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" <[log in to unmask]>
> Sent by: "CCP4 bulletin board" <[log in to unmask]>
> 23-Jul-2007 00:29
> Please respond to "Artem Evdokimov" <[log in to unmask]>
>
>
> To
> [log in to unmask]
> 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:[log in to unmask]] On Behalf Of
> Lucas
> Bleicher
> Sent: Sunday, July 22, 2007 11:02 AM
> To: [log in to unmask]
> 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 <[log in to unmask]>
> 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: [log in to unmask] Tel +49 7531
>> 88 4049 Fax 3183
>> Fachbereich Biologie, Universität Konstanz, Box
>> M647, D-78457 Konstanz
>>
>>
>
>
>
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