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, herman.schreu...@sanofi-aventis.com 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:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Peter
Canning
Sent: Wednesday, October 05, 2011 4:42 PM
To: CCP4BB@JISCMAIL.AC.UK
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
