Re: [ccp4bb] xds and cell refinement in cI

- Protein crystallography

Main steps:

- Protein purification
- Crystallisation

Special:

- Programs for crystallography
- X-ray detectors

Basic tutorials:

   - Chemistry
   - Protein
   - Peptide
   - Amino Acids

Xtal community:

- CCP4BB

CCP4bb navigation

CCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999

Previous message:
Subject: Re: question about pore size calculation
From: Sudharsan Sridharan sudhaarsan {- at -} GMAIL {- dot -} COM
Date: 2009-10-14

Next message:
Subject: Re: question about pore size calculation
From: David Briggs drdavidcbriggs {- at -} GMAIL {- dot -} COM
Date: 2009-10-14

Subject: Re: xds and cell refinement in cI
From: Graeme Winter graeme {- dot -} winter {- at -} GOOGLEMAIL {- dot -} COM
Date: 2009-10-14

Hi Jan,

While the results from integration with a triclinic lattice should be
fine (you appear to be happy with them) the integration with a cubic
lattice thing is odd. I just ran XDS on a cubic insulin data set via
xia2 and - even when the symmetry is set - the cell constant is
refined. This is cI like the example you describe below. When working
like this however I do explicitly set REFINE(INTEGRATE)=ORIENTATION
CELL as I like that to be refined, while keeping the experimental
hardware settings at the postrefined values.

What have you set REFINE(INTEGRATE)= to in XDS.INP?

Cheers,

Graeme

2009/10/14 Jan Abendroth :
> Hi all,
> thanks a lot for numerous replies.
> Graeme's suggestion to integrate in triclinic and let CORRECT sort out the
> space group worked and yielded nice data with reasonable Rsyms, I/sig etc.
>
> When I then, though, re-enter the cell parameters etc (cp GXPARM.XDS
> XPARM.XDS) and just run INTEGRATE and CORRECT, the cell parameters won't
> refine any further, they stay right at the value given by XPARM.XDS. As Kay
> suggested, no cell parameter refinement in cubic (cI)?
>
> Cheers
> Jan
>
>
>
> On Oct 8, 2009, at 12:28 AM, Graeme Winter wrote:
>
>> Hi Jan,
>>
>> Always worth a try is to process the data in P1 then assigning the
>> symmetry in CORRECT - that way the cell constants can refine to what
>> they want to. It also means you can check that the symmetry actually
>> is cubic.
>>
>> For the majority of data sets in my experience it makes little
>> difference whether you assign the lattice constraints during
>> integration, unless they're wrong.
>>
>> Cheers,
>>
>> Graeme
>>
>>
>>
>> 2009/10/8 Jan Abendroth :
>>>
>>> Hi all,
>>> I am running into a strange behaviour fo xds for a primitive cubic data
>>> set.
>>> Neither in the INTEGRATE nor in the CORRECT step the cell parameters are
>>> refined and stay exactly at the value specified in XDS.INP. R-factors and
>>> I/sigmas of the XSCALE run look suspiciously high/low. When I reduce the
>>> symmetry to tetragonal and run an otherwise identical XDS.INP script, the
>>> cell parameters are refined again.
>>> Any ideas?
>>> Thanks a bunch
>>> Jan
>>> --
>>> Jan Abendroth
>>> deCODE biostructures
>>> Seattle / Bainbridge Island WA, USA
>>> work: JAbendroth_at_decode.is
>>> home: Jan.Abendroth_at_gmail.com
>>>
>>>
>>>
>>>
>
> --
> Jan Abendroth
> deCODE biostructures
> Seattle / Bainbridge Island WA, USA
> work: JAbendroth_at_decode.is
> home: Jan.Abendroth_at_gmail.com
>

CCP4bb navigation

CCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999

Previous message:
Subject: Re: question about pore size calculation
From: Sudharsan Sridharan sudhaarsan {- at -} GMAIL {- dot -} COM
Date: 2009-10-14

Next message:
Subject: Re: question about pore size calculation
From: David Briggs drdavidcbriggs {- at -} GMAIL {- dot -} COM
Date: 2009-10-14