Dear community, Thanks for your valuable suggestions.
Best regards, Sudipta. On Thu, Jul 17, 2014 at 8:04 AM, Eleanor Dodson <eleanor.dod...@york.ac.uk> wrote: > 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. >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> > >
