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: [log in to unmask] [mailto:[log in to unmask]]
> On
>> Behalf Of Clemens Vonrhein
>> Sent: 12 September 2008 17:06
>> To: Phil Evans
>> Cc: [log in to unmask]
>> 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 [log in to unmask] 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
|