Re: [ccp4bb] Fwd:
How we can define NCS in phenix.refine. phenix.refine uses torsion ncs and top-out restraints target, which all in all means no need to do anything special apart from enabling using ncs in refinement. Details: http://journals.iucr.org/d/issues/2014/05/00/rr5054/index.html Acta Cryst. (2014). D70, 1346-1356 Flexible torsion-angle noncrystallographic symmetry restraints for improved macromolecular structure refinement Pavel
Re: [ccp4bb] Proper detwinning?
I would recommend to run ZANUDA in the default mode from ccp4i or on CCP4 web server. ZANUDA has resolved several similar cases for me. Misha From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Chris Fage [cdf...@gmail.com] Sent: 10 July 2014 01:14 To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] Proper detwinning? Hi Everyone, Despite modelling completely into great electron density, Rwork/Rfree stalled at ~38%/44% during refinement of my 2.0-angstrom structure (P212121, 4 monomers per asymmetric unit). Xtriage suggested twinning, with |L| = 0.419, L^2 = 0.245, and twin fraction = 0.415-0.447. However, there are no twin laws in this space group. I reprocessed the dataset in P21 (8 monomers/AU), which did not alter Rwork/Rfree, and in P1 (16 monomers/AU), which dropped Rwork/Rfree to ~27%/32%. Xtriage reported the pseudo-merohedral twin laws below. P21: h, -k, -l P1: h, -k, -l; -h, k, -l; -h, -k, l Performing intensity-based twin refinement in Refmac5 dropped Rwork/Rfree to ~27%/34% (P21) and ~18%/22% (P1). Would it be appropriate to continue with twin refinement in space group P1? How do I know I'm taking the right approach? Interestingly, I solved the structure of the same protein in P212121 at 2.8 angstroms from a different crystal. Rwork/Rfree bottomed out at ~21%/26%. One unit cell dimension is 9 angstroms greater in the twinned dataset than in the untwinned. Thank you for any suggestions! Regards, Chris
Re: [ccp4bb] Naccess
hi, I found the following reference in a paper- Hubbard S. PhD thesis. University College of London, Department of Biochemistry and Molecular Biology; 1992. NACCESS: a Program for Calculating Accessibilities. On Wednesday, 9 July 2014 8:20 PM, FOOS Nicolas nicolas.f...@synchrotron-soleil.fr wrote: Hello, i cited this program with : Hubbard, S.J., and Thornton, J.M. (1993). NACCESS (Computer Program, Department of Biochemistry and Molecular Biology, University College London.). I am not absolutly certain that's th best way. Nicolas De : CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] de la part de Armando Albert [xalb...@iqfr.csic.es] Envoyé : mercredi 9 juillet 2014 17:02 À : CCP4BB@JISCMAIL.AC.UK Objet : [ccp4bb] Naccess Dear all, Does anyone know how to properly cite Naccess for calculation of solvent accessible area (http://www.bioinf.manchester.ac.uk/naccess/)? Armando
Re: [ccp4bb] question about powder diffraction
Tim Yes the diffraction pattern can certainly be seen as an interference phenomena. However, this paper disagrees that everything except the Bragg peaks vanishes in the noise. The (simple) Bragg condition assumes an infinite lattice whereas the lattice is truncated in real samples. The original question related to how many reflections occur in a powder sample and where they would be. This paper addresses the issues in some detail. However, I haven't read the paper in detail and don't want to comment at this stage on whether the title A new theory of x-ray diffraction is justified. Regards Colin -Original Message- From: Tim Gruene [mailto:t...@shelx.uni-ac.gwdg.de] Sent: 09 July 2014 10:49 To: Nave, Colin (DLSLtd,RAL,LSCI); ccp4bb Subject: Re: [ccp4bb] question about powder diffraction -BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Hi Colin, On 07/09/2014 09:52 AM, Colin Nave wrote: [...] If the whole diffraction process is considered as an interference problem then the contributions are not confined to the Bragg condition. Isn't this how textbooks on crystallography usually start? Drenth, e.g. starts with the scattering from a single electron, then builds up a molecule and the lattice and you find the everything except the Bragg peaks vanish in the noise. How does one NOT see the diffraction process as an interference 'problem'? Curiously, Tim Colin -Original Message- From: Gerard Bricogne [mailto:g...@globalphasing.com] Sent: 09 July 2014 00:38 To: ccp4bb Subject: Re: [ccp4bb] question about powder diffraction Dear all, The downstream end of this thread seems to have drifted into learned considerations of spelling, so I am getting back to this early reply. I am surprised that nobody has mentioned the role of the wavelength in all this: there is no way that one can directly link the first four planes in a Nickel crystal to a fixed set of 2theta values. The values you quote, Kianoush, must have been observed for a certain wavelength, but they would be different for another wavelength. So if you want one of the powder rings to come out at a 2theta of 45 degrees, adjust the wavelength accordingly so that Bragg's law be satisfied for the spacing between the corresponding planes. There also seems to be a confusion in the last question (unless I have completely misunderstood it) about the orientation of a crystal and the Bragg angle at which it will contribute to the ring pattern of the powder it belongs to. If there is a crystal oriented with some if its planes at 45 degrees from the X-ray beam, that will simply determine where on each ring its diffraction spots will contribute: it will have no effect on the Bragg angles of those spots, that depend purely on the internal spacings between atoms within the crystal, not on the orientation of the crystal. At the same wavelength at which you quote the 2theta values for those four rings, the crystal at 45 degrees from the beam will still have its diffraction spots contribute to the rings at 44, 52, 76 and 93 degrees. Again, forgive me if I have completely misunderstood the initial question. With best wishes, Gerard. -- On Tue, Jul 08, 2014 at 04:13:59PM -0400, Edward A. Berry wrote: The plane will scatter, and all atoms in the plane will scatter in phase if angle of incidence equals angle of reflection. this is how a mirror reflects. Furthermore all the parallel planes will also reflect at this angle. Trouble is the beams scattered from the different parallel planes are systematically out of phase with each other unless Bragg's law is met for that set of planes, so interference is destructive and adds up to nothing. At least that's how I understand it, eab On 07/08/2014 03:53 PM, Kianoush Sadre-Bazzaz wrote: Hi If a sample of powder crystal (say Nickel) is shot with monochromatic x-rays, one will observe reflections from planes that satisfy Bragg's Law. For Ni the first four planes are (111, 200, 202, 311) with 2theta (44, 52, 76, 93 degrees) respectively. Why doesn't one observe a reflection at, say, 45 degrees? There will be a grain oriented in the powder such that x-rays reflect at 45 degrees and so forth. I would expect a continuum of reflections... thanks for the insight. Kianoush - -- - -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A -BEGIN PGP SIGNATURE- Version: GnuPG v1.4.12 (GNU/Linux) Comment: Using GnuPG with Icedove - http://www.enigmail.net/ iD8DBQFTvRAeUxlJ7aRr7hoRAoJAAKDA0VZMXMz7+sbOxVjGB/lPLzI+tgCePKu9 uDKSAlSudLR0OGprtltg9oE= =eNZt -END PGP SIGNATURE- -- This e-mail and any attachments may contain confidential, copyright and or privileged material, and are for the use of the intended addressee only. If you are not the intended addressee or an authorised recipient of the addressee please notify us of
[ccp4bb] New PDB validation reports
Hi all, I've been playing with the new PDB validation service. It is very pretty and kudos to all the hard work that has clearly gone into it. I did notice however that the way the information is presented, there seems to be a bias towards truncating side chains versus modeling them with higher b-factors. The disordered side chains have higher RSRZs (rightfully so), but there doesn't seem to be any indicator for missing atoms. As a results I can make my validation report prettier by truncating versus modeling with high Bs. I don't want to kick an ant pile here, but given this rather significant difference in quality reporting, I was wondering if the community had reached a consensus on this issue that I had missed. Cheers, Katherine -- Nil illegitimo carborundum* - *Didactylos
Re: [ccp4bb] New PDB validation reports
Glad you brought it up Katherine. Debasish From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Katherine Sippel Sent: Thursday, July 10, 2014 2:26 PM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] New PDB validation reports Hi all, I've been playing with the new PDB validation service. It is very pretty and kudos to all the hard work that has clearly gone into it. I did notice however that the way the information is presented, there seems to be a bias towards truncating side chains versus modeling them with higher b-factors. The disordered side chains have higher RSRZs (rightfully so), but there doesn't seem to be any indicator for missing atoms. As a results I can make my validation report prettier by truncating versus modeling with high Bs. I don't want to kick an ant pile here, but given this rather significant difference in quality reporting, I was wondering if the community had reached a consensus on this issue that I had missed. Cheers, Katherine -- Nil illegitimo carborundum - Didactylos
[ccp4bb] Postdoctoral Position in Complex Carbohydrate Biosynthesis
Dear colleagues, I would like to draw your attention to an open postdoctoral position in my laboratory. The DOE-funded position aims at unraveling how processive membrane-embedded glycosyltransferases synthesize, assemble and secrete polysaccharides. Polysaccharides represent the most abundant biopolymers on earth and perform a wide range of biological functions. As non-templated biopolymers, polysaccharides can reach several thousand sugar units in length, yet, under certain conditions, are efficiently transported across biological membranes to form essential components of plant cell walls, the extracellular matrix or biofilms. We are employing structural and molecular biology techniques to unravel the mechanisms by which these polymers are translocated and deposited outside the cell. The successful candidate will join a multi-disciplinary and highly dedicated group. The laboratory is integrated into the Center for Membrane Biology at the University of Virginia (membranebiology.virginia.edu), which offers state-of-the-art resources including crystallization robotics, an electron microscopy core facility, NMR and EPR spectroscopy, SAXS and single molecule fluorescence microscopy. Applicants should have at least one first author peer-reviewed publication as well as experience in membrane protein expression in pro- and eukaryotic systems. An in-depth training in molecular biology and biophysics and the ability to work independently yet integrate well in a diverse group is important. Interested candidates should contact me directly for further information (jochen_zim...@virginia.edu). Sincerely, Jochen _ The University of Virginia is an affirmative action/equal opportunity employer committed to diversity, equity, and inclusiveness. Women, minorities, veterans and persons with disabilities are encouraged to apply. For Thomas Jefferson, learning was an integral part of life. The academical village was created around the assumption that learning is a lifelong and shared process, and that interaction between scholars and students enlivens the pursuit of knowledge. University Human Resources strives to identify applicants who will contribute as high potential employees, leaders and managers. We employ individuals who foster and promote the University mission and purpose. Successful candidates exemplify uncommon integrity; they are honest, trusted, team-oriented and live the core values of the University. These candidates display great judgment, by practicing evidence-based decision-making. They are strategically focused by contributing to and achieving department goals and vision. They set high performance standards and hold themselves accountable by aggressively executing these standards. These employees also develop a deep passion for the University and the impact it has on students, faculty, alumni and community. Successful candidates identify their personal career goals and development opportunities, and as supervisors, help their staff do the same. They contribute to team success by leading talent, through their individual efforts and by leading and developing their teams. _ Jochen Zimmer, D. Phil. Assistant Professor Molecular Physiology and Biological Physics University of Virginia 480 Ray C. Hunt Dr. Charlottesville, VA 22908 Phone: 434 243 6506 http://people.virginia.edu/%7ejz3x/
