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 notget 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 chainsb. 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
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