Re: [ccp4bb] Rfree statistics in SHELXL

- 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: CCP4 needs your help, part 2 a reminder
From: Jim Naismith naismith {- at -} ST-ANDREWS {- dot -} AC {- dot -} UK
Date: 2007-10-08

Next message:
Subject: How to number atoms in a ligand
From: Zheng Zhou zhengzhouzz {- at -} GMAIL {- dot -} COM
Date: 2007-10-08

Subject: Re: Rfree statistics in SHELXL
From: Oliv Eidam eidamo {- at -} BIOC {- dot -} UNIZH {- dot -} CH
Date: 2007-10-08

It is actually possible to calculate R(free) with SHELXL for the outer
most resolution shell. Gabor Bunkoczi indicated the solution and I
forward it here to the public:
- Rename the .res file of the last refinement run to .ins
- adjust the CGLS parameter in the .ins file to 0 -1 (Zero refinement
cycles, selection of reference set with the flag -1):
CGLS 0 -1
- Set the resolution limits to the ones of the outer most resolution
shell (in my case 1.39-1.34 Angstroem):
SHEL 1.39 1.34
- re-run the job with the modified .ins file
- the R1(Free) values in the output .res file correspond to those of the
highest resolution shell.

Gabor, thank you very much for this great suggestion!

Oliv

Dr G. Bunkoczi schrieb:
> Hi Oliv,
>
> you can include a SHELL command (set to the highest resolution shell),
> and CGLS 0 -1 and re-run the job. The R-factors you get are those of
> the highest resolution shell.
>
> BW, Gabor
>
> On Oct 8 2007, Oliv Eidam wrote:
>
>> Dear all,
>>
>> I used SHELXL for anisotropic structure refinement of high-resolution
>> data (1.3 Angstroem) and a reviewer asked me to include refinement
>> statistics for the outer most resolution shell in the
>> crystallographic table. While R-factors for the outer most resolution
>> shell belong to the standard output in REFMAC or CNS, it seems to me
>> that SHELXL calculates R-factors only for reflections of the work
>> set. I also noticed that test reflections are missing in the
>> structure factor file (.fcf file) generated by shelxpro, preventing
>> me to use the [S] or [L] options in shelxpro to calculate R(free)
>> statistics.
>> Is it simply not possible to calculate the R(free) factor for the
>> outer most shell after SHELX refinement? Or is there a problem with
>> my SHELX program?
>>
>> Many thanks for your answers and suggestions,
>>
>> Oliv
>>
>>
>>
>

--
Oliv Eidam

Department of Biochemistry
University of Zurich
Winterthurerstrasse 190
8057 Zurich, Switzerland

Phone: 0041-44-635-6563
Email: eidamo@bioc.uzh.ch
Web: http://www.bioc.uzh.ch/gruetter
NCCR: http://www.structuralbiology.ethz.ch

CCP4bb navigation

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

Previous message:
Subject: CCP4 needs your help, part 2 a reminder
From: Jim Naismith naismith {- at -} ST-ANDREWS {- dot -} AC {- dot -} UK
Date: 2007-10-08

Next message:
Subject: How to number atoms in a ligand
From: Zheng Zhou zhengzhouzz {- at -} GMAIL {- dot -} COM
Date: 2007-10-08