Hey, When was the announcement made? I can't claim to read all the CCP4 mail very carefully, so I probably missed the it...
The wiki I've set up is essentially a sandlot - something to play with and something to give people ideas (in other terms, not intended as a final product), but I'll gladly remove it so as not to cause confusion. Artem > Yes, this is how a wiki page for CCP4 might look like. However, to make a > wiki successful we have to make sure it is secure and that there is a > dedicated core team to maintain it. Kevin was asked by the CCP4 to lead > the wiki project and while he is setting things up, it would be > counterproductive to start setting up independent "CCP4 wiki" sites. > > Tadeusz > > > > > > > > "Artem Evdokimov" <[EMAIL PROTECTED]> > Sent by: "CCP4 bulletin board" <[email protected]> > 23-Jul-2007 00:29 > Please respond to "Artem Evdokimov" <[EMAIL PROTECTED]> > > > To > [email protected] > cc > > Subject > [ccp4bb] CCP4 Wiki > > > > > > > Hi, > > Would something like this work? > > http://www.xtals.org/wiki/ > > I've only set it up today, but it seems to work just fine. Feel free to > play > with it. > > Artem > > -----Original Message----- > From: CCP4 bulletin board [mailto:[EMAIL PROTECTED] On Behalf Of > Lucas > Bleicher > Sent: Sunday, July 22, 2007 11:02 AM > To: [email protected] > Subject: Re: [ccp4bb] Suggestion: Wiki -- was:Re: [ccp4bb] need > help--Rfree > is not decreasing > > 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/ > > > > ----------------------------------------------------------- > This e-mail was sent by GlaxoSmithKline Services Unlimited > (registered in England and Wales No. 1047315), which is a > member of the GlaxoSmithKline group of companies. The > registered address of GlaxoSmithKline Services Unlimited > is 980 Great West Road, Brentford, Middlesex TW8 9GS. > ----------------------------------------------------------- >
