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 PROTECTED]> escreveu: > 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 > > > > > -- > Kay Diederichs > http://strucbio.biologie.uni-konstanz.de > email: [EMAIL PROTECTED] Tel +49 7531 > 88 4049 Fax 3183 > Fachbereich Biologie, Universität Konstanz, Box > M647, D-78457 Konstanz > > Flickr agora em português. Você cria, todo mundo vê. http://www.flickr.com.br/
