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
