Re: [ccp4bb] Ca or Zn
Dear Ethan, Yes indeed. An exciting development underway at Diamond Light Source led by Armin Wagner will greatly improve the ease of measurement at eg the calcium edge but also extending that wavelength range. The furin paper I quoted did nevertheless successfully show structural detail from those measurements. The Ga and Zn edges wavelengths are an easier challenge to access, i agree of course, rather the interest I tried to stress was the getting of the sigmas on the occupancies as well as the occupancies themselves, and how we did that and checked them via more than one software is also hopefully of interest. Greetings from Taipei, John Prof John R Helliwell DSc On 31 Oct 2012, at 10:37, Ethan Merritt merr...@u.washington.edu wrote: On Tuesday, 30 October 2012, Jrh wrote: This paper describes use of data either side of the calcium edge:- http://dx.doi.org/10.1107/S0907444905002556 I think that counts as not amenable (which is not quite the same as impossible. From the Methods section of that paper: Measurements in the vicinity of the K absorption edge of calcium (3.07 Å) are close to or beyond the physical limit of most beamlines typically used for X-ray crystallography [...] It was not possible to observe interpretable diffraction patterns at λ = 3 Å with the weakly diffracting furin crystals using the MAR CCD detector and exposure times up to 20 min per degree of rotation. They did soldier on and managed to collect extremely weak data below the Ca edge and stronger but still very weak data above the edge where the Ca f term was appreciable. But this is far from a routine experiment. Another approach dating back to work in 1972 by Peter Coleman and Brian Matthews http://dx.doi.org/10.1016/0006-291X(72)90750-4 is to replace the Ca with a rare earth having similar chemistry (e.g. La, whose L-1 edge is at 1.98Å). This next paper describes a case of gallium and zinc mix at one site with occupancy AND sigmas estimated with different software. This example is however much better diffraction resolution than that you may have. But hopefully will still be of interest:- http://dx.doi.org/10.1107/S0108768110011237 Ga and Zn, sure. That's an easy one. The Ga edge is at 1.196Å and the Zn edge is at 1.284Å, both edges are nicely in range for data collection and they are close enough together that little or no beamline readjustment is needed when jumping from one to the other. Ethan Prof John R Helliwell DSc On 31 Oct 2012, at 04:53, Ethan Merritt merr...@u.washington.edu wrote: On Tuesday, October 30, 2012 01:44:43 pm Adrian Goldman wrote: The coordination is indicative but not conclusive but, as I responded to the original poster, I think the best approach is to use anomalous scattering. You can measure just below and above the Ca edge, Actually, you can't. The Ca K-edge is at 3.07Å, which is not a wavelength amenable to macromolecular data collection. cheers, Ethan and similarly with the Zn, and those maps will be _highly_ indicative of the relative amounts of metal ion present. In fact, you can deconvolute so that you know the occupancy of the metals at the various sites. Adrian On 30 Oct 2012, at 22:37, Chittaranjan Das wrote: Veerendra, You can rule out if zinc has replaced calcium ions (although I agree with Nat and others that looking at the coordination sphere should give a big clue) by taking a few crystals, washing them a couple of times and subjecting them to ICP-MS analysis, if you have access to this technique. You can learn how many zinc, if any, have bound per one protein molecule in the dissolved crystal. Best Chitta - Original Message - From: Veerendra Kumar veerendra.ku...@uconn.edu To: CCP4BB@JISCMAIL.AC.UK Sent: Tuesday, October 30, 2012 2:55:33 PM Subject: [ccp4bb] Ca or Zn Dear CCP4bb users, I am working on a Ca2+ binding protein. it has 4-5 ca2+ binding sites. I purified the protein in presence of Ca2+ and crystallized the Ca2+ bound protein. I got crystal and solved the structure by SAD phasing at 2.1A resolution. I can see the clear density in the difference map for metals at the expected binding sites. However I had ZnCl2 in the crystallization conditions. Now i am not sure whether the observed density is for Ca or Zn or how many of them are ca or zn? Since Ca (20 elctron) and Zn (30 electron), is this value difference can be used to make a guess about different ions? is there any way we can find the electron density value at different peaks? Thank you Veerendra
Re: [ccp4bb] Coot 0.7 Saving Dialog opens behind main window
Le 30/10/12 20:28, Jason Busby a écrit : Another work-around is to use the command-tilde (⌘ + ~) keystroke. That will cycle through all the windows of the current program. Jason. -- Jason Busby PhD Student Laboratory of Structural Biology School of Biological Sciences University of Auckland Thomas Building 110 3a Symonds St Private Bag 92019 Auckland 1142 New Zealand ph: +64 9 3737599 ext 84155 fx: +64 9 3737414 On 31/10/2012, at 4:58 AM, Damian Niegowski wrote: If you choose to use the excellent Mac OSX feature Exposé and Active screen corners this becomes less of a problem. Damian Niegowski Ph.D. Institute of Medical Biochemistry and Biophysics Karolinska Institutet Scheeles väg 2 171 77 STOCKHOLM e-mail: damian.niegow...@ki.se phone: 0046 8 524 876 33 fax: 0046 8 736 04 39 On Oct 30, 2012, at 4:32 PM, Eike Schulz wrote: Dear Coot-users, I am running Coot-0.7 on OSX 10.6.8. Installation from the 'Scott'-package was no problem at all it runs very smoothly. However, whenever I want to save the coordinates the saving dialog open -behind- the main window. To be more precise: the coordinate molecule selector opens in front of it but the -file name selector- opens behind the main window. This is over the time a bit frustrating when you have to minimize/move the main window every time you want to save your structure. Does it happen to others as well, or is this specific to my system? If its possible, how could it be changed to open in front of the main window? Best regards Eike Hi, I don't know for your osx version (mine is 10.6.8) but the short-cut I know is command-grave accent (⌘ + `). One problem with this is that osx considers all X11-based applications to be a single X11 application, so it can take a while until you reach the window you want if you have other X11-based applications open. Another problem is that, contrary to what you have in aqua-based applications, the X11 windows don't cycle. Apple developers have known about these issues for a long, long time. Perhaps they solved them in more recent versions of osx. Best regards, -- Miguel Architecture et Fonction des Macromolécules Biologiques (UMR7257) CNRS, Aix-Marseille Université 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 mailto:miguel.ortiz-lombar...@afmb.univ-mrs.fr http://w2.afmb.univ-mrs.fr/Miguel-Ortiz-Lombardia
Re: [ccp4bb] Coot 0.7 Saving Dialog opens behind main window
Choosing one of the desired program/instance windows and pressing F10 is probably the most simple way. F10 will show you all windows open accosiated with the one you choose. Damian Niegowski Ph.D. Institute of Medical Biochemistry and Biophysics Karolinska Institutet Scheeles väg 2 171 77 STOCKHOLM e-mail: damian.niegow...@ki.se phone: 0046 8 524 876 33 fax: 0046 8 736 04 39 On Oct 31, 2012, at 10:13 AM, Miguel Ortiz Lombardía wrote: Le 30/10/12 20:28, Jason Busby a écrit : Another work-around is to use the command-tilde (⌘ + ~) keystroke. That will cycle through all the windows of the current program. Jason. -- Jason Busby PhD Student Laboratory of Structural Biology School of Biological Sciences University of Auckland Thomas Building 110 3a Symonds St Private Bag 92019 Auckland 1142 New Zealand ph: +64 9 3737599 ext 84155 fx: +64 9 3737414 On 31/10/2012, at 4:58 AM, Damian Niegowski wrote: If you choose to use the excellent Mac OSX feature Exposé and Active screen corners this becomes less of a problem. Damian Niegowski Ph.D. Institute of Medical Biochemistry and Biophysics Karolinska Institutet Scheeles väg 2 171 77 STOCKHOLM e-mail: damian.niegow...@ki.se phone: 0046 8 524 876 33 fax: 0046 8 736 04 39 On Oct 30, 2012, at 4:32 PM, Eike Schulz wrote: Dear Coot-users, I am running Coot-0.7 on OSX 10.6.8. Installation from the 'Scott'-package was no problem at all it runs very smoothly. However, whenever I want to save the coordinates the saving dialog open -behind- the main window. To be more precise: the coordinate molecule selector opens in front of it but the -file name selector- opens behind the main window. This is over the time a bit frustrating when you have to minimize/move the main window every time you want to save your structure. Does it happen to others as well, or is this specific to my system? If its possible, how could it be changed to open in front of the main window? Best regards Eike Hi, I don't know for your osx version (mine is 10.6.8) but the short-cut I know is command-grave accent (⌘ + `). One problem with this is that osx considers all X11-based applications to be a single X11 application, so it can take a while until you reach the window you want if you have other X11-based applications open. Another problem is that, contrary to what you have in aqua-based applications, the X11 windows don't cycle. Apple developers have known about these issues for a long, long time. Perhaps they solved them in more recent versions of osx. Best regards, -- Miguel Architecture et Fonction des Macromolécules Biologiques (UMR7257) CNRS, Aix-Marseille Université 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 mailto:miguel.ortiz-lombar...@afmb.univ-mrs.fr http://w2.afmb.univ-mrs.fr/Miguel-Ortiz-Lombardia
Re: [ccp4bb] Coot 0.7 Saving Dialog opens behind main window
Unfortunately, that very much depends on which OSX you are running (Leopard, Snow Leopard, Lion, Mountain Lion) and which keyboard you have…! On my keyboard it's F3 and not F10. T. --- Dr Antony W Oliver Senior Research Fellow CR-UK DNA Repair Enzymes Group Genome Damage and Stability Centre Science Park Road University of Sussex Falmer, Brighton, BN1 9RQ email: antony.oli...@sussex.ac.uk tel (office): +44 (0)1273 678349 tel (lab): +44 (0)1273 677512 On Oct 31, 2012, at 9:30 AM, Damian Niegowski wrote: Choosing one of the desired program/instance windows and pressing F10 is probably the most simple way. F10 will show you all windows open accosiated with the one you choose. Damian Niegowski Ph.D. Institute of Medical Biochemistry and Biophysics Karolinska Institutet Scheeles väg 2 171 77 STOCKHOLM e-mail: damian.niegow...@ki.se phone: 0046 8 524 876 33 fax: 0046 8 736 04 39 On Oct 31, 2012, at 10:13 AM, Miguel Ortiz Lombardía wrote: Le 30/10/12 20:28, Jason Busby a écrit : Another work-around is to use the command-tilde (⌘ + ~) keystroke. That will cycle through all the windows of the current program. Jason. -- Jason Busby PhD Student Laboratory of Structural Biology School of Biological Sciences University of Auckland Thomas Building 110 3a Symonds St Private Bag 92019 Auckland 1142 New Zealand ph: +64 9 3737599 ext 84155 fx: +64 9 3737414 On 31/10/2012, at 4:58 AM, Damian Niegowski wrote: If you choose to use the excellent Mac OSX feature Exposé and Active screen corners this becomes less of a problem. Damian Niegowski Ph.D. Institute of Medical Biochemistry and Biophysics Karolinska Institutet Scheeles väg 2 171 77 STOCKHOLM e-mail: damian.niegow...@ki.se phone: 0046 8 524 876 33 fax: 0046 8 736 04 39 On Oct 30, 2012, at 4:32 PM, Eike Schulz wrote: Dear Coot-users, I am running Coot-0.7 on OSX 10.6.8. Installation from the 'Scott'-package was no problem at all it runs very smoothly. However, whenever I want to save the coordinates the saving dialog open -behind- the main window. To be more precise: the coordinate molecule selector opens in front of it but the -file name selector- opens behind the main window. This is over the time a bit frustrating when you have to minimize/move the main window every time you want to save your structure. Does it happen to others as well, or is this specific to my system? If its possible, how could it be changed to open in front of the main window? Best regards Eike Hi, I don't know for your osx version (mine is 10.6.8) but the short-cut I know is command-grave accent (⌘ + `). One problem with this is that osx considers all X11-based applications to be a single X11 application, so it can take a while until you reach the window you want if you have other X11-based applications open. Another problem is that, contrary to what you have in aqua-based applications, the X11 windows don't cycle. Apple developers have known about these issues for a long, long time. Perhaps they solved them in more recent versions of osx. Best regards, -- Miguel Architecture et Fonction des Macromolécules Biologiques (UMR7257) CNRS, Aix-Marseille Université 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 mailto:miguel.ortiz-lombar...@afmb.univ-mrs.fr http://w2.afmb.univ-mrs.fr/Miguel-Ortiz-Lombardia
Re: [ccp4bb] Coot 0.7 Saving Dialog opens behind main window
On OSX 10.6.8.(Show Leopard) which was the system in question this option exist, but you are right, the key used might be different. Damian Niegowski Ph.D. Institute of Medical Biochemistry and Biophysics Karolinska Institutet Scheeles väg 2 171 77 STOCKHOLM e-mail: damian.niegow...@ki.se phone: 0046 8 524 876 33 fax: 0046 8 736 04 39 On Oct 31, 2012, at 10:38 AM, Antony Oliver wrote: Unfortunately, that very much depends on which OSX you are running (Leopard, Snow Leopard, Lion, Mountain Lion) and which keyboard you have…! On my keyboard it's F3 and not F10. T. --- Dr Antony W Oliver Senior Research Fellow CR-UK DNA Repair Enzymes Group Genome Damage and Stability Centre Science Park Road University of Sussex Falmer, Brighton, BN1 9RQ email: antony.oli...@sussex.ac.uk tel (office): +44 (0)1273 678349 tel (lab): +44 (0)1273 677512 On Oct 31, 2012, at 9:30 AM, Damian Niegowski wrote: Choosing one of the desired program/instance windows and pressing F10 is probably the most simple way. F10 will show you all windows open accosiated with the one you choose. Damian Niegowski Ph.D. Institute of Medical Biochemistry and Biophysics Karolinska Institutet Scheeles väg 2 171 77 STOCKHOLM e-mail: damian.niegow...@ki.se phone: 0046 8 524 876 33 fax: 0046 8 736 04 39 On Oct 31, 2012, at 10:13 AM, Miguel Ortiz Lombardía wrote: Le 30/10/12 20:28, Jason Busby a écrit : Another work-around is to use the command-tilde (⌘ + ~) keystroke. That will cycle through all the windows of the current program. Jason. -- Jason Busby PhD Student Laboratory of Structural Biology School of Biological Sciences University of Auckland Thomas Building 110 3a Symonds St Private Bag 92019 Auckland 1142 New Zealand ph: +64 9 3737599 ext 84155 fx: +64 9 3737414 On 31/10/2012, at 4:58 AM, Damian Niegowski wrote: If you choose to use the excellent Mac OSX feature Exposé and Active screen corners this becomes less of a problem. Damian Niegowski Ph.D. Institute of Medical Biochemistry and Biophysics Karolinska Institutet Scheeles väg 2 171 77 STOCKHOLM e-mail: damian.niegow...@ki.se phone: 0046 8 524 876 33 fax: 0046 8 736 04 39 On Oct 30, 2012, at 4:32 PM, Eike Schulz wrote: Dear Coot-users, I am running Coot-0.7 on OSX 10.6.8. Installation from the 'Scott'-package was no problem at all it runs very smoothly. However, whenever I want to save the coordinates the saving dialog open -behind- the main window. To be more precise: the coordinate molecule selector opens in front of it but the -file name selector- opens behind the main window. This is over the time a bit frustrating when you have to minimize/move the main window every time you want to save your structure. Does it happen to others as well, or is this specific to my system? If its possible, how could it be changed to open in front of the main window? Best regards Eike Hi, I don't know for your osx version (mine is 10.6.8) but the short-cut I know is command-grave accent (⌘ + `). One problem with this is that osx considers all X11-based applications to be a single X11 application, so it can take a while until you reach the window you want if you have other X11-based applications open. Another problem is that, contrary to what you have in aqua-based applications, the X11 windows don't cycle. Apple developers have known about these issues for a long, long time. Perhaps they solved them in more recent versions of osx. Best regards, -- Miguel Architecture et Fonction des Macromolécules Biologiques (UMR7257) CNRS, Aix-Marseille Université 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 mailto:miguel.ortiz-lombar...@afmb.univ-mrs.fr http://w2.afmb.univ-mrs.fr/Miguel-Ortiz-Lombardia
Re: [ccp4bb] Phaser MR with partial solution, 8 molecules/ASU
On the whole it is good practice to refine the 7 molecules you have - correct sequence etc etc, all with NCS restraints a 3A, then if you like use one of your improved molecules as the search model. But don't you have some NC symmetry such as dimers or tetramers - if so take one of the complete units and fit over the partner of the missing molecule - it is very probable then that you have positioned the lost one. Or if you want to be completely automated - use the dimer/tetramer whatever as the search model.. Eleanor MOLREP is good at this - On 30 Oct 2012, at 14:53, Mark J van Raaij wrote: if you are sure about it's position, why not put the 8th molecule by hand? why believe what a program does more than you can see by eye? (this is nothing against Phaser, it is a great program) Mark J van Raaij Laboratorio M-4 Dpto de Estructura de Macromoleculas Centro Nacional de Biotecnologia - CSIC c/Darwin 3 E-28049 Madrid, Spain tel. (+34) 91 585 4616 http://www.cnb.csic.es/~mjvanraaij On 30 Oct 2012, at 15:44, Jacob Wong wrote: Dear all, I have this (3.0 A) structure that has 8 molecules per ASU - Phaser was able to find 7 molecules correctly, but not the last one, as indicated by the .sol file (TFZ=5.1) below and the resultant density map. I tried to delete the entry of the last molecule and give the truncated .sol file for another round of MR but Phaser returned with the same solution that has the 8th molecule misplaced. I am tempted to place the 8th molecule by hand but before that would like to learn from you a better way of handling it. One thing I could think of is to refine/rebuild the partial structure with the 7 molecules so as to resolve any potential packing clashes due to model/structure variations and then let Phaser find/position the 8th one for me, but it appears that Phaser doesn't accept .pdb file for a MR with partial solution routine? Thank you, Jacob # [No title given] SPACEGROUP P 21 21 21 SOLU SET RFZ=3.7 TFZ=8.2 PAK=0 LLG=78 RFZ=3.7 TFZ=16.0 PAK=0 LLG=248 TFZ==17.2 RFZ=3.7 TFZ=17.8 PAK=0 LLG=463 TFZ==19.7 RFZ=2.9 TFZ=23.0 PAK=0 LLG=765 TFZ==23.2 RFZ=2.8 TFZ=28.6 PAK=0 LLG=1201 TFZ==30.0 RFZ=3.9 TFZ=23.1 PAK=0 LLG=1537 TFZ==24.3 RFZ=2.6 TFZ=19.5 PAK=1 LLG=2096 TFZ==32.1 RFZ=3.0 TFZ=5.1 PAK=1 LLG=1945 TFZ==7.0 SOLU 6DIM ENSE ensemble1 EULER 333.533 143.979 14.880 FRAC -0.30547 0.22985 -0.12420 BFAC 0.0 SOLU 6DIM ENSE ensemble1 EULER 287.095 31.031 200.132 FRAC -0.01202 0.48107 -0.12591 BFAC 0.0 SOLU 6DIM ENSE ensemble1 EULER 220.563 33.756 203.275 FRAC -0.33196 0.18927 -0.27514 BFAC 0.0 SOLU 6DIM ENSE ensemble1 EULER 125.978 23.511 167.527 FRAC 0.36411 -0.45096 -0.17121 BFAC 0.0 SOLU 6DIM ENSE ensemble1 EULER 148.925 162.593 356.498 FRAC -0.41711 -0.09462 -0.07282 BFAC 0.0 SOLU 6DIM ENSE ensemble1 EULER 323.033 34.903 192.073 FRAC -0.53201 -0.04754 -0.02533 BFAC 0.0 SOLU 6DIM ENSE ensemble1 EULER 113.904 157.019 345.596 FRAC 0.09892 -0.60041 -0.17986 BFAC 0.0 SOLU 6DIM ENSE ensemble1 EULER 79.967 95.631 1.727 FRAC -0.41239 0.07915 -0.05760 BFAC 0.0
Re: [ccp4bb] refmac
Please send an extract - you probably have a format error.. Or do you have 1500 chais?) Eleanor On 30 Oct 2012, at 22:43, jp d wrote: hi, i have a large pdb file and i keep getting this error with refmac ERROR: number of chains 1500 i suspect something needs to be done to my pdb any suggestions ? thanks jpd
Re: [ccp4bb] oof topic: pH effect on substrate analog
On Tue, 2012-10-30 at 16:12 +, Peter Hsu wrote: I'm wondering, since I lack activity at this pH point, would it lead to no binding of a substrate analog? Not necessarily. You should check pH dependence of the Km - it might be that lower activity is primarily due to reduction in kcat. Binding studies are always a good idea before trying to soak/cocrystallize. With that said, it's entirely possible that you don't see ligand in the electron density because the enzyme is stuck in a wrong conformation or binding site is blocked. I wonder if you can get resolve pH issue by cross-linking the crystals at which point you can use whichever soaking buffer pH you want (assuming no loss of diffraction) Cheers, Ed. -- I'd jump in myself, if I weren't so good at whistling. Julian, King of Lemurs
[ccp4bb] Position: Project Manager for the International Year of Crystallography
PROJECT MANAGER FOR THE INTERNATIONAL YEAR OF CRYSTALLOGRAPHY Organisation: International Union of Crystallography Location: Chester, UK Highly Competitive Salary: £40K minimum Term: Fixed term (2 years) Description: The UN General Assembly has designated 2014 as the International Year of Crystallography. As part of IYCr2014, the International Union of Crystallography (IUCr), which is a scientific union and publisher of several leading scientific journals, is developing a wide-ranging agenda for publicly oriented events across the globe and is looking to appoint an ambitious person for IYCr2014 events management and delivery. You will be responsible for fund-raising and sponsorship activities for the IYCr, helping to publicise the economic and social contributions that crystallography makes by submitting articles to the press and to magazines, promoting poster and museum exhibitions highlighting the usefulness of crystallography, assisting with the development of the IYCr2014 web site, and interacting with the regional and national crystallographic organisations in formulating global sets of events. You will act as the focal point for IYCr2014 and work with all potential partners to make the international year a global success reaching out to schools, colleges and the general public. You will help to assemble a team of enthusiasts to inspire and coordinate worldwide activities. You will be supported by, and will be expected to work with, the various IUCr committees that will oversee the IYCr2014 activities. In addition, we are in the process of appointing a Business Development Executive with primary responsibility for publications development for IYCr2014, and you will work closely with him/her. You will ideally be a graduate with a knowledge of crystallography and experience of writing scientific articles for the general public. We are looking for someone with excellent communication skills and prior experience of raising funds from industrial and private sponsors. Experience with media and journalistic media will be a major advantage. The ability to communicate in another major language in addition to English will also be beneficial. In return, the IUCr offers a competitive salary with excellent benefits and a unique working environment. You will be primarily based in Chester, UK, with some travel opportunities. To be considered for the position please send a CV and covering letter to Carol Cook (c...@iucr.org) by 2 December 2012.
[ccp4bb] PhD student opening, Department of Drug Design and Pharmacology, University of Copenhagen
Please note the opening for the project: Neutron and X-ray structural studies of the epigenetic regulator KDM5B and its interaction partners in oncogene regulation With application deadline 8 november 2012. More details at http://www.farma.ku.dk/index.php?id=11675 Best wishes Michael Gajhede Michael Gajhede Professor Faculty of Health and Medical Sciences Biostructural Research University of Copenhagen Jagtvej 162 2100 Copnhagen Ø Denmark TEL +45 35336000 DIR +45 35336407 m...@sund.ku.dkmailto:m...@sund.ku.dk www.ku.dkhttp://www.ku.dk/ [SUND_bomaerke_UK] inline: image001.gif
[ccp4bb] fragment searching
Does anyone know a good way to search for a fragment matches(~16 residue long helix or loop) from pdb?I have a fragment of pdb and want to pull out all the similar structures from the pdb, any easy way to do that? Thanks a lot. On Tue, Oct 30, 2012 at 9:34 AM, David Briggs drdavidcbri...@gmail.comwrote: Hello Adrian, I use Research Gate and there are a few occasions where I have found it useful, particularly the questions feature. HTH, Dave David C. Briggs PhD http://about.me/david_briggs On 30 October 2012 16:13, Adrian Goldman adrian.gold...@helsinki.fi wrote: Hi, At the risk of starting another series of rants, and somewhat off-topic, is anyone actively using ResearchGate? It is bombarding me with email messages, but I am uncertain as to whether people are really using it or whether it is just scientific spam. Adrian Goldman Adrian Goldman Institute of Biotechnology, University of Helsinki, Finland
[ccp4bb] Workshop Computational challenges in Structural Biology Strasbourg November 14 15 2012
Workshop Computational challenges in Structural Biology Strasbourg November 14 15 2012. See web site : http://ccsb2012.loria.fr/ This mail is to announce the forthcoming workshop Computational challenges in Structural Biology which will be held in Strasbourg November 14 15 2012.The main aim of this workshop is to highlight current computational challenges in cryo-electron microscopy and to brain-storm possible solutions. Cryo-electron microscopy is becoming an increasingly powerful technique for solving the structures of large biomolecules. However, in order to reconstruct the 3D structures or large molecular machines with atomic resolution, it is necessary to process many thousands or even millions of 2D micrographs and to use advanced 3D modeling techniques. This workshop brings together experimental and molecular modeling experts in the above fields in order to identify current bottlenecks and to explore possible solutions using high performance computing and integrative modeling techniques. Registration Information Registration for this workshop is free, but the number of participants is limited. If you are interested please register through the web site. We still have some places available. Thank you for your interest in the workshop The organizers. David Ritchie, Annick Dejaegere, Patrick Schultz.
[ccp4bb] Faculty positions at Molecular Biophysics Unit, IISc, Bangalore
Dear Sham Well-done , You did a great job by raising this issue on CCP4, I am sure most of the Indian post docs/ scientists working outside India will agree with you. Sham ! I think you are wrong here:* You said In all cases, (I would say only 95 % cases) it is their mutual understanding to fix their own people, through the back-door deal. Here those people will disagree who got into a position through the same means.* I agree with Garib that we should stop this discussion on CCP4bb. This would not yield any positive outcomes, Instead it would hurt sentiments and emotions of many Indians (mainly beneficiaries of this scam /civic crime). But just to conclude this, I really appreciate Sham for bringing up this issue on CCP4 and making international scientific community aware of what is happening in Indian Science/Research institutes as far as faculty recruitment process is concerned. Some of the international scientist will be invited to attend conference on International Conference on Biomolecular Forms and Functions: celebrating 50 years of the Ramachandran Map at IISc Bangalore,in January 2013, , I am sure some of the big Indian bosses (those who control these institutes) within india, will be attending this conference,if you get a chance to have informal discussion on these issues with some of these people, please raise these issues, this will be really helpful for Indian post docs those who are struggling to find a job in India, despite of having a very strong CV and skills in the field. Thanks and regards
[ccp4bb] Position in Structural Biology at OIST, Okinawa, Japan
Postdoctoral Position in Structural Biology at OIST, Okinawa, Japan A Postdoctoral position in Structural Biology (Protein X-ray crystallography) is available in the Trans-membrane Trafficking Unit at Okinawa Institute of Science and Technology, Okinawa Japan. We are seeking for an innovative, talented and highly motivated independent scientist to work on the structure of membrane proteins. Applications should be sent to Prof. Fadel Samatey at tmt.012j...@oist.jp and must include a CV and contact information of up to three referees. Experience in cloning, protein expression, protein purification, protein crystallization and protein structure determination is required. The position will initially be for one year, with a possibility of extension for a total of four years. Inquiries about the position are welcome. Review of applications will begin immediately.Application deadline is December 27, 2012. OIST offers a very competitive salary and comprehensive benefits package. OIST embraces diversity and recognizes it as being a key to success. We believe in developing and maintaining a diverse workforce. Further information about the institute can be found at http://www.oist.jp/
Re: [ccp4bb] fragment searching
CCP4's gesamt should help you here. It can search a collection of PDB/mmCIF files for a structural match, any mainchain fragment with C-alphas would do. For searching through an archive, you need to use it off-line, from a terminal window. Run $CCP4/bin/gesamt without parameters, it will print usage instructions, you need 2nd or 3rd command line template depending on how you'd like to specify your query fragment. Beware that SSM/Superpose is not the best choice here and may not work at all. Gesamt should be reasonably fast on short fragments, I'd expect that execution time will be that required for opening/reading all files in the PDB :) Hope this helps, Eugene On 31 Oct 2012, at 15:31, rui wrote: Does anyone know a good way to search for a fragment matches(~16 residue long helix or loop) from pdb?I have a fragment of pdb and want to pull out all the similar structures from the pdb, any easy way to do that? Thanks a lot. On Tue, Oct 30, 2012 at 9:34 AM, David Briggs drdavidcbri...@gmail.commailto:drdavidcbri...@gmail.com wrote: Hello Adrian, I use Research Gate and there are a few occasions where I have found it useful, particularly the questions feature. HTH, Dave David C. Briggs PhD http://about.me/david_briggs On 30 October 2012 16:13, Adrian Goldman adrian.gold...@helsinki.fimailto:adrian.gold...@helsinki.fi wrote: Hi, At the risk of starting another series of rants, and somewhat off-topic, is anyone actively using ResearchGate? It is bombarding me with email messages, but I am uncertain as to whether people are really using it or whether it is just scientific spam. Adrian Goldman Adrian Goldman Institute of Biotechnology, University of Helsinki, Finland -- Scanned by iCritical.
