Re: [ccp4bb] Very weird

Protein crystallography Programs for crystallography X-ray detectors
Basic tutorials:
Protein Peptide

CCP4bb navigation

CCP4bb <-- 2007 <-- March 2007 <-- 07 March 2007

Previous message:
Subject: Re: Easy proteins to crystallize
From: "Douglas L {- dot -} Theobald" dtheobald {- at -} BRANDEIS {- dot -} EDU
Date: 2007-03-07

Next message:
Subject: XDS to MTZ for SOLVE
From: "Santarsiero, Bernard D {- dot -} " bds {- at -} UIC {- dot -} EDU
Date: 2007-03-07

Subject: Re: Very weird
From: Edwin Pozharski epozh001 {- at -} UMARYLAND {- dot -} EDU
Date: 2007-03-07

I believe Phaser places CRYST1 record at the top of an output
pdb-file... Yanming, did you try lower symmetry spacegroups?

Eleanor Dodson wrote:
> It seems very odd..in fact almost impossible. You still have 3 correct
> molecules
> I wonder if there is some error in the coordinate file?
> Errors I make are:
>
> leaving and end record, between 2 parts. - many programs stop
> reading coordinates at the first END
>
> leaving CRYST1 and SCALE cards in the middle of the file..
> Getting the CRYST record wrong somewhere - REFMAC does not seem to
> check that the cell dimensions are consistent
>
> Eleanor
>
>
>
> Yanming Zhang wrote:
>> Dear all,
>>
>> I am sorry to trouble you again because I am facing a very weird
>> situation:
>>
>> Three copies from Phaser are the right solutions based upon:
>> 1, Rfree 42% R 39%
>> 2, No packing clash
>> 3, The packing within the 3 makes good sense
>> 4, Density evenly distributed among the 3 copies even without NCS
>>
>> Then fix these 3, asking Phaser to find one more (here I adopt the
>> strategy one copy at a time). Phaser did find one more, So now I have
>> 4 copies in total.
>>
>> Using the phase calculated from the previous 3 copies(because Rfree
>> 42%), the 4th copy can exactly match one junk of the density, even
>> the side chain matchs, demonstrating the 4th copy is correct.
>>
>> Checking the crystallographic packing, The density which the 4th
>> occupies, is an extra density which did not account for by the
>> previous 3 copies or their symmetry mates.
>>
>> No Clash exists
>>
>> Then I use the 4 copies to do the refinement, forseeing that there
>> will be a huge Rfree drop from 42% because I account for the extra
>> density using the 4th copy. BUT TO MY SURPRISE, THE RFREE INCREASE TO
>> 65%.
>>
>> Can you teach me what is going wrong? Thank you
>> Yanming
>>
>>

--
Edwin Pozharski, PhD, Assistant Professor
University of Maryland, Baltimore
----------------------------------------------
When the Way is forgotten duty and justice appear;
Then knowledge and wisdom are born along with hypocrisy.
When harmonious relationships dissolve then respect and devotion arise;
When a nation falls to chaos then loyalty and patriotism are born.
------------------------------ / Lao Tse /

CCP4bb navigation

CCP4bb <-- 2007 <-- March 2007 <-- 07 March 2007

Previous message:
Subject: Re: Easy proteins to crystallize
From: "Douglas L {- dot -} Theobald" dtheobald {- at -} BRANDEIS {- dot -} EDU
Date: 2007-03-07

Next message:
Subject: XDS to MTZ for SOLVE
From: "Santarsiero, Bernard D {- dot -} " bds {- at -} UIC {- dot -} EDU
Date: 2007-03-07