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 better to go to an external wiki
hosting service. I have investigated a number of these and have a couple
of candidates which meet our requirements.
I'm hoping it will be possible to make the service broader than just
CCP4 - the CNS and other queries we get on CCP4BB show that there is at
least some demand for this.
I'm intersted in any feedback anyone has to offer. There will be
developments on this over the next few months.
Kevin
Kay Diederichs wrote:
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 postings of this mailing list (which to me _is_ a
very valuable ressource).
A Wiki is not difficult to set up. Maybe it could be part of the CCP4
pages? We set up a Wiki for our lab at the beginning of the year, and it
was a great success, in particular because it works the same way as
Wikipedia - anybody can contribute. There should be some means of
controlling "write access", but that could simply be granted to people
who are subscribed to the CCP4 mailing list.
I'd at least volunteer in helping to get a Wiki started. And one way to
get it filled with articles would be that those people who used to write
a "summary" of responses would simply compose a new Wiki article, and
report to the mailing list that this article exists, which could then be
expanded by others.
best,
Kay
Anastassis Perrakis schrieb:
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 job, to be able to
compare. The fact that weight is 0.3 says nothing.
The correct weight can vary wildly from 0.02 to 0.5, in my experience.
for 2.0 data 0.3 sound loose, 0.15-0.2 is what I am used to,
depending on dataset. But, The only way to tell what is right is
inspecting the geometry and aim for a 'reasonable' rms 1-2 distances
deviation.
What is 'reasonable', can cause yet another long discussion, but my
personal favorite for 1-2 distances rms deviation is between 0.015-0.020.
In Refmac these also give the lowest R factors, in my hands.
The invisible side chains is yet another long discussion that you can
retrieve from the ccp4bb archives.
Again, my personal preference is to leave them in and let them get
very high B factors, as long as they do not
get negative density in difference maps, that I presume you are
inspecting.
I dont mind deleting them (but dont like it) and I think mutating to
ALA is worse since its misleading to users.
Finally, given that you have 2.0 A data you should try and model not
only waters, but also:
a. double conformations of side chains
b. solvent and cryoprotectant molecules; glycerol, SO4 etc should be
different than waters and easy to model.
... and I still cant help wondering how people do their phd's or
post-docs in labs that no-one can explain
such trivialities. Or why people prefer not to ask their colleagues
and supervisors, but to mail ccp4bb. Or why do I bother answering such
emails on a Saturday morning, and then complaining, only to have the
likes of Dr. Walsh commenting about my humor ;-)))
I find all these really scary.
Tassos
On 21 Jul 2007, at 0:29, JOE CRYSTAL wrote:
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/delete water in Coot followed by 10 cycles refmac
refinement, but Rwork/Rfree are still around 22.5/27.5%. I also
noticed a few side chains without density. Will setting those atoms
to 0 occupancy or high B factor or mutating to Ala help decrease
Rfree substantially? If not, is there any better strategies to lower
down R factors? I will be very appreciative if you have any
suggestions or comments to offer. Thank you in advance.
Best,
Joe
