Re: [ccp4bb] Out of topic: Plot Ligand-protein interactions
Dear Wenhe, You don't need any skills to use Ligplot. Only thing you have to give is the residue number of the ligand or the small molecule you are interested in the command line. There are other commercial software but i don't know whether they are of any interest to you ! MOE or MAESTRO also provides 2D plotting. HTH ! Regards, Krishna Chinthalapudi, PhD Hannover Medical School On Fri, Jan 20, 2012 at 8:46 AM, Kimi wenhezhong.xmu@gmail.com wrote: Dear all, I would like to know what program/software you usually use to plot the 2D interactions between ligand and protein. As far as I know, LigPlot is powerful but need some skills. Also a web-based program from PDB server is easy to use but not very powerful. What is your recommendation? Thank you. King regards, Wenhe
[ccp4bb] PhD and Postdoc opportunities in Singapore in Structural Biology.
PhD and Postdoc opportunities in Singapore in Structural Biology. The Bob Robinson laboratory is looking for candidates to apply for a range of scholarships and fellowships in conjunction with the laboratory. Joining the laboratory will be conditional on securing the award. The laboratory, in the Institute of Molecular and Cell Biology (IMCB), uses structural biology techniques to study 1) how the power generated from actin-filament polymerization is harnessed by biological processes, 2) the breadth of structures and dynamics that are formed by diverse bacterial actin-like filament systems, and 3) how these structures may be interfered with in the search for novel drug candidates. The laboratory uses a variety of techniques, including: protein crystallography, electron microscopy, TIRF microscopy and SILAC mass spectrometry. 1) European-based researchers to apply for the EMBO Long-Term Fellowship (postdoc). http://www.embo.org/programmes/fellowships/long-term.html 2) Potential PhD students to apply for NGS and SINGA scholarships. https://www.singa.a-star.edu.sg/ http://www.nus.edu.sg/ngs/scholarships.html 3) Potential joint PhD students to apply for ARAP Scholarships. http://www.a-star.edu.sg/tabid/424/default.aspx 4) Singaporean Students to apply for AGS scholarships. http://www.a-star.edu.sg/tabid/424/default.aspx Interested candidates should contact Bob directly: Website: http://www.imcb.a-star.edu.sg/php/robinson.php email: rrobin...@imcb.a-star.edu.sg
Re: [ccp4bb] Out of topic: Plot Ligand-protein interactions
Wenhe There is a ligand environment viewer at the URL below that plots environments of ligands in various view types. At the moment is only works on existing structures since the ligands have to be correctly typed with correct dictionaries. This has a number of export formats. http://www.ebi.ac.uk/pdbe-srv/leview/ The EBIAstexViewer http://www.ebi.ac.uk/pdbe-srv/view/entry/1cbs/viewer Also has a chemistry viewer (menu - Chemistry) which shows the ligand in 2D with the environment and various options. You asked for plotting - so I guess you want an export format so I am not sure if this is suitable. Regards Tom Oldfield Dear all, I would like to know what program/software you usually use to plot the 2D interactions between ligand and protein. As far as I know, LigPlot is powerful but need some skills. Also a web-based program from PDB server is easy to use but not very powerful. What is your recommendation? Thank you. King regards, Wenhe
Re: [ccp4bb] native gels
Hi Anita, I have recently performed it following this protocol I found in the Internet: http://wolfson.huji.ac.il/purification/Protocols/PAGE_Acidic.html I hope this helps! Good luck, Federica -- Federica Basilico Ph.D. student Department of Experimental Oncology European Institute of Oncology Via Adamello 16 20139 Milan (Italy) anita p (crystals...@gmail.com) wrote: Hi All, Has anyone run a native gel for proteins at pI8 . I want to pour my own native gel. Do I run a discontinuous page or a continuous one?? Please help with regards to the buffer system to be used, and the dye to be used. With regards Rashmi
[ccp4bb] International Max Planck Research School (IMPRS) “From Molecules to Organisms”
Regarding our IMPRS: Talented junior scientists are offered the opportunity to earn a doctorate under excellent research conditions in Tübingen, Germany. Doctoral students benefit from regular workshops and supervising tutors at the Max Planck Institute for Developmental Biology, the Friedrich Miescher Laboratory and the University of Tübingen. Research Fields: IMPRS students tackle research projects bridging the gap from molecules to organisms. Transcending the boundaries of traditional life science disciplines, methodologies and scientific approaches from different fields are combined to address topics inaccessible by isolated research areas. How to apply: We are now accepting applications to join the school in September 2012. Application is a three step online procedure: first fill in the online application form, then upload your certificates, and lastly arrange for two reference letters to be submitted directly to our application system. Your application must be complete by March 15, 2012. Please visit: http://imprs.tuebingen.mpg.de/de/home.html
Re: [ccp4bb] MAD
For those of you interested, the reply to Tassos' question can be found here: http://www.iucr.org/resources/commissions/crystallographic-computing/schools/school96/ccp4-program-system (on-line) as well as here, http://www.*ccp4*.ac.uk/manual.ps (a ps file). McLaughlin, Terry and Zelinka. And yes, I'm over 40 ! I have also dealt with LCF files... Fred. Anastassis Perrakis wrote: A, yes, inventor's names. Anyone reading who is less than 40 and knows what MTZ stands for? ;-) My favorite technique remains SADDAM - a side product of Gerard's War On Error, that never did catch-up with the masses - experimentally or as an acronym. A. On 19 Jan 2012, at 21:51, Petr Leiman wrote: It would be so much more convenient to call these techniques (MAD, SAD, etc.) by their inventor's name. This would simplify things immensely simultaneously eliminating CCP4BB MADisagreements. Although in our days of copyrights wars, the journals and perhaps conferences where these methods were presented for the first time would insist on using their names as part of the method's name... Petr On Jan 19, 2012, at 7:42 PM, Ethan Merritt wrote: On Thursday, 19 January 2012, Ian Tickle wrote: So what does this have to do with the MAD acronym? I think it stemmed from a visit by Wayne Hendrickson to Birkbeck in London some time around 1990: he was invited by Tom Blundell to give a lecture on his MAD experiments. At that time Wayne called it multi-wavelength anomalous dispersion. Tom pointed out that this was really a misnomer for the reasons I've elucidated above. Wayne liked the MAD acronym and wanted to keep it so he needed a replacement term starting with D and diffraction was the obvious choice, and if you look at the literature from then on Wayne at least consistently called it multi-wavelength anomalous diffraction. Ian: The change-over from dispersion to diffraction in MAD protein crystallography happened a couple of years earlier, at least with regard to work being done at SSRL. I think the last paper using the term dispersion was the 1988 Lamprey hemoglobin paper. The next two papers, one a collaboration with Wayne's group and the other a collaboration with Hans Freeman's group, used the term diffraction. WA Hendrickson, JL Smith, RP Phizackerley, EA Merritt. Crystallographic structure-analysis of lamprey hemoglobin from anomalous dispersion of synchrotron radiation. PROTEINS-STRUCTURE FUNCTION AND GENETICS, 4(2):77–88, 1988. JM Guss, EA Merritt, RP Phizackerley, B Hedman, M Murata, KO Hodgson, HC Freeman. Phase determination by multiple-wavelength X-ray-diffraction - crystal-structure of a basic blue copper protein from cucumbers. SCIENCE, 241(4867):806–811, AUG 12 1988. WA Hendrickson, A Pahler, JL Smith, Y Satow, EA Merritt, RP Phizackerley. Crystal structure of core streptavidin determined from multiwavelength anomalous diffraction of synchrotron radiation. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 86(7):2190–2194, APR 1989. On the other hand, David and Lilo Templeton continued to use the term anomalous dispersion for at least another decade, describing their diffraction experiments exploring polarization effects and other characteristics of near-edge X-ray scattering by elements all over the periodic table. Ethan Cheers -- Ian On 18 January 2012 18:23, Phil Jeffrey pjeff...@princeton.edu wrote: Can I be dogmatic about this ? Multiwavelength anomalous diffraction from Hendrickson (1991) Science Vol. 254 no. 5028 pp. 51-58 Multiwavelength anomalous diffraction (MAD) from the CCP4 proceedings http://www.ccp4.ac.uk/courses/proceedings/1997/j_smith/main.html Multi-wavelength anomalous-diffraction (MAD) from Terwilliger Acta Cryst. (1994). D50, 11-16 etc. I don't see where the problem lies: a SAD experiment is a single wavelength experiment where you are using the anomalous/dispersive signals for phasing a MAD experiment is a multiple wavelength version of SAD. Hopefully one picks an appropriate range of wavelengths for whatever complex case one has. One can have SAD and MAD datasets that exploit anomalous/dispersive signals from multiple difference sources. This after all is one of the things that SHARP is particularly good at accommodating. If you're not using the anomalous/dispersive signals for phasing, you're collecting native data. After all C,N,O,S etc all have a small anomalous signal at all wavelengths, and metalloproteins usually have even larger signals so the mere presence of a theoretical d difference does not make it a SAD dataset. ALL datasets contain some anomalous/dispersive signals, most of the time way down in the noise. Phil Jeffrey Princeton On 1/18/12 12:48 PM, Francis E Reyes wrote: Using the terms 'MAD' and 'SAD' have always been confusing to me when considering more complex phasing cases. What happens if you have
Re: [ccp4bb] Merging data collected at two different wavelength
Let's have some more info here. What resolution we talking about? What are the space groups? What is the nature of the Co (is it a heavy atom soak?, a bound Co?) Have you tried to find heavy atom sites? (anomalous Patterson, or some other automated method) Are they believable? You say the dataset is twinned. How do you know this is the case? You're looking for help (and you've come to the right place) but knowing a little bit more about your system will help others suggest a suitable phasing scenario. F On Jan 19, 2012, at 12:39 PM, arka chakraborty wrote: Hi all, Thanks a lot for the valuable suggestions.I have tried detwinning it but the detwinning program in CCP4 takes care of only merohedral data( if I am not wrong) and the other program( I guess Cell-now in Apex 2 by Bruker?) which takes care of non-merohedral twinning is not accessible to it( as I can't buy it). Also, the anomalous signal in the home source data is pretty weak. So, I was thinking about trying to get a better result by trying to merge the two data sets, though I am aware of the problem posed by twinning. But since we were not being able to get crystals of size mountable at home source, I thought why not try whatever is possible! Thanking you, Regards, ARKO On Thu, Jan 19, 2012 at 10:13 PM, James Holton jmhol...@lbl.gov wrote: Oh dear. You definitely cannot de-twin a dataset by mergeing it with a non-twinned dataset! And if the twin fraction of your synchrotron set is much greater than 0.3 then it is unlikely that you will be able to use the anomalous differences to solve the phase problem. If I were you, I would focus on the non-twinned crystal system. You CAN average anomalous differences across different crystals, provided they are reasonably isomorphous. http://dx.doi.org/10.1107/S0907444910046573 And I should add the caveat that twinning is equivalent to non-isomorphism until after you have solved the structure because it dramatically changes the intensity you have available for any given hkl index. -James Holton MAD Scientist On 1/19/2012 8:20 AM, arka chakraborty wrote: Hi all, Thanks for providing multiple solutions to my problem. Prof . Tim Gruene and Prof. James Holton provided some nice solutions. However since the data are collected from different crystals, I am not sure whether I can do MAD phasing. My aim is to merge the two data-sets to circumvent the problem posed by the fact that the synchroton data is twinned. So maybe merging the data sets will provide better phases from SAD phasing? My main concern was how to do scaling adjustments before using the data-sets together. Thanking you, Regards, ARKO On Thu, Jan 19, 2012 at 1:46 AM, Soisson, Stephen M stephen_sois...@merck.com wrote: But if we were to follow that convention we would have been stuck with Multi-wavelength Resonant Diffraction Experimental Results, or, quite simply, MuRDER. -Original Message- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Jacob Keller Sent: Wednesday, January 18, 2012 3:13 PM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Merging data collected at two different wavelength This begs the question* whether you want the lemmings to understand you. One theory of language, gotten more or less from Strunk and White's Elements of Style, is that the most important feature of language is its transparency to the underlying thoughts. Bad language breaks the transparency, reminds you that you are reading and not simply thinking the thoughts of the author, who should also usually be invisible. Bad writing calls attention to itself and to the author, whereas good writing guides the thoughts of the reader unnoticeably. For Strunk and White, it seems that all rules of writing follow this principle, and it seems to be the right way to think about language. So, conventions, even when somewhat inaccurate, are important in that they are often more transparent, and the reader does not get stuck on them. Anyway, a case in point of lemmings is that once Wayne Hendrickson himself suggested that the term anomalous be decommissioned in favor of resonant. I don't hear any non-lemmings jumping on that bandwagon... JPK *Is this the right use of beg the question? On Wed, Jan 18, 2012 at 1:57 PM, Phoebe Rice pr...@uchicago.edu wrote: Can I be dogmatic about this ? I wish you could, but I don't think so, because even though those sources call it that, others don't. I agree with your thinking, but usage is usage. And 10,000 lemmings can't be wrong? -- *** Jacob Pearson Keller Northwestern University Medical Scientist Training Program email: j-kell...@northwestern.edu *** Notice: This e-mail message, together with any attachments, contains
Re: [ccp4bb] Merging data collected at two different wavelength
Hi all, There is a good news and it is that we have got crystals this morning which have diffracted upto 2.5 ang at home source and data collection is going on. I hope this solves the problem though the not so good anomalous signal at home source will probably make SAD phasing difficult. However to provide some additional information asked for by Prof. Francis E Reyes: The data is in all probability twinned because of two reasons: 1) At the time of data collection the two fused crytsals( or crystallites?) could be seen clearly which unfortunately could not be separated. 2) The data shows clear interference of lattices with one lattice showing much higher intensity for the first half or so of the 360 images collected and the other lattice for the second half. I have tried separating the frames and solving but it didnt work out. The spacegroup is P41212 in all data. The synchroton data has resolution of 2.75 ang collected at 1.60428 ang wavelength and the home data 3.0 ang. collected at CuKalpha wavelength. All are Co soaks. I should restate that it is a DNA oligomer and though I have been able to get heavy atom positions and the occupancies look ok but the phased map is too noisy to be interpreted. Regards, ARKO On Fri, Jan 20, 2012 at 9:46 PM, Francis E Reyes francis.re...@colorado.edu wrote: Let's have some more info here. What resolution we talking about? What are the space groups? What is the nature of the Co (is it a heavy atom soak?, a bound Co?) Have you tried to find heavy atom sites? (anomalous Patterson, or some other automated method) Are they believable? You say the data set is twinned. How do you know this is the case? You're looking for help (and you've come to the right place) but knowing a little bit more about your system will help others suggest a suitable phasing scenario. F On Jan 19, 2012, at 12:39 PM, arka chakraborty wrote: Hi all, Thanks a lot for the valuable suggestions.I have tried detwinning it but the detwinning program in CCP4 takes care of only merohedral data( if I am not wrong) and the other program( I guess Cell-now in Apex 2 by Bruker?) which takes care of non-merohedral twinning is not accessible to it( as I can't buy it). Also, the anomalous signal in the home source data is pretty weak. So, I was thinking about trying to get a better result by trying to merge the two data sets, though I am aware of the problem posed by twinning. But since we were not being able to get crystals of size mountable at home source, I thought why not try whatever is possible! Thanking you, Regards, ARKO On Thu, Jan 19, 2012 at 10:13 PM, James Holton jmhol...@lbl.gov wrote: Oh dear. You definitely cannot de-twin a dataset by mergeing it with a non-twinned dataset! And if the twin fraction of your synchrotron set is much greater than 0.3 then it is unlikely that you will be able to use the anomalous differences to solve the phase problem. If I were you, I would focus on the non-twinned crystal system. You CAN average anomalous differences across different crystals, provided they are reasonably isomorphous. http://dx.doi.org/10.1107/S0907444910046573 And I should add the caveat that twinning is equivalent to non-isomorphism until after you have solved the structure because it dramatically changes the intensity you have available for any given hkl index. -James Holton MAD Scientist On 1/19/2012 8:20 AM, arka chakraborty wrote: Hi all, Thanks for providing multiple solutions to my problem. Prof . Tim Gruene and Prof. James Holton provided some nice solutions. However since the data are collected from different crystals, I am not sure whether I can do MAD phasing. My aim is to merge the two data-sets to circumvent the problem posed by the fact that the synchroton data is twinned. So maybe merging the data sets will provide better phases from SAD phasing? My main concern was how to do scaling adjustments before using the data-sets together. Thanking you, Regards, ARKO On Thu, Jan 19, 2012 at 1:46 AM, Soisson, Stephen M stephen_sois...@merck.com wrote: But if we were to follow that convention we would have been stuck with Multi-wavelength Resonant Diffraction Experimental Results, or, quite simply, MuRDER. -Original Message- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Jacob Keller Sent: Wednesday, January 18, 2012 3:13 PM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Merging data collected at two different wavelength This begs the question* whether you want the lemmings to understand you. One theory of language, gotten more or less from Strunk and White's Elements of Style, is that the most important feature of language is its transparency to the underlying thoughts. Bad language breaks the transparency, reminds you that you are reading and not simply thinking the thoughts of the
[ccp4bb] New Faster-than-fast Fourier transform
New Fourier transform algorithm supposedly improves the speed of Fourier transforms get up to a tenfold increase in speed depending upon circumstances. Hopefully this will get incorporated into our refinement programs. http://web.mit.edu/newsoffice/2012/faster-fourier-transforms-0118.html -- Jim Fairman, Ph D. Crystal Core Leader I/Project Leader I Emerald BioStructures http://www.emeraldbiostructures.com/ Tel: 206-780-8914 Cell: 240-479-6575 E-mail: fairman@gmail.com jfair...@embios.com
Re: [ccp4bb] New Faster-than-fast Fourier transform
On Fri, Jan 20, 2012 at 9:37 AM, Jim Fairman fairman@gmail.com wrote: New Fourier transform algorithm supposedly improves the speed of Fourier transforms get up to a tenfold increase in speed depending upon circumstances. Hopefully this will get incorporated into our refinement programs. Perhaps if source code were available (freely and without restrictions)... although I don't know enough theory to tell whether this is applicable to X-ray crystallography or not. However, because of the way most programs are structured it is unlikely to make a huge difference in refinement speed in any case - maybe 25% faster, but certainly not an order of magnitude. -Nat
Re: [ccp4bb] New Faster-than-fast Fourier transform
On Friday, 20 January 2012, Jim Fairman wrote: New Fourier transform algorithm supposedly improves the speed of Fourier transforms get up to a tenfold increase in speed depending upon circumstances. Hopefully this will get incorporated into our refinement programs. http://web.mit.edu/newsoffice/2012/faster-fourier-transforms-0118.html This report is interesting, but it is not immediately obvious to me that crystallographic transforms are in the class of problems for which this algorithm is applicable. From reading the very non-technical article linked above, I conclude that a better summary would be New approach to Fourier approximation provides a very cheap (fast) way of identifying and then discarding components that contribute very little to the signal. In other words, it seems to be a way of increasing the compression ratio for lossy image/audio compression without increasing the amount of time required for compression. So if you're doing map fitting while listening to streamed mp3 music files, perhaps your map inversion will get a slightly larger slice of the CPU time relative to LastFM. On the other hand, it is possible that somewhere in here lies a clever approach to faster solvent flattening. Ethan
Re: [ccp4bb] New Faster-than-fast Fourier transform
The problem is however, that the coffee break is lost in the noise of this FFT. Jürgen On Jan 20, 2012, at 12:57 PM, Ethan Merritt wrote: On Friday, 20 January 2012, Jim Fairman wrote: New Fourier transform algorithm supposedly improves the speed of Fourier transforms get up to a tenfold increase in speed depending upon circumstances. Hopefully this will get incorporated into our refinement programs. http://web.mit.edu/newsoffice/2012/faster-fourier-transforms-0118.html This report is interesting, but it is not immediately obvious to me that crystallographic transforms are in the class of problems for which this algorithm is applicable. From reading the very non-technical article linked above, I conclude that a better summary would be New approach to Fourier approximation provides a very cheap (fast) way of identifying and then discarding components that contribute very little to the signal. In other words, it seems to be a way of increasing the compression ratio for lossy image/audio compression without increasing the amount of time required for compression. So if you're doing map fitting while listening to streamed mp3 music files, perhaps your map inversion will get a slightly larger slice of the CPU time relative to LastFM. On the other hand, it is possible that somewhere in here lies a clever approach to faster solvent flattening. Ethan .. Jürgen Bosch Johns Hopkins University Bloomberg School of Public Health Department of Biochemistry Molecular Biology Johns Hopkins Malaria Research Institute 615 North Wolfe Street, W8708 Baltimore, MD 21205 Office: +1-410-614-4742 Lab: +1-410-614-4894 Fax: +1-410-955-2926 http://web.mac.com/bosch_lab/
[ccp4bb] Protein Fold Motifs- off-topic
Hello Everyone, Does anyone know of a quick (yet somewhat reliable) sort of cheat-sheet/quick reference sheet with the more common folds with an illustrative example?
Re: [ccp4bb] Protein Fold Motifs- off-topic
Hi Yuri, I don't know of a cheat-sheet, but I find the Introduction to Protein Structure book by Branden and Tooze to useful for illustrations of common folds. Jeff On Fri, Jan 20, 2012 at 10:13 AM, Yuri Pompeu yuri.pom...@ufl.edu wrote: Hello Everyone, Does anyone know of a quick (yet somewhat reliable) sort of cheat-sheet/quick reference sheet with the more common folds with an illustrative example?
Re: [ccp4bb] Protein Fold Motifs- off-topic
A very similar question: how about smaller motifs, such as various turn types, etc.? JPK On Fri, Jan 20, 2012 at 12:37 PM, Jeff Headd jjhe...@lbl.gov wrote: Hi Yuri, I don't know of a cheat-sheet, but I find the Introduction to Protein Structure book by Branden and Tooze to useful for illustrations of common folds. Jeff On Fri, Jan 20, 2012 at 10:13 AM, Yuri Pompeu yuri.pom...@ufl.edu wrote: Hello Everyone, Does anyone know of a quick (yet somewhat reliable) sort of cheat-sheet/quick reference sheet with the more common folds with an illustrative example? -- *** Jacob Pearson Keller Northwestern University Medical Scientist Training Program email: j-kell...@northwestern.edu ***
Re: [ccp4bb] New Faster-than-fast Fourier transform
From the rather non-technical inofrmation available so far, it seems to me that it is like leaving out all but the strongest reflections (or perhaps the strongest normalized structure factors). This is unlikely to improve the quality of structure refinement, the importance of using as much data as possible and not leaving out the weakest reflections has often been emphasized. This is quite different to data compression of music. However there is one case where we are already doing this, namely small molecule direct methods or using the same programs to find the heavy atoms in SAD and MAD experiments. These programs use only the strongest 15-20% of the normalized structure factors (E-values). This is possible because the data to parameter ratio is still sufficient, and these reflections contain much of the useful information. However the Fourier routines used by these programs (at least the ones I wrote) are not taking full advantage of the 'sparseness' of the data, so if the MIT people have found a clever way of doing this it might still be useful for heavy atom location (though FFTW and the Intel MKL FFT will be difficult to beat). George On 01/20/2012 06:57 PM, Ethan Merritt wrote: On Friday, 20 January 2012, Jim Fairman wrote: New Fourier transform algorithm supposedly improves the speed of Fourier transforms get up to a tenfold increase in speed depending upon circumstances. Hopefully this will get incorporated into our refinement programs. http://web.mit.edu/newsoffice/2012/faster-fourier-transforms-0118.html This report is interesting, but it is not immediately obvious to me that crystallographic transforms are in the class of problems for which this algorithm is applicable. From reading the very non-technical article linked above, I conclude that a better summary would be New approach to Fourier approximation provides a very cheap (fast) way of identifying and then discarding components that contribute very little to the signal. In other words, it seems to be a way of increasing the compression ratio for lossy image/audio compression without increasing the amount of time required for compression. So if you're doing map fitting while listening to streamed mp3 music files, perhaps your map inversion will get a slightly larger slice of the CPU time relative to LastFM. On the other hand, it is possible that somewhere in here lies a clever approach to faster solvent flattening. Ethan
Re: [ccp4bb] Protein Fold Motifs- off-topic
In addition to the book recommended by Jeff, another good one is Protein Structure and Function by Petsko and Ringe. A bit less cumbersome than Branden and Tooze, but not as complete (it's a relatively thin paperback, rather than a full-blown textbook). If you just want a nice protein domain cheat sheet, it should be adequate. Mike - Original Message - From: Jeff Headd jjhe...@lbl.gov To: CCP4BB@JISCMAIL.AC.UK Sent: Friday, January 20, 2012 10:37:51 AM GMT -08:00 US/Canada Pacific Subject: Re: [ccp4bb] Protein Fold Motifs- off-topic Hi Yuri, I don't know of a cheat-sheet, but I find the Introduction to Protein Structure book by Branden and Tooze to useful for illustrations of common folds. Jeff On Fri, Jan 20, 2012 at 10:13 AM, Yuri Pompeu yuri.pom...@ufl.edu wrote: Hello Everyone, Does anyone know of a quick (yet somewhat reliable) sort of cheat-sheet/quick reference sheet with the more common folds with an illustrative example? -- Michael C. Thompson Graduate Student Biochemistry Molecular Biology Division Department of Chemistry Biochemistry University of California, Los Angeles mi...@chem.ucla.edu
Re: [ccp4bb] New Faster-than-fast Fourier transform
George Sheldrick gshe...@shelx.uni-ac.gwdg.de a écrit : For all those interested in the technical details about this new Fourier stuff, I saw that the whole paper is available from the web site, not only the simplified account (look at right of this awfully wrong 3-term Fourier synthesis illutration that I would never show to beginners!) P. Dumas From the rather non-technical inofrmation available so far, it seems to me that it is like leaving out all but the strongest reflections (or perhaps the strongest normalized structure factors). This is unlikely to improve the quality of structure refinement, the importance of using as much data as possible and not leaving out the weakest reflections has often been emphasized. This is quite different to data compression of music. However there is one case where we are already doing this, namely small molecule direct methods or using the same programs to find the heavy atoms in SAD and MAD experiments. These programs use only the strongest 15-20% of the normalized structure factors (E-values). This is possible because the data to parameter ratio is still sufficient, and these reflections contain much of the useful information. However the Fourier routines used by these programs (at least the ones I wrote) are not taking full advantage of the 'sparseness' of the data, so if the MIT people have found a clever way of doing this it might still be useful for heavy atom location (though FFTW and the Intel MKL FFT will be difficult to beat). George On 01/20/2012 06:57 PM, Ethan Merritt wrote: On Friday, 20 January 2012, Jim Fairman wrote: New Fourier transform algorithm supposedly improves the speed of Fourier transforms get up to a tenfold increase in speed depending upon circumstances. Hopefully this will get incorporated into our refinement programs. http://web.mit.edu/newsoffice/2012/faster-fourier-transforms-0118.html This report is interesting, but it is not immediately obvious to me that crystallographic transforms are in the class of problems for which this algorithm is applicable. From reading the very non-technical article linked above, I conclude that a better summary would be New approach to Fourier approximation provides a very cheap (fast) way of identifying and then discarding components that contribute very little to the signal. In other words, it seems to be a way of increasing the compression ratio for lossy image/audio compression without increasing the amount of time required for compression. So if you're doing map fitting while listening to streamed mp3 music files, perhaps your map inversion will get a slightly larger slice of the CPU time relative to LastFM. On the other hand, it is possible that somewhere in here lies a clever approach to faster solvent flattening. Ethan Philippe DUMAS, responsable d'équipe Directeur de Recherche au CNRS Equipe de Biophysique Biologie Structurale Unité 'Architecture Réactivité de l'ARN', UPR9002 Institut de Biologie Moléculaire et Cellulaire 15, rue René Descartes F67084 STRASBOURG +33 (0)388 41 70 02 http://www-ibmc.u-strasbg.fr/arn/Dumas/index_dum_fr.html
Re: [ccp4bb] Protein Fold Motifs- off-topic
Thanks guys
Re: [ccp4bb] New Faster-than-fast Fourier transform
After quick look at the manuscript: It is applicable to sparse signals (i.e. number of non-zero elements is not whole space). It would be applicable to inverse FFT after density modification and gain would not be that much. k-sparse approximation would loose signal (strictly speaking it does not produce exact FFT but an approximation, i.e. very weak signals (electron density, fourier coefficients) may be ignored) At the moment I am a bit sceptical about its use in crystallography. Although with careful implementation twice speed up crystallographic FFT could be possible. Garib On 20 Jan 2012, at 17:37, Jim Fairman wrote: New Fourier transform algorithm supposedly improves the speed of Fourier transforms get up to a tenfold increase in speed depending upon circumstances. Hopefully this will get incorporated into our refinement programs. http://web.mit.edu/newsoffice/2012/faster-fourier-transforms-0118.html -- Jim Fairman, Ph D. Crystal Core Leader I/Project Leader I Emerald BioStructures Tel: 206-780-8914 Cell: 240-479-6575 E-mail: fairman@gmail.com jfair...@embios.com Garib N Murshudov Structural Studies Division MRC Laboratory of Molecular Biology Hills Road Cambridge CB2 0QH UK Email: ga...@mrc-lmb.cam.ac.uk Web http://www.mrc-lmb.cam.ac.uk
[ccp4bb] protein structure for high schoolers
Hi- I am trying to help my former chemistry teacher set up a demonstration of protein structure for her class. I'd like to include electron density maps, and maybe show an enzyme active site. Are there suggestions from the BB on the easiest way to do this? Would pymol be the program of choice, or is there a simpler program that could show electron density? Has anyone already created such a demonstration they could and have advice on it? James
Re: [ccp4bb] protein structure for high schoolers
Hi, I think that spdbv (deepview) and the tutorial has some of what you need. The program is very simple to implement on any Mac or PC, although it's not the nicest program to use in the long run. It'll take you 5 minutes to install and test the features you'd like from the tutorial. Cheers, Boaz Boaz Shaanan, Ph.D. Dept. of Life Sciences Ben-Gurion University of the Negev Beer-Sheva 84105 Israel E-mail: bshaa...@bgu.ac.il Phone: 972-8-647-2220Skype: boaz.shaanan Fax: 972-8-647-2992 or 972-8-646-1710 From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of James Whittle [whit...@crystal.harvard.edu] Sent: Friday, January 20, 2012 11:41 PM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] protein structure for high schoolers Hi- I am trying to help my former chemistry teacher set up a demonstration of protein structure for her class. I'd like to include electron density maps, and maybe show an enzyme active site. Are there suggestions from the BB on the easiest way to do this? Would pymol be the program of choice, or is there a simpler program that could show electron density? Has anyone already created such a demonstration they could and have advice on it? James
Re: [ccp4bb] protein structure for high schoolers
Hi, I've given a couple talks/demos to HS students. As much as I love enzymes, I found it more effective to show structures of proteins binding to other biological molecules (not just other proteins). I typically show phosphatidylinositol binding protein (PITP) bound to phosphatidylcholine, simply because that is a structure I solved and am comfortable with. I think DNA binding proteins would also be effective. p53 might be a good candidate, especially because of its association with cancer - that will get their attention. I used pymol, it was easy to install on the teachers computer, then they could easily use it after I left. Regards, Marilyn Marilyn D. Yoder Division of Cell Biology Biophysics School of Biological Sciences University of Missouri-Kansas City 5007 Rockhill Rd. Kansas City, MO 64110 Phone: 816-235-1986 From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of James Whittle Sent: Friday, January 20, 2012 3:41 PM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] protein structure for high schoolers Hi- I am trying to help my former chemistry teacher set up a demonstration of protein structure for her class. I'd like to include electron density maps, and maybe show an enzyme active site. Are there suggestions from the BB on the easiest way to do this? Would pymol be the program of choice, or is there a simpler program that could show electron density? Has anyone already created such a demonstration they could and have advice on it? James
[ccp4bb] Fwd: [ccp4bb] Off Topic: Good Mass Spec Facility?
Thanks everyone for the helpful responses! For the curious, here is a list of the postings: * I have two to recommend. I don't know how many outside samples they process but Oak Ridge National lab has a spectacular mass spec facility that we used extensively while i was at the University of Tennessee doing my Ph D (http://www.ornl.gov/sci/csd/Research_areas/obms_staff.html). Another lab I know if is the Proteomics Center at Case Western Reserve in Cleveland ( http://proteomics.case.edu/instruments_and_computational_facilities.aspx). Jim Fairman, Ph D. Crystal Core Leader I/Project Leader I Emerald BioStructures Tell me about it. I'm tearing my hair right now because of two projects that are stalled waiting for the UIC small molecule MS facility to get us results. Having said that: We have had pretty good results with the facility at Wash U, doing intact mass on large peptides and smallish (30 kD) proteins (I assume you're looking at intact masses?). They typically get us results within 1-2 weeks. They have a couple of quirks (for example, they typically mail us hard copies of printouts, instead of emailing us PDFs), but have been reliable and good about tweaking their analyses to fit our samples. http://msr.dom.wustl.edu/ Good luck, Pat Loll * Hi Austin: I know about Proteomics Center at Stonybrook, NY. It may be far for you. The website is :http://www.osa.sunysb.edu/Proteomics/ Thanks Rakhi Agarwal * Thanks again, Austin. -- Forwarded message -- From: Dima Klenchin klenc...@facstaff.wisc.edu Date: Fri, Jan 20, 2012 at 11:52 AM Subject: Re: [ccp4bb] Off Topic: Good Mass Spec Facility? To: Austin Rice austinrice2...@u.northwestern.edu I am trying to accurately quantify disulfide bond formation. I would like to use a mass spec method involving two thiol reactive labels: one with ethyl attached reacted before disulfide reduction and the other with methyl attached reacted after disulfide reduction. I can label my own samples, the issue is finding a mass spec facility capable of gathering and processing the data in a timely manner. Can someone recommend a mass spec facility? Austin, Judging from no replies on CCP4bb, you are probably getting most replies by private email. If you are not going to post a summary, would you mind sending me an email with the recommended places? I have the same question as you. Our facility is pretty bad - expensive and too frequently pathetically incompetent. Thanks, Dima
[ccp4bb] chemical state of trimethyl lead in the crystal
Does trimethyl lead tend to lose the Me in aqueous buffers? A colleague is preparing to deposit a 2.9A structure that was refined against the TML derivative (higher resolution than native). Since the Pb was added as trimethyllead, the first inclination is to report the heavy atoms as TML, ligand ID PBM. However there is no density for the Me's, not surprising at this resolution and because they are probably rotationally disordered. So she doesn't know where to put them, and if they are omitted they will add to the missing atoms list in her PDB file. Also the Pb tend to be around Arg and Lys, whereas TML is apparently a cation (TML-Acetate?). So I wonder if the compound hydrolyzes to some kind of possibly anionic Pb(OH)n Also, if it is TML what should the Pb-C bond lengths be? Parameter file from HicUp (based on PDB) has ~2.2, but phenix.elbow puts it at 2.5 A. eab
Re: [ccp4bb] protein structure for high schoolers
James, I would like to recommend the free ICM-Browser http://www.molsoft.com/icm_browser.html . It is widely used for teaching structural biology and it is easy to make fun and interesting fully interactive 3D slides and animations of protein structures. The students can view the fully interactive 3D files in the browser, PowerPoint or on the web using ActiveICM http://www.molsoft.com/activeicm.html The files can also be viewed on the *iPad**/iPhone* using iMolview http://www.molsoft.com/iMolview.html We will be happy to send you some examples if you would like them. Thanks, Andy On 1/20/2012 1:41 PM, James Whittle wrote: Hi- I am trying to help my former chemistry teacher set up a demonstration of protein structure for her class. I'd like to include electron density maps, and maybe show an enzyme active site. Are there suggestions from the BB on the easiest way to do this? Would pymol be the program of choice, or is there a simpler program that could show electron density? Has anyone already created such a demonstration they could and have advice on it? James -- Andrew Orry Ph.D. MolSoft LLC Senior Research Scientist 11199 Sorrento Valley Road, S209 San Diego CA 92121 Tel: 858-625-2000 x108 Fax: 828-625-2888 www.molsoft.com
Re: [ccp4bb] protein structure for high schoolers
foldit doesn't do electron densities and I don't recall if there are any puzzles in it that mention active sites/docking (it's been more than a year since I played it), but it's worth a mention. Hi- I am trying to help my former chemistry teacher set up a demonstration of protein structure for her class. I'd like to include electron density maps, and maybe show an enzyme active site. Are there suggestions from the BB on the easiest way to do this? Would pymol be the program of choice, or is there a simpler program that could show electron density? Has anyone already created such a demonstration they could and have advice on it? James
