[ccp4bb] Align linux version
Dear CCP4 users, We are trying to align two different structures. It would be helpful for us if anybody has linux compiled align version? Regards, Mintu Chandra
Re: [ccp4bb] Align linux version
-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Dear Mintu Chandra, Do you mean by 'has linux compiled align version', that 'align' is a program you use for the alignment? I wonder because I have not heard of it. If you would be happy with any alignment software, you could use coot (graphical) or lsqkab (command line). Both programs areavailable once you installed ccp4. Regards, Tim Gruene On 11/10/2013 01:30 PM, Mintu Chandra wrote: Dear CCP4 users, We are trying to align two different structures. It would be helpful for us if anybody has linux compiled align version? Regards, Mintu Chandra - -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A -BEGIN PGP SIGNATURE- Version: GnuPG v1.4.15 (GNU/Linux) Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/ iD8DBQFSf/YeUxlJ7aRr7hoRAvhHAJ4+LUkvSIMPWjbTkKdw3+6LMtztfQCgztjN lG+aflDaFBmC8kBvJYA4WoE= =Vpsr -END PGP SIGNATURE-
[ccp4bb] postdoctoral position at Brown University
Dear colleagues, Please see below an announcement regarding an opening for a postdoctoral associate in structural biology at Brown University. Brown University, an Ivy League institution, is located in Providence, Rhode Island, less than one hour away from Boston and three hours away from New York City. The structural biology facility at Brown’s Laboratories of Molecular Medicine (LMM) includes, among others, new X-ray crystallography instrumentation (Rigaku FR-E+ SuperBright with VariMax-HF ArcSec optics, a Saturn 944 CCD detector and ACTOR robotic crystal mounting system), a BIOSAXS-1000 small angle X-ray scattering instrument, and an 850 MHz NMR spectrometer. Many thanks, Alexandra Title: Postdoctoral Research AssociateThe Department of Molecular Biology, Cell Biology and Biochemistry at Brown University is seeking a Postdoctoral Research Associate. The position is in the laboratory of Dr. Alexandra Deaconescu. The laboratory's interest is the interplay between DNA repair and other cellular processes including transcription and chromatin remodeling, and is focused on elucidating the function and mechanochemistry of DNA-based motors using a combination of biochemical, biophysical and structural techniques. (e.g. X-Ray crystallography, small-angle X-ray scattering and transmission electron microscopy). A successful candidate should have the following qualifications. A Ph.D. in the field of Molecular Biology, Cell Biology, Biochemistry or related field. An established track-record of publications in peer-reviewed journals. Solid experience in biochemistry of complex DNA-binding proteins (such as chromatin remodeling factors or DNA repair proteins) and eukaryotic expression systems. Prior knowledge of crystallography would be a plus, but not required. Must be highly motivated; work independently as well as in a team. Excellent spoken and written English is required. New Ph.D. graduates are encouraged to apply. Salary, starting date and project details are negotiable. For more information about the lab, visit, https://research.brown.edu/research/profile.php?id=1379608523r=1 Interested candidates should send a CV, one page research experience summary and contact information for three references to alexandra_deacone...@brown.edu. Please write Postdoctoral Candidate in the e-mail subject header. Brown University is an EEO/AA employer and actively solicits applications from minorities and women. -- Alexandra M. Deaconescu, Ph.D. Research Associate, HHMI c/o Grigorieff Laboratory Rosenstiel Center MS029 Brandeis University 415 South St. Waltham, MA 02454 phone: 781-736-2498 For FEDEX Brandeis University Kalman Receiving Dock 415 South St. Waltham, MA 02454
Re: [ccp4bb] Align linux version
Mintu Chandra, align is gerson cohen's program. Unless you talk about another align. I googled align for linux Gerson Cohen and here is what I found -- the linux version http://software.compbio.washington.edu/ramp/ramp/src/other_source/align.save.f Test it and see if it works. If not, there is a superpose server as well that you can use in the internet. just google superpose. Also coot. Phenix has some option as I recall I have seen it. lsqman does the job as well. jackie vitali On Sun, Nov 10, 2013 at 4:09 PM, Tim Gruene t...@shelx.uni-ac.gwdg.de wrote: -BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Dear Mintu Chandra, Do you mean by 'has linux compiled align version', that 'align' is a program you use for the alignment? I wonder because I have not heard of it. If you would be happy with any alignment software, you could use coot (graphical) or lsqkab (command line). Both programs areavailable once you installed ccp4. Regards, Tim Gruene On 11/10/2013 01:30 PM, Mintu Chandra wrote: Dear CCP4 users, We are trying to align two different structures. It would be helpful for us if anybody has linux compiled align version? Regards, Mintu Chandra - -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A -BEGIN PGP SIGNATURE- Version: GnuPG v1.4.15 (GNU/Linux) Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/ iD8DBQFSf/YeUxlJ7aRr7hoRAvhHAJ4+LUkvSIMPWjbTkKdw3+6LMtztfQCgztjN lG+aflDaFBmC8kBvJYA4WoE= =Vpsr -END PGP SIGNATURE-
Re: [ccp4bb] monovalent cation binding sites
Dear John, many thanks for the reference. Discussions of spatial autocorrelation measures seem to come up mostly in the econometrics and geography literature. An expert (I am not ) will no doubt supply better citations, but the chapters by Haining and Getis in Handbook of Applied Spatial Analysis http://www.springer.com/economics/regional+science/book/978-3-642-03646-0 may be of use. There is a discussion of testing for white noise with no spatial dependence in the context of image analysis (courtesy of Peyman Milanfar ) in section III of http://www.lx.it.pt/~mtf/Almeida_Figueiredo_TIP2013.pdf What I was asking about is a fairly simple-minded application of these tests. Density from calculated structure factors for a 10A cube P1 unit cell with either O or Na at the center shows clear difference up to 2A from the peak: http://diablo.ucsc.edu/~afyfe/navso/navso.pdf Pearson correlation ignores position and only considers density values. For distinguishing Na and water amidst the noise of a real map however, it might (or not..) be helpful to test whether a cluster of positive/negative values near the peak differs from what can be expected randomly in the map. Best, Alastair Fyfe On 11/09/2013 11:27 PM, Jrh wrote: Dear Alastair, This reference:- http://dx.doi.org/10.1107/S0907444903004219 seems related to your email input below. I would be grateful though to be guided with a couple of references from you on the topics you raise. Thankyou in anticipation, Best wishes, John Prof John R Helliwell DSc FInstP CPhys FRSC CChem F Soc Biol. Chair School of Chemistry, University of Manchester, Athena Swan Team. http://www.chemistry.manchester.ac.uk/aboutus/athena/index.html On 9 Nov 2013, at 20:30, Alastair Fyfe af...@ucsc.edu wrote: A related question on this topic: calculated density curves drop off at different rates even for isoelectronic ions/water. Thus the neighborhood of a mismodeled peak in the error map would be expected to show detectable, non-random, spatial dependence. On the other hand the neighborhood of a well-modeled peak should be indistinguishable from white noise. Though there are statistics (Moran's I, Geary's C ) for testing spatial effects in variable correlation that could be applied to DFc/ 2mFo-DFc correlation, I haven't seen them applied to this problem. Can anyone suggest a relevant reference? This seems a useful adjunct to bond-valence/non-bonding contact methods. thanks, Alastair Fyfe On 11/09/2013 03:24 AM, Robbie Joosten wrote: Hi Ed, WHAT_CHECK checks water that may be ions and also checks the identity of ions already built. The check my metal server is also very good for final validation of ions. Cheers, Robbie Sent from my Windows Phone Van: Edward A. Berry Verzonden: 9-11-2013 7:29 Aan: CCP4BB@JISCMAIL.AC.UK Onderwerp: Re: [ccp4bb] monovalent cation binding sites Thanks, all! Ed Nat Echols wrote: In the latest Phenix: mmtbx.water_screen model.pdb data.mtz elements=NA,K The data are required right now, but I could be convinced to make that optional. -Nat Diana Tomchick wrote: There's a command in coot that identifies waters that have an unusually high coordination number. You then need to manually inspect the electron density map and bond lengths, atom type, etc. Diana Shekhar Mande wrote: Ed, I dont about monovalent metals (they are typically liganded by hydroxyls of Ser/Thr, or the main chain carbonyls). But we did an analysis of divalent metals in proteins, and found several instances, where crystallographers might have mistaken a metal to be a water. Thus, in the PDB, what is reported to be a water, might actually turn out to be a metal! Some of our sites have used to predict functions of proteins, where enzyme assays required addition of metals, and hence, I am gratified that it is useful! I am enclosing a PDF with this. We also have a server. Shekhar Dunten, Pete W. wrote: Ed, O had a command that scrutinized waters and helped find metals modeled as water. Victor Lamzin has a program whose name I'be momentarily forgotten which gives plots of e-density at atomic centers versus B-factor, for each atom type. Points off the lines are candidates for incorrectly modeled metals. Pete Dunten, Pete W. wrote: See attached and the reference noted therein. Best wishes, Pete Parthasarathy Sampathkumar wrote: Hi Ed, WASP analyse water molecules in high-resolution protein structure to check if some of those could be metal ions. WASP could be run as a part of STAN server. STAN - the STructure ANalysis server from USF ( http://xray.bmc.uu.se/cgi-bin/gerard/rama_server.pl ) One could also identity potential metal ions within COOT as well. HTH, Best Wishes, Partha On Fri, Nov 8, 2013 at 9:09 PM, Edward A. Berry ber...@upstate.edu mailto:ber...@upstate.edu wrote: Is there a server or program to predict binding
