[phenixbb] Funky message on phaser MR

[Rafael Lemos Miguez Counago]

Dear Randy,

Thanks for the prompt reply and updating the documentation.  It definitely
helped me understand Phaser's workings a bit better.

Best wishes,

Rafael.


Dr. Rafael LM Couñago
Postdoctoral Research Fellow

Kobe Lab - Bacterial Pathogenesis Group
School of Chemistry and Molecular Biosciences
Bldg76 / room 340 ­ ph. 07 334 69073
The University of Queensland
St Lucia, QLD 4072
Australia 

 


On 27/08/12 9:07 PM, "Randy Read" <rjr27 at cam.ac.uk> wrote:

> Dear Rafael,
> 
> We haven't yet published the theory used to estimate the LLG that will be
> achieved with a particular model and then to adjust the strategies based on
> that.  And I realised, after your email, that it hadn't even been discussed in
> the documentation.  So I've just added a couple of sections to the
> documentation on molecular replacement:
> http://www.phaser.cimr.cam.ac.uk/index.php/Molecular_Replacement#Should_Phaser
> _Solve_It.3F.  I hope that helps!
> 
> Regards,
> 
> Randy
> 
> -----
> Randy J. Read
> Department of Haematology, University of Cambridge
> Cambridge Institute for Medical Research    Tel: +44 1223 336500
> Wellcome Trust/MRC Building                         Fax: +44 1223 336827
> Hills Road                                                            E-mail:
> rjr27 at cam.ac.uk
> Cambridge CB2 0XY, U.K.
> www-structmed.cimr.cam.ac.uk
> 
> On 27 Aug 2012, at 10:23, Rafael Lemos Miguez Counago wrote:
> 
>> Hi Rob.
>> 
>> I think I have two out of three offenders - the low identity between the
>> model and the crystallised protein; and the low completeness of the model - I
>> am using just the most conserved domain as a search model.
>> 
>> I did noticed that when I repeated the search with a more complete model the
>> expected LLG (at the start of the run) went up.
>> 
>> Thanks for clarifying this issue for me.
>> 
>> Best wishes,
>> 
>> Rafael.
>> 
>> 
>> ________________________________________
>> From: phenixbb-bounces at phenix-online.org [phenixbb-bounces at phenix-online.org]
>> on behalf of R.D. Oeffner [rdo20 at cam.ac.uk]
>> Sent: Monday, 27 August 2012 6:54 PM
>> To: PHENIX user mailing list
>> Subject: Re: [phenixbb] Funky message on phaser MR
>> 
>> Hi Rafael,
>> 
>> Phaser contains new methods to estimate what the expected LLG value will be
>> by the end of the calculation. The expected LLG value depends on
>> 
>> 1) the resolution of the data
>> 2) the RMSD of your MR model,
>> 3) the size of the MR model compared to the structure you are trying to
>> solve.
>> 
>> For LLG values less than about 60 (I think) there is no certainty that the MR
>> model will be placed correctly and you get this warning. Improving any of the
>> three parameters above will help you avoiding this message.
>> 
>> 
>> Regards,
>> 
>> Rob
>> 
>> 
>> On Aug 27 2012, Rafael Lemos Miguez Counago wrote:
>> 
>>> Dear all,
>>> 
>>> I am getting this message when running Phaser-MR in Phenix (1.8-1069):
>>> 
>>> "Warning: Resolution of data does not achieve (half) expected LLG target:
>>> placement of one/first ensemble will be
>>> very difficult"
>>> 
>>> The data scales/merges OK. - 99% complete at 2.2A, Rmerge 8.4%. TNCS is
>>> detected by Xtriage and Phaser tries to
>>> account for that.
>>> 
>>> Coincidently (?) my molecular replacement solution is not looking very good.
>>> Any ideas?
>>> 
>>> Best wishes,
>>> 
>>> Rafael.
>>> 
>>> 
>>> 
>>> 
>>> 
>>> 
>> 
>> --
>> Robert Oeffner, Ph.D.
>> Research Associate, The Read Group
>> Department of Haematology, University of Cambridge
>> Cambridge Institute of Medical Research
>> Wellcome Trust / MRC Building, Hills Road, Cambridge, CB2 0XY
>> www-structmed.cimr.cam.ac.uk, tel:01223763234, mobile:07712 887162
>> 
>> 
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