First suggestion - use WEIGHT AUTO in REFMAC - you may have restrained
the geometry too tightly..
And have you tried TLS ?
And at what level do you see no density - remember sigma levels in
maps need to vary with B factor - very easy to achieve this with COOT..
Eleanor
JOE CRYSTAL wrote:
That would be a great idea. In fact, I keep on my
mailbox dozens of great postings (most of them
summaries) in CCP4 which would be very useful to
everybody if there's an online resource, with
information organized in topics. I would gladly copy
them to this wiki.
Lucas
--- Kay Diederichs <[EMAIL
On Sat, Jul 21, 2007 at 05:22:42PM +0100, Winter, G (Graeme) wrote:
> ... or alternatively just start something on wikipedia?
Wikipedia actually has a policy against articles that are too technical in
nature, so it might not be the appropriate place for this kind of content.
http://en.wikipedia.o
I would happily contribute to this, and migrate anything relevant from my
own stuff. I think this could be a very valuable resource. The PyMOL
wiki is a good example of what could be done. The main requirement for
success I think is having a few dedicated users who want to see it
succeed. We shou
Hi!
A crystallography wiki was discussed at the last CCP4 developers
meeting, and I've been looking into it.
Setting up a wiki is not hard, but keeping it up-to-date and secure is.
(We've had problems with this at York, where we've been running one for
a few years). Therefore I suggest it is
: [ccp4bb] Suggestion: Wiki -- was:Re: [ccp4bb] need help--Rfree is not
decreasing
So - rather than repeat things that are obvious to some people, would it
not be good to have a crystallography-FAQ that one could point people
to? This should be part of a Wiki where "we crystallographers&q
So - rather than repeat things that are obvious to some people, would it
not be good to have a crystallography-FAQ that one could point people
to? This should be part of a Wiki where "we crystallographers" could
collect our wisdom. This would be much more systematic, and less
volatile, than the
Sorry for the cliche, but the goal of refinement is not to reduce R
factors, but to produce a good model.
ARP/wARP uses the 'WEIGHT AUTO' option of REFMAC5 to get a good
geometry.
You should set the weight to a value that produces 1-2 and 1-3
distances rms deviations similar to the ARP/wARP
Dear all,
I am refining a structure at 2.0 A. The water molecules have been added
using arp/warp resulting Rwork/Rfree=21/26% (about 370 HOH for 360
residues). After 10 cycles of refmac refinement (wt 0.3), Rwork/Rfree went
up about 1.5% to 22.5/27.5%. I did some minor adjustments and add/del
