Re: [ccp4bb] shipping heavy-atom solutions using Fedex
Does anyone has experience in shipping these compounds Try Hampton Research. Christopher J. Law, PhD., Skirball Institute, NYU Medical Center, New York, NY 10016, U.S.A On 11/02/2008, David Aragao [EMAIL PROTECTED] wrote: Dear All, We need to ship small amounts ( 100ul, [ ] 5mM) of heavy atom (HA) solutions to a synchrotron for onsite HA soaking. Fedex is able to do so but is asking for the corresponding UN numbers. All the HAs are from Hampton Research kit. We have found the UN number for three HA but we cannot find for the other 3. Does anyone has experience in shipping these compounds or knows where we could get these numbers for: ethyl mercuric phosphate (EMP) - C2H5HgO)HPO2 potassium tetranitroplatinate - K2Pt(NO2)4 potassium tetracyanoplatinate - K2Pt(CN)4 We are thinking in leaving EMP out but to ship the above platinum HAs with the same UN number as K2PtCl4 (UN 3288.61 toxic solid, inorganic). any comment would be extremely useful, Thanks in advance, David --- David platinum, Ph. D. Postdoctoral Researcher Membrane Structural and Functional Biology group CES department, University of Limerick Ireland
Re: [ccp4bb] Thermofluor
Hi Jeroen, We used a BioRad iCycler iQ for the measurements in Thermofluor-based high-throughput stability optimization of proteins for structural studies. Ericsson, et. al. Analytical Biochemistry (2006) 357:289-298. The wavelengths for excitation and detection were ~490 and ~575 nm, respectively (for Sypro Orange). See http://probes.invitrogen.com/handbook/figures/0020.html for wavelength (band) selection. The iCycler iQ is highly dependable and very sensitive. Best regards, Martin On Feb 12, 2008, at 6:07 PM, mesters wrote: Sorry for the off-topic but can somebody recommend highly a sensitive RT-PCR machine for the thermofluor experiment (sypro orange). That would imply excitation below 500 nm (ideally 470) and detection at about 570 nm, right? I know several simple machines have a problem with the 570 nm... Jeroen. . B. Martin Hallberg, PhD Assistant professor Department of Cell and Molecular Biology Medical Nobel Institute Karolinska Institutet von Eulers v. 1 SE-171 77 Stockholm Sweden
[ccp4bb] AW: [ccp4bb] Thermofluor
Hi Jeroen, I assume you are planning to use Sypro Orange. We are using the Roche LC480 (simply because it's around in the lab next door) and it does the job although it's a little inconvenient to tweak the settings. Many people use the iCycler from Biorad. This machine is a little more flexible and can be customized: You can introduce filter pairs of your choice and play with other dyes such as ANS-1.8. We intend to do that since sypro orange binds to quite a number of our proteins before heating (which perhaps tells you something about our proteins but lets blame the dye first). Ralf Ralf Jauch Genome Institute of Singapore 60 Biopolis Street #02-01Genome Singapore 138672 Tel: (65) 6478 8102 Mobile: (65) 96398715 [EMAIL PROTECTED] -Ursprüngliche Nachricht- Von: CCP4 bulletin board im Auftrag von mesters Gesendet: Mi 13.02.2008 01:07 An: CCP4BB@JISCMAIL.AC.UK Betreff: [ccp4bb] Thermofluor Sorry for the off-topic but can somebody recommend highly a sensitive RT-PCR machine for the thermofluor experiment (sypro orange). That would imply excitation below 500 nm (ideally 470) and detection at about 570 nm, right? I know several simple machines have a problem with the 570 nm... Jeroen. -- Jeroen Raymundus Mesters, Ph.D. Institut fuer Biochemie, Universitaet zu Luebeck Zentrum fuer Medizinische Struktur und Zellbiologie Ratzeburger Allee 160, D-23538 Luebeck Tel: +49-451-5004070, Fax: +49-451-5004068 E-mail: [EMAIL PROTECTED] Http://www.biochem.uni-luebeck.de Http://www.iobcr.org Http://www.opticryst.org -- If you can look into the seeds of time and say which grain will grow and which will not - speak then to me (Macbeth) --
Re: [ccp4bb] Fit2D?
You can download the latest FIT2D executables from: http://ftp.esrf.eu/pub/expg/FIT2D/ Make sure to use the http protocol to download the files, ftp will not work. The most recent version of FIT2D is for MacOSX. Updates and support for other OS were apparently discontinued. Alexander Johs ORNL Richard Gillilan wrote: I've been trying to get a copy of Fit2D for MacOSX, but the esrf web site with the executables has been unavailable for some time. The actual documentation is still online, including mirrors, but not the link to the executable. The author has also not responded. Anyone know what's up with Fit2D? Is it still being supported? Richard Gillilan MacCHESS Cornell
Re: [ccp4bb] an over refined structure
Edward Berry wrote: Dirk Kostrewa wrote: Dear Dean and others, Peter Zwart gave me a similar reply. This is very interesting discussion, and I would like to have a somewhat closer look to this to maybe make things a little bit clearer (please, excuse the general explanations - this might be interesting for beginners as well): 1). Ccrystallographic symmetry can be applied to the whole crystal and results in symmetry-equivalent intensities in reciprocal space. If you refine your model in a lower space group, there will be reflections in the test-set that are symmetry-equivalent in the higher space group to reflections in the working set. If you refine the (symmetry-equivalent) copies in your crystal independently, they will diverge due to resolution and data quality, and R-work and R-free will diverge to some extend due to this. If you force the copies to be identical, the R-work R-free will still be different due to observational errors. In both cases, however, the R-free will be very close to the R-work. Ah- that's going way to fast for the beginners, at least one of them! Can someone explain why the R-free will be very close to the R-work, preferably in simple concrete terms like Fo, Fc, at sym-related reflections, and the change in the Fc resulting from a step of refinement? Ed Dear Ed, Some years ago I was castigated in group meeting for stating that the question posed by a post-doc was a bad question. I gather this is considered rude behavior. My belief is that if you say good question to all questions you degrade the value of those truly good questions when they come along. Yours is a good question and demands a proper answer. Like all good questions, however, the answer is neither easy nor short. I'm going to make a stab at it, and I may end up far from the mark, but I'm sure someone will point out my failings in follow-up letters. At least I'll get these ideas out of my head so I can get back to my real work. The other attempts to answer this question, including my own, have included terms such as error and bias and, without definitions for these terms, are ultimately unsatisfying. It seems to me that the whole point of refinement is to bias the model to the observations, so the real matter is inappropriate bias. This brings up the question of what a model is intended to fit and what it is not. When I first implemented an overall anisotropic B correction in TNT I noticed that the correction for a given model would grow larger as more refinement cycles were run. It appears that a model consisting of only atomic positions and isotropic B's can be created where the Fc's have an anisotropic fall off in resolution. When the isotropic model was refined with the anisotropy uncorrected the parameters managed to find a way to fit that anisotropy. When the anisotropy was properly modeled the positions and isotropic B's could go back to their job of fitting the signal they were designed to fit. This is what I would define a inappropriate bias. The parameters of the model are attempting to fit a signal they were not designed to fit. In this example, the distortion of the parameters is distributed over a large number and each parameter is changed by a small amount; an amount usually considered too small to be significant, but in aggregate they produce a significant signal (the anisotropic falloff of the model's Fc's). A more trivial example would the the location of the side chains of amino acids near the density of an unmodeled ligand. Refinement will tend to move the side chains away from the center of their own density toward the unfilled density, perhaps even inappropriately placing a side chain in the ligand density instead of its own. Again, the fit of the parameters to the signal they were designed to fit has been degraded by the attempt to fit a signal they were not, and could never, fit properly. When well designed parameters fit the signal they were designed to fit the model has predictive power. I guess that is what designed is defined to mean in this case. A model that can't predict things is useless, and that is why the free R is such a good test of a model. If the parameters of a model are fitting signal in the data that they were not designed to fit, all bets are off. There is no reason to expect that they will have the same predictive power, except by happenstance or (bad) luck. Placing the end of an arginine residue in the density of a ligand does, at least, put a few atoms in places where atoms should be, and that will tend to lower the free R, but the requirement that there be bridging atoms linking those atoms to the main chain of the protein will cause the parameters of the middle atoms to engage is contortions to try to fit the data, and those contortions will harm the ability of the model to make correct predictions. Going back to the first example, there is also no reason to expect that the small perturbations in an
Re: [ccp4bb] summary: sgi dials on intel mac
The protocol (ftp://)from the link is wrong, ftp is not supported by the esrf site (which one is told when actually ftp'ing there. Try http://ftp.esrf.eu/pub/expg/FIT2D/, it works for me Tim -- Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A On Tue, 12 Feb 2008, Andreas Förster wrote: Juergen Bosch and Ben Eisenbraun were quick to forward my request to Dave Gohara who's at WUSTL now. Dave was equally quick in pointing out that a universal binary of the USB-to-serial driver resides on his homepage (http://smackfumaster.com) in the Software - Crystallography and EM Binaries section. Thank you! All it takes is installing the driver, rebooting, and plugging the adapter and dials in. Now I just have to find out which programs will actually take orders from dials. Andreas - Hey all, I've been trying to get SGI dials to work with a MacBook Pro running Leopard. I can't get my digitus USB-to-serial adaptor to work. The supplied driver is PPC only. As the chip is from Prolific, I tried the driver from sbgrid (David Gohara's work). That also seems to be PPC only. I tried to contact David Gohara directly, but he doesn't appear to be at Harvard anymore. Does anyone have dials working with a Leopard Intel Mac and would like to let me in on the secret? I should probably be using a PowerMate, but the dials were lying around collecting dust. I thought I might give them a second lease on life. Thanks. Andreas
Re: [ccp4bb] Thermofluor
Hi Jeroen, We just bought a Stratagene Mx3005p for the Thermofluor method (also known as differential scanning fluorimetry). This was after talking to Martin, among others, he he... We haven't had it long and did our first experiments last Friday, but it produced good results straight away. We chose the Stratagene for a couple of reasons: a) the iQ5 required a manual change of filter which would make it unuseable for qPCR, and while we don't anticipate a great deal of usage for qPCR it would be a shame to cripple such an expensive machine. The filter for the Mx3005p can be chosen in software. b) the Mx3005p uses a photomultiplier instead of a CCD to read the plate. This (according to Stratagene) leads to better uniformity of detection across the plate. I believe the iQ5 requires some kind of calibration run each time you use it. Our first impression of the Stratagene software is very positive. We haven't tried the iQ5 but others say it's a perfectly fine machine. A couple of people who know more than most are Helena Berglund at SGC Stockholm (BioRad) and Frank Niesen at SGC Oxford (Stratagene). Whichever of these two machines you choose, SGC have produced an excellent detailed protocol and from their FTP site ftp.sgc.ox.ac.uk you can download Excel spreadsheets to calculate Tm and produce at-a- glance output for up to 96 wells from either iQ5 or Mx3005p output. SGC intend to continue supporting output from both machines. There are cheaper models by BioRad which we didn't look into (we got a grant for the Mx3005p!) but I imagine they have sensitivity/wavelength issues. The link to the SGC protocol is: http://www.ncbi.nlm.nih.gov/pubmed/17853878?ordinalpos=3itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_RVDocSum HTH Derek On Feb 12, 2008, at 18:07, mesters wrote: Sorry for the off-topic but can somebody recommend highly a sensitive RT-PCR machine for the thermofluor experiment (sypro orange). That would imply excitation below 500 nm (ideally 470) and detection at about 570 nm, right? I know several simple machines have a problem with the 570 nm... Jeroen. -- Jeroen Raymundus Mesters, Ph.D. Institut fuer Biochemie, Universitaet zu Luebeck Zentrum fuer Medizinische Struktur und Zellbiologie Ratzeburger Allee 160, D-23538 Luebeck Tel: +49-451-5004070, Fax: +49-451-5004068 E-mail: [EMAIL PROTECTED] Http://www.biochem.uni-luebeck.de Http://www.iobcr.org Http://www.opticryst.org -- If you can look into the seeds of time and say which grain will grow and which will not - speak then to me (Macbeth) --
[ccp4bb] Fit2D?
I've been trying to get a copy of Fit2D for MacOSX, but the esrf web site with the executables has been unavailable for some time. The actual documentation is still online, including mirrors, but not the link to the executable. The author has also not responded. Anyone know what's up with Fit2D? Is it still being supported? Richard Gillilan MacCHESS Cornell
[ccp4bb] summary: sgi dials on intel mac
Juergen Bosch and Ben Eisenbraun were quick to forward my request to Dave Gohara who's at WUSTL now. Dave was equally quick in pointing out that a universal binary of the USB-to-serial driver resides on his homepage (http://smackfumaster.com) in the Software - Crystallography and EM Binaries section. Thank you! All it takes is installing the driver, rebooting, and plugging the adapter and dials in. Now I just have to find out which programs will actually take orders from dials. Andreas - Hey all, I've been trying to get SGI dials to work with a MacBook Pro running Leopard. I can't get my digitus USB-to-serial adaptor to work. The supplied driver is PPC only. As the chip is from Prolific, I tried the driver from sbgrid (David Gohara's work). That also seems to be PPC only. I tried to contact David Gohara directly, but he doesn't appear to be at Harvard anymore. Does anyone have dials working with a Leopard Intel Mac and would like to let me in on the secret? I should probably be using a PowerMate, but the dials were lying around collecting dust. I thought I might give them a second lease on life. Thanks. Andreas
Re: [ccp4bb] sgi dials on intel mac
On Tue, Feb 12, 2008 at 05:16:14PM +, Andreas Förster wrote: I've been trying to get SGI dials to work with a MacBook Pro running Leopard. I can't get my digitus USB-to-serial adaptor to work. The supplied driver is PPC only. As the chip is from Prolific, I tried the driver from sbgrid (David Gohara's work). That also seems to be PPC only. The version on our webpage is out of date. Sorry about that. I tried to contact David Gohara directly, but he doesn't appear to be at Harvard anymore. He's at Washington University now. You can get the latest driver from his personal page: http://gohara.wustl.edu/software/crystallography_and_em_bina/ I don't know if he's on this list, but his email address is in the PDF of dials set up instructions linked off that page. -ben -- Ben Eisenbraun Structural Biology Grid http://sbgrid.org/
[ccp4bb] 13th Annual UTMB Sealy Center for Structural Biology Symposium
Dear Colleague: You and your colleagues are cordially invited to join us for the 13th Annual Structural Biology Symposium to be held at the University of Texas Medical Branch at Galveston on May 16th and 17th, 2008. The meeting is organized by the Sealy Center for Structural Biology Molecular Biophysics and co-sponsored by the Keck Center for Computational Structural Biology. In previous years, over 300 scientists from the U.S. and abroad, have participated in the annual event. The goal of the symposia is to bring together leaders in all areas of structural biology to present current topics. The program of the 2008 Symposium includes the following prominent speakers: Keynote Speaker: Thomas A. Steitz, Ph.D. Sterling Professor of Molecular Biophysics and Biochemistry Professor of Chemistry Yale University David A. Agard, Ph.D., University of California at San Francisco, San Francisco, CA William E. Balch, Ph.D., The Scripps Research Institute, La Jolla, CA José Barral, M.D., Ph.D., The University of Texas Medical Branch, Galveston, TX Tracy M. Handel, Ph.D., University of California, San Diego, CA Arthur E. Johnson, Ph.D., Texas AM Health Science Center, College Station, TX Susan Marqusee, M.D., Ph.D., University of California, Berkeley, Berkeley, CA Joseph Puglisi, Ph.D., Stanford University School of Medicine, Stanford, CA Yousif Shamoo, Ph.D., Rice University, Houston, TX Thomas Walz, Ph.D., Harvard Medical School, Boston, MA Poster sessions and social events, included in the program, provide ample opportunity for formal and informal discussions with the speakers. Awards will be given to graduate students and post-docs for best poster presentations. To insure maximum participation, the costs of attending the symposium have been kept to a minimum. Reasonably priced rooms have been reserved at the historic beachfront Hotel Galvez on Galveston Island for symposium participants and meals are provided on-site during the Symposium. Please visit our symposium web-site at http://www.scsb.utmb.edu/symposium/ or contact Angelina Johnson, Phone: (409) 772-8083, Fax: (409) 772-6334 or email at: [EMAIL PROTECTED], for on-line registration and abstract submission. Registration for the Symposium will open February 1, 2008 and we encourage you and your colleagues to go on-line and register. We are looking forward to seeing you on May 16th 17th, 2008. On behalf of the Organizing Committee: Sincerely yours, Robert O. Fox, Ph.D. Vince Hilser, Ph.D. Symposium Chair Symposium Co-Chair Deputy Director Director Sealy Center for Structural Biology and Sealy Center for Structural Biology and Molecular Biophysics Molecular Biophysics Professor Professor Department of Biochemistry and Molecular Biology Department of Biochemistry and Molecular Biology Yours sincerely, Mark A. White, Ph.D. Assistant Professor, Dept. Biochemistry and Molecular Biology, Manager, Sealy Center for Structural Biology and Molecular Biophysics X-ray Crystallography Laboratory, Basic Science Building, Room 6.660 C University of Texas Medical Branch Galveston, TX 77555-0647 Tel. (409) 747-4747 Fax. (409) 747-4745 mailto://[EMAIL PROTECTED] http://xray.utmb.edu http://xray.utmb.edu/~white
Re: [ccp4bb] an over refined structure
Dale Tronrud wrote:
In summary, this argument depends on two assertions that you can
argue with me about:
1) When a parameter is being used to fit the signal it was designed
for, the resulting model develops predictive power and can lower
both the working and free R. When a signal is perturbing the value
of a parameter for which is was not designed, it is unlikely to improve
its predictive power and the working R will tend to drop, but the free
R will not (and may rise).
2) If the unmodeled signal in the data set is a property in real
space and has the same symmetry as the molecule in the unit cell,
the inappropriate fitting of parameters will be systematic with
respect to that symmetry and the presence of a reflection in the
working set will tend to cause its symmetry mate in the test set
to be better predicted despite the fact that this predictive power
does not extend to reflections that are unrelated by symmetry.
This bias will occur for any kind of error as long as that
error obeys the symmetry of the unit cell in real space.
Dear Dale,
Thanks for taking the time to think about my problem and for
composing what is obviously a well-thought-out explanation.
I am a little over my head here, but I think I see your point.
Inappropriate fitting of this residual error has poor predictive
power so does not reduce {Fc-Fo| for general free reflections.
However the error is symmetrical, so attempts to fit it will
result in symmetrical changes which reduce |Fo-Fc| for those
free reflections that are related to working reflections.
I need to read the references that were mentioned in this
discussion, and think about it a little more in order to
resolve some remaining conflicts in my thinking.
But I don't need to bother everyone else with my
struggles, unless I come up with something useful.
Thanks for the guidance!
Ed
[ccp4bb] Protein-protein docking
I would recommend giving Dave Ritchie's Hex program a go - it is blisteringly quick. It's limited to local searches so it is best if you have a reasonable idea where you expect the docking surface to be (mutations, NMR shift data etc). We used it to refine solutions from searches with crosslinking restraints. It works nicely interactively if you explore the receptor surface by centring the search on different residues. Best wishes Martyn Martyn Symmons Department of Pathology University of Cambridge
[ccp4bb] sgi dials on intel mac
Hey all, I've been trying to get SGI dials to work with a MacBook Pro running Leopard. I can't get my digitus USB-to-serial adaptor to work. The supplied driver is PPC only. As the chip is from Prolific, I tried the driver from sbgrid (David Gohara's work). That also seems to be PPC only. I tried to contact David Gohara directly, but he doesn't appear to be at Harvard anymore. Does anyone have dials working with a Leopard Intel Mac and would like to let me in on the secret? I should probably be using a PowerMate, but the dials were lying around collecting dust. I thought I might give them a second lease on life. Thanks. Andreas
[ccp4bb] xprep vs shelxc
Dear All, A very simple stupid question: is it worth while getting xprep instead of shelxc to do the same job? i realize xprep does a lot of other things, but also seem to get the idea from some places that it does a better job than shelxc at preparing data from shelxd, or is there any difference (getting xprep will cost some money so i would like to know where the difference lies if there is any significant difference??) Thanks for advice, Tommi -- Tommi Kajander, Ph.D. Macromolecular X-ray Crystallography Research Program in Structural Biology and Biophysics Institute of Biotechnology P.O. Box 65 (Street address: Viikinkaari 1, 4th floor) University of Helsinki FIN-00014 Helsinki, Finland Tel. +358-9-191 58903 Fax +358-9-191 59940
[ccp4bb] Thermofluor
Sorry for the off-topic but can somebody recommend highly a sensitive RT-PCR machine for the thermofluor experiment (sypro orange). That would imply excitation below 500 nm (ideally 470) and detection at about 570 nm, right? I know several simple machines have a problem with the 570 nm... Jeroen. -- Jeroen Raymundus Mesters, Ph.D. Institut fuer Biochemie, Universitaet zu Luebeck Zentrum fuer Medizinische Struktur und Zellbiologie Ratzeburger Allee 160, D-23538 Luebeck Tel: +49-451-5004070, Fax: +49-451-5004068 E-mail: [EMAIL PROTECTED] Http://www.biochem.uni-luebeck.de Http://www.iobcr.org Http://www.opticryst.org -- If you can look into the seeds of time and say which grain will grow and which will not - speak then to me (Macbeth) --
