Re: [ccp4bb] Translational NCS and molecular replacement.
No need to reindex - just do this to change the space group in the scala header. mtzutils hklin1 scala.mtz hklout scala-P22121.mtz symm P22121 end There are other ways of course.. Eleanor On 16 July 2014 13:28, Vajdos, Felix wrote: > Dear Sudipta— > > > > Herman is correct, you just need to reindex your scala.mtz file to the > correct space group. > > > > Regarding translational NCS, it has been many years since I’ve dealt with > this, but it is my impression that modern refinement methods treat this > much better, especially with maximum likelihood targets, as the low(er) > intensity reflections will have systematically lower sig/noise than the > other parity groups. > > > > *Felix F. Vajdos* > > * Associate Research Fellow Structural Biology & Biophysics* > *Pfizer Inc* > *Eastern Point Road * > *MS 8220-3273* > *Groton, CT 06334* > > *860-715-6504 <860-715-6504>* > > > > > > > > *From:* CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] *On Behalf Of * > herman.schreu...@sanofi.com > *Sent:* Wednesday, July 16, 2014 3:08 AM > *To:* CCP4BB@JISCMAIL.AC.UK > *Subject:* [ccp4bb] AW: [ccp4bb] Translational NCS and molecular > replacement. > > > > Dear Sudipta, > > you are correct, your original scala.mtz has the wrong space group in it, > resulting in very high Rfactors (and presumably bad electron density). > > In these cases, I usually reprocess (remerge) the data in the correct > space group to get the statistics right (and gain probably a few extra h00 > reflections that got rejected in P212121). If you use the same a, b and c > axes as before, you do not need to rerun Phaser, otherwise you have to. > > If you have translational NCS, you have to live with it. The only way to > get rid of it is to find another crystal with a different crystal packing. > > > > Best, > > Herman > > > > *Von:* CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK > ] *Im Auftrag von *Sudipta Bhattacharyya > *Gesendet:* Dienstag, 15. Juli 2014 20:32 > *An:* CCP4BB@JISCMAIL.AC.UK > *Betreff:* [ccp4bb] Translational NCS and molecular replacement. > > > > Dear Community, > > > > I have some doubts to clarify. In a way to solve a structure by Phaser-MR, > I found phaser ended up with a potentially good MR solution (with good > statistics, packing and electron density, and as we know the homolog > structure so in a reasonable biological assembly also). However, the space > group where phaser found the potential solution (P22121) is different what > we got in pointless (P212121), and phaser also indicated the presence of > translational NCS (NCS translation vector = 0.500, 0.494 0.391). Now when > we try to refine the structure with its original scala.mtz file (which is > indexed and sclaled in P212121) and phaser generated pdb file, the R/Rfree > is very high (around 0.5) but when I tried refining with mtz file generated > by phaser, it was reasonable, at least for first cycle of refinement > (R/Rfree, 0.41/0.46). Now my question is, can I use the phaser generated > mtz file instead of the original scala.mtz for further refinement? Or I > have to reindex my original data into phaser suggested spacegroup and run > the MR again? Translational NCS are generally associated with high R > values, is there any way to get rid of that problem? > > > > Best regards, > > Sudipta. > > > > > > > > > > > > > > > > > > > > > > > > >
[ccp4bb] dtrek2scala
Does anyone have experience using the dtrek2scala program? According to the documentation the reflexions should by default be batched by the oscillation range read from the dtintegrate.head file but what it has actually done is put all the reflexions in the same batch (#33, despite setting 'BATCH 1'). It would appear that this has resulted in aimless failing with "ERROR in ScaleModel: run 1 has insufficent information for smooth scaling". Also the output MTZ file from dtrek2scala has all zeros in the ROT column and the aimless doc says "The scale factor is a function of the primary beam direction, either as a smooth function of Phi (the rotation angle ROT), or expressed as BATCH (image) number (__deprecated__)." (my emphasis). Any pointers to the correct operation of dtrek2scala greatly appreciated! Cheers -- Ian
[ccp4bb] Postdoctoral Position in X-ray and Neutron Crystallography at ORNL
Purpose: The Biology and Soft Matter Division of the Neutron Sciences Directorate of ORNL runs world-class scientific neutron crystallography and neutron scattering programs. The Biology and Soft Matter Division, in partnership with collaborators at the University of California-San Diego and the University of Utah, has an immediate opening for a Postdoctoral Research Associate to participate in an NIH-funded collaborative translational project directed to developing a new generation of accelerated oxime reactivators of nerve agent and pesticide organophosphate(OP)-inhibited human acetylcholinesterase (hAChE). The successful candidate will investigate the structure and function of hAChE, and identify structurally imposed limiting factors in oxime reactivation of the enzyme inhibited by OP. The postdoctoral researcher will join the research team that uses a multidisciplinary approach combining biochemistry, X-ray and neutron crystallography, small-angle scattering (SAXS, TR-SAXS, SANS), neutron spectroscopy and computational modeling (QM/MM/MD) to understand how slow molecular motions, protonation and ionization states in the mechanism of oxime reactivation of OP-inhibited hAChE influence and in effect limit antidotes’ efficacy. Major Duties/Responsibilities: --Responsible for protein purification, protein-ligand complexes preparation, crystal growth, and X-ray and neutron crystallographic studies. --Assist in sample preparation for SANS and neutron spectroscopic measurements, and with data collection. --Assist with collaborative crystallographic projects of ORNL neutron diffractometers MaNDi and IMAGINE at the 25% level of effort, including data collection, processing, structure refinement/analysis. --Responsible for publishing papers based on this research and assist with publishing collaborative manuscripts. --Present results at national and international conferences. Qualifications Required: A Ph.D. in biochemistry, biophysics or a related discipline completed within the last 5 years is required. Research experience with biochemical methods for production, purification and crystallization of proteins, and X-ray crystallography is required. Candidates should be self-motivated, have good interpersonal, communication and presentation skills and a demonstrated ability to interact effectively with staff at all levels. The ability to work as a member of a multi-disciplinary team is a critical asset. Qualifications Desired: Knowledge of mechanistic biochemistry is highly desirable. The aspiration to learn is highly desirable. Other Requirements: Applicants must have received their PhD within five years of this application and must complete all degree requirements before starting their appointment. To apply, please send the most current CV and a list of publications directly to Andrey Kovalevsky (kovalevsk...@ornl.gov)
