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 should also try not to fall into the trap of re-writing Blundell and Johnson but instead make judicious use of external links and other resources.
Kevin Cowtan wrote: > 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 >>> >> >> >
