (WW) NVIDIA(0): Stereo is only available on Quadro cards (II) NVIDIA(0): Disabling stereo. I was wondering whether anyone could explain what is so un-Quadro about this card? (Currently, the display is an LCD, but the same messages came up when the display was a CRT) Thank you for your help, Tim -- Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A
Re: [ccp4bb] stereo with Nvidia Quadro
Just check out the cards on the back - it should have the small round port that a 60GX plug would fit into. The NuVision site has a list of cards that are compatible with their emitters. I don't remember them all right off, but it's fairly straightforward. By the way, I buy all my video cards and memory on e-bay. Those quadro FX cards are often packaged in Dell systems that are leased to companies, and when the leases are up, the cards get parted out. I've purchased at least 7 this way, only paying 1/3 or so for each (compared to retail prices). I haven't had an issue with any thus far (until today that is - I'm sure something will happen now). Be sure to check the vendors out, but it is a source that isn't too crazy. I don't remember the prices I paid, but it was small compared to buying them new online somewhere. As I furnished 6 computers at once, I looked for package deals (they were even better). Good luck with that. Dave Tim Gruene wrote: Dear David, thank you for your answer. Do you (or anyone on the list) know if any FX-card would work with NuVision 60GX (like FX370, FX570), or only the dear ones (FX1400 and above)? Tim -- Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A On Thu, 8 May 2008, David J. Schuller wrote: The nVidia cards used for stereo are the Quadro FX series. The Quadro NVS series are for running multiple monitors, but not fancy 3D graphics. You can explore the manufacturer's web site for details. - === With the single exception of Cornell, there is not a college in the United States where truth has ever been a welcome guest - R.G. Ingersoll === David J. Schuller modern man in a post-modern world MacCHESS, Cornell University [EMAIL PROTECTED] On Thu, 2008-05-08 at 15:01 +0200, Tim Gruene wrote: Good day, I have been trying to enable stereo mode on a PC (SuSE10.1) with an NVIDIA NV37GL [Quadro FX 330/Quadro NVS280] graphics card (according to Xorg.0.log). (--) PCI:*(5:0:0) nVidia Corporation NV37GL [Quadro FX 330/Quadro NVS280] rev 162, Mem @ 0xdd00/24, 0xc000/28, 0xde00/24, BIOS @ 0xdfc0/17 (II) NVIDIA(0): NVIDIA GPU Quadro NVS 280 PCI-E at PCI:5:0:0 (GPU-0) Accroding to some web page about O, the options are set to (**) NVIDIA(0): Option Stereo 3 (**) NVIDIA(0): Option NvAGP 1 (**) NVIDIA(0): Option IgnoreEDID false (**) NVIDIA(0): Option UseEdidFreqs true Yet, the log file says (WW) NVIDIA(0): Stereo is only available on Quadro cards (II) NVIDIA(0): Disabling stereo. I was wondering whether anyone could explain what is so un-Quadro about this card? (Currently, the display is an LCD, but the same messages came up when the display was a CRT) Thank you for your help, Tim -- Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A
[ccp4bb] 2008 Gordon Research Conference on Diffraction Methods in Structural Biology
There is still time to apply to attend this GRC, relevant to researchers interested in Methods Development - details below! The official closing date is 22nd June, but places are limited to a total of 125. Best wishes Elspeth Garman and Andrew Leslie Gordon Research Conference on Diffraction Methods in Structural Biology July 13-18, 2008, Bates College, Lewiston, Maine, USA Co-Chairs: Elspeth Garman Andrew Leslie The 2008 Gordon Research Conference on Diffraction Methods in Structural Biology will encompass advances in the methodology for macromolecular X-ray crystallography, and other diffraction/scattering applications. The full confirmed programme and timetable for the meeting can now be found below and at: http://www.grc.org/programs.aspx?year=2008program=diffrac as well as details on how to register (registration closes on 22nd June 2008 but attendance is limited to 125 researchers). All macromolecular crystallographers interested in Methods development are encouraged to apply. To promote a lively meeting, we hope that all participants will present a poster and contribute to the discussions. *Confirmed Program as at 8th May 2008.* *MACROMOLECULAR STRUCTURES: PUSHING THE BOUNDARIES * Discussion Leader: *Janet Smith* (University of Michigan at Ann Arbor, USA) *Jens Preben Morth* (Aarhus University, Denmark) Structure determination of the sodium-potassium pump *Jack Johnson* (Scripps Research Institute, USA) Crystallography of Viral Maturation Intermediates: Large Unit Cells, Particle Dynamics, and Energy Landscapes *EXPERIMENTAL ASPECTS* Discussion Leader: *James Holton* (University of California, Berkeley, USA) *Douglas Juers* (Whitman College, USA) Rational approaches to cryo-crystallography protocols *Zbyszek Dauter* (Frederick Cancer Institute, USA) A thoughtful approach to data collection *Eddie Snell* (Hauptman-Woodward Medical Research Institute, USA) Are X-rays damaging to structural biology? A case study with xylose isomerase *Martin Weik* (Institut de Biologie Structurale, Grenoble, France) Temperature-controlled cryo-crystallography to study the structural dynamics of proteins *COMPLEMENTARY TECHNIQUES* Discussion Leader: *Peter Kuhn* (Scripps Research Institute, USA) *Junko Yano* (Lawrence Berkeley National Laboratory, USA) Combination of XAS and XRD for studying a high-resolution structure of the photosynthetic water-splitting catalyst *Dean Myles* (Oak Ridge National Laboratory USA) New opportunities for neutron structural biology *Carrie Wilmot* (University of Minnesota, USA) Single crystal spectroscopy coupled to crystallography *FUTURE DIRECTIONS IN SYNCHROTRON BASED MACROMOLECULAR CRYSTALLOGRAPHY * Discussion Leader: *Elizabeth Duke* (Diamond Light Source, UK) *Soichi Wakatsuki* (KEK, Japan) Microfocus and low energy PX developments looking towards next generation synchrotron sources *Ed Mitchell* (ESRF, Grenoble, France) Bigger, better, faster, more: The ESRF Upgrade Programme *Aina Cohen* (SSRL, USA) Automation, Robotics and Remote Access at the SSRL Protein Crystallography Beam Lines *Frank von Delft* (Structural Genomics Consortium, Oxford, UK) A User's Wish: An Experiment-Focussed Beamline Interface *EMERGING TECHNOLOGIES* Discussion Leader: *Andrew Leslie* (MRC-LMB, Cambridge, UK) *Robert F. Fischetti* (GM/CA-CAT, Argonne National Laboratory, USA) Where have all the photoelectrons gone? *Clemens Schulze-Briese* (Swiss Light Source, Villigen, Switzerland) PILATUS 6M - the first year of regular user operation *COMPUTATIONAL METHODS* Discussion Leader: *Airlie McCoy* (University of Cambridge, UK) *Sasha Popov* (ESRF, Grenoble, France) BEST SAD data collection *Paul Adams* (Lawrence Berkeley Laboratory, USA) Automated structure solution with PHENIX *Kevin Cowtan* (University of York, UK) The 3 R's of automated model building: R-factors, resolution, and refinement *George Phillips* (University of Wisconsin-Madison, USA) Interpretation of electron density maps from protein crystals *CHALLENGING PROBLEMS / MEMBRANE PROTEINS * Discussion Leader: *Tom Terwilliger* (Los Alamos National Laboratory, USA) *Chris Tate* (LMB-MRC Cambridge, UK) Thermostabilisation and structure determination of a beta1 adrenergic receptor *Mike Lawrence* (The Walter and Eliza Hall Institute of Medical Research, Melbourne, Australia) Pursuit of the structure of the human insulin receptor ectodomain *Mark Mayer* (NIH, Bethesda, USA) Structure and function of allosteric ion binding sites in glutamate receptor ligand binding domains *TALKS SELCETCED FROM POSTERS* *VALIDATION* Discussion Leader: *Ana Gonzales* (Stanford Synchrotron Radiation Laboratory, USA) *Gerard Kleywegt* (University of Uppsala, Sweden) Validation *Jane Richardson* (Duke University, USA) MolProbity Progress: RNA, Auto-corrections, and H redux *IMAGING METHODS OF THE FUTURE* Discussion Leader: *Raimond Ravelli* (Leiden University Medical Centre, The
Re: [ccp4bb] HKL2000 and gcc4 - redux
On May 7, 2008, at 3:07 PM, Chris Waddling wrote: so even temporarily putting a library where it doesn't belong Actually, this is what /usr/lib is for (except for the doesn't part). According to the Filesystem Hierarchy Standard 4.7 regarding the general requirements and limitations of files placed in /usr/lib: /usr/lib includes object files, libraries, and internal binaries that are not intended to be executed directly by users or shell scripts. If it fulfills the definition and is not expressly forbidden, then its reasonable to assume its allowed. James -- James Stroud UCLA-DOE Institute for Genomics and Proteomics 611 Charles E. Young Dr. S. Los Angeles, CA 90095 http://www.jamesstroud.com
Re: [ccp4bb] stereo with Nvidia Quadro
Dear David, thank you for your answer. Do you (or anyone on the list) know if any FX-card would work with NuVision 60GX (like FX370, FX570), or only the dear ones (FX1400 and above)? Nvidia has been progressively dropping support from their lower-end cards. For example the older FX1100 has stereo, but the newer FX1700 does not. Currently you have to buy the FX 3500 or above to get stereo. Look at this chart under the row Display Connectors for cards which have Stereo listed: http://www.nvidia.com/object/IO_11761.html The 3500 series is moderately expensive. If you are on a budget maybe you could snag an older used card online somewhere. -- -- Eric Bennett Hofstadter's Law: It always takes longer than you expect, even when you take into account Hofstadter's Law.
Re: [ccp4bb] stereo with Nvidia Quadro
The 3500 series is moderately expensive. If you are on a budget maybe you could snag an older used card online somewhere. You can still buy new 1400's (OEM) for less than $160. Go to compuvest.com and search for quadro 1400.
[ccp4bb] How to generate two molecules of proteins and two chains of RNA in CNS 1.2
Dear All, When I used CNS 1.2 to generate the pdb file for two molecules of proteins and two chains of RNA (with different chain ids in format of CCP4), only one RNA chain is generated. Can anyone tell me how to correctly generate the files used for refinement with CNS 1.2? I downloaded the input files from the CNS website and I tried true and false for the renaming segid but all did not work. Thank you very much! Best, Sun Tang - Be a better friend, newshound, and know-it-all with Yahoo! Mobile. Try it now.
