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 <felix.vaj...@pfizer.com> 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 > <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. > > > > > > > > > > > > > > > > > > > > > > > > >
