Your split between Rfree and R suggests you are using refmac. (I also
got a hint when you explicitly said you were using refmac.) Although
there are many efficient ways to get stuck in a refinement, I have
found the most effective by far is underweighting the structure
factors and falling into the viscous cycle of model bias, which is why
I have religiously avoided refmac in the past. Try upping the
"weighting term" from the default of 0.3 and building into the maps
that result. I got this latter advice recently from our x-ray admin
who was also kind enough not to give me a forehead slap for my
cluelessness.
James
On Apr 15, 2009, at 2:39 AM, ANDY DODDS wrote:
Hi James,
I usually use DM in teh CCP4 suite to do DM. It gives you options to
do solvent flattening, Histogram matching and NCS averaging.
If you compare the FOM to the DMFOM in the mtz files, you can usually
see and improvement in the score. That is usually all I bother my
arse to look at. Any comments as to what else I should be looking at
generally, would be welcomed.
I am currently working on a difficult structure at 2.9 Angstrom that I
cant get to lower the RFree any more and am stuck at 32% with a R fact
of about 21%. I went back and performed density modification right at
the start, then performed MR and the same refinement as before and saw
absolutely no improvement in refinement statistics at all. They were
identical using the non-DM modified mtz file. I was surprised, but
this may be due more to the fact that I don't fully appreciate what is
going on here.
For the record I performed flattening and matching and tried this and
then both plus NCS (there is NCS in my model) averaging and still
absolutely identical refinement statistics. This is using refmac by
the way TLS + restrained refinement.
Sorry for the thread hijack James, but at least it is related! ;)
cheers
andy
2009/4/15 James Stroud <xtald...@gmail.com>:
Hello All,
What is the current state of the art with respect to density
modification
after molecular replacement? In other words, what programs are
people having
the best luck with these days?
Thanks in advance for any hints.
James
