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
