Dear Herman In some cases density modification starting with MR phases can indeed prove very powerful. We recently used Parrot to bootstrap a difficult case at 4.3 angs and were able to obtain very good maps for entire missing domains. See Supplementary Fig 1 in:Verstraete et al 2011 BLOOD 118:60-68 and more technical info and fig5 in: Verstraete et al 2011 Acta F67:325-331.
The "Ncs mask radius" card in parrot proved to be an important one to experiment with, and is probably more important to do so at medium-low resolution. We provide details of our observations/implementation on page 330 of the actaF paper. We also found that post-MR HL coefficients written out by Phaser were also key. So in subsequent runs, after having built and refined partial models, we would do a phase calculation run in Phaser to obtain HL by 'fixing' the partial model via a template .sol file with 0 values for rotation/translation across the board. Best wishes Savvas On 05 Oct 2011, at 17:13, [email protected] wrote: > Dear CCP4'ers, > > I do have a similar case with 8 molecules in the asymmetric unit, related by > improper symmetry and the structure is solved by molecular replacement. I do > have 2 questions: > > 1) Does it make sense to average to improve phases? The molecular replacement > phases perfectly obey the non-crystallographic symmetry? > 2) For refinement I do not need average maps since Buster and other > refinement programs are very capable to handle ncs. However, I am not a > computer and for manual rebuilding and display purposes it would be very good > to use averaged maps. Which program could I best use for this: Parrot, DM, > Solomon, other? None of them seem to be really made for molecular replacement > phases. > > Also my many thanks for any help, advice etc. > Herman Schreuder > > From: CCP4 bulletin board [mailto:[email protected]] On Behalf Of Peter > Canning > Sent: Wednesday, October 05, 2011 4:42 PM > To: [email protected] > Subject: [ccp4bb] Parrot NCS averaging > > Dear CCP4’ers, > > > > I am working on refining the structure of a protein complex consisting of two > different chains. Data were collected to 2.3A in space group C2 and phased by > molecular replacement without any problem, but the ASU contains 6 complexes > (so 12 chains in total). In the ASU, the 6 complexes form 3 dimers. Dimer 1 > is related to dimer 2 by a rotation operation and to dimer 3 by translation – > I hope that makes sense! > > > > When I run Parrot to do density improvement and NCS averaging, Parrot works > beautifully (final FOM is 0.87) but NCS averaging causes the average NCS > correlation coefficient to drop (from 0.94 to 0.64) and the average mask > volume to increase from 0.31 to 0.7 (minimum volume increases from 0.05 to > 0.07 and maximum volume goes from 1.2 to 2), which seems a bit high. > > > > Unless I have misunderstood something, I thought the NCS correlation > coefficient should increase during averaging and the average mask volume > should decrease. If this is the case, has anyone any idea what I’m doing > wrong? > > > > Also, at the risk of asking a dumb question, is there a particular way my > Parrot modified file should be input into Refmac to get the best results? The > FOM from my refmac runs never seems to be as good as that output by Parrot. > > > > Thanks in advance, all advice gratefully received, etc etc… > > > > Peter Canning > > SGC > > > > >
