For low resolution data (~7-8 Angstroms or so), there are cases where any type of occupancy refinement isn't tremendously stable. I'm much less bothered by occupancies>1 (for phasing sites) than I am with cases where all of the occupancies are refined to 0 (especially when fixing the occupancies produced a usable map).
It may always be a good thing to try initial occupancy-only refinement, but it might not be a good idea to assume it's always what you want to do. Pete Ian Tickle wrote: > I would have thought that it would always be a good idea to refine only > the occupancies in the first few cycles and only refine co-ords & B > factors once the occupancies have settled down to sensible values. But > in that case wouldn't the Fcalc's be linearly dependent on the > occupancies so the occupancy-only refinement should be reasonably > well-behaved, even from a distant starting point? The initial > guesstimates of the occupancies could be significantly off even if the > data is correctly scaled so the refinement still needs to be reasonably > robust. > > But I agree with you, there can't be any harm in applying the Wilson > scale factor, so you may as well always do it, at least it ensures that > the range of values for the F's is roughly right (and you're less likely > to get questions like "why are my occupancies more than 1 ?"!). > > -- Ian > >> -----Original Message----- >> From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] > On >> Behalf Of Clemens Vonrhein >> Sent: 12 September 2008 17:06 >> To: Phil Evans >> Cc: CCP4BB@JISCMAIL.AC.UK >> Subject: Re: [ccp4bb] Wilson plot from truncated.mtz >> >> On Sun, Aug 24, 2008 at 08:08:00PM +0100, Phil Evans wrote: >>> As you say, the linear fit is only used to put data on a very rough >>> absolute scale. This isn't necessary, but it doesn't hurt >> It might be necessary after all for experimental phasing using heavy >> atoms: you want to start refinement of the occupancies from something >> not too far away. If your data is off by 1000 starting with values of >> 1.0 might be too bad for the minimizer to get anywhere. >> >> This becomes especially tricky if you have poor data (low resolution >> and/or quality), a poor initial heavy atom solution or no real idea of >> the numbner of molecules per asymmetric unit (especially difficult for >> large numbers). >> >> Unfortunately you often have to deal with a combination or even all of >> the above. But if you're lucky your resolution is so low that you >> don't have to worry about the other things anway ;-) >> >> So in general I think it is a good thing to do. >> >> Cheers >> >> Clemens >> >> -- >> >> *************************************************************** >> * Clemens Vonrhein, Ph.D. vonrhein AT GlobalPhasing DOT com >> * >> * Global Phasing Ltd. >> * Sheraton House, Castle Park >> * Cambridge CB3 0AX, UK >> *-------------------------------------------------------------- >> * BUSTER Development Group (http://www.globalphasing.com) >> *************************************************************** > > > > Disclaimer > This communication is confidential and may contain privileged information > intended solely for the named addressee(s). It may not be used or disclosed > except for the purpose for which it has been sent. If you are not the > intended recipient you must not review, use, disclose, copy, distribute or > take any action in reliance upon it. If you have received this communication > in error, please notify Astex Therapeutics Ltd by emailing [EMAIL PROTECTED] > and destroy all copies of the message and any attached documents. > Astex Therapeutics Ltd monitors, controls and protects all its messaging > traffic in compliance with its corporate email policy. The Company accepts no > liability or responsibility for any onward transmission or use of emails and > attachments having left the Astex Therapeutics domain. Unless expressly > stated, opinions in this message are those of the individual sender and not > of Astex Therapeutics Ltd. The recipient should check this email and any > attachments for the presence of computer viruses. Astex Therapeutics Ltd > accepts no liability for damage caused by any virus transmitted by this > email. E-mail is susceptible to data corruption, interception, unauthorized > amendment, and tampering, Astex Therapeutics Ltd only send and receive > e-mails on the basis that the Company is not liable for any such alteration > or any consequences thereof. > Astex Therapeutics Ltd., Registered in England at 436 Cambridge Science Park, > Cambridge CB4 0QA under number 3751674
