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On Mon, 5 Jun 2006, Yoder, Marilyn wrote:
> Hi all,
>
> I have a reviewer challenging the number of digits to the right of the
> decimal point that I have reported in a submitted manuscript. I had
> reported 3 digits to the right, frankly because that is what most of the
> programs I use report and the PDB coordinate file reports 3 digits to
> the right of the decimal in the CRYST1 record. The reviewer doubts that
> the value is accurate to that many digits, and suggested reporting to
> the tenth of an Angstrom. In corresponding with the PDB, they allow 3
> digits to the right of the decimal, but even if one gives the PDB, say
> 51.1 A as an axis, the CRYST1 record will be padded and will appear as
> 51.100A.
>
> So my question is .... how does one determine what is a valid accuracy
> or precision in unit cell axes? To be honest, I'm not sure what all the
> numbers are, and how many significant digits they have, that are used in
> calculating unit cell axes.
>
> In my particular case, I have data to 1.73 A, synchrotron radiation,
> 0.41 degree mosacity. All unit cells are less than 115 A.
>
> Thanks for any insight.
>
> Regards,
> Marilyn
>
> Marilyn D. Yoder
> Division of Cell Biology & Biophysics
> School of Biological Sciences
> University of Missouri-Kansas City
> 5007 Rockhill Rd.
> Kansas City, MO 64110-2499
> phone 816-235-1503
> fax 816-235-1503
Hi,
Take 2 crystals (one of which you've already collected the diffraction
data from) and collect a second data set from the second crystal using any
source and any detector you like. Or even collect a second data set
from the "first" crystal if it is still around sitting in a Dewar. Then
process the new data set and check whether or not the cell parameters
agree to the 3rd decimal point: I think that they won't. Do check for
yourself, one should always question statements if one has no idea if the
statement is correct or not.
So I think the reviewer is right in requesting that the paper should not
give too accurate values for the cell parameters (1 or 2 decimal points is
sufficient). However nothing prevents you from leaving the values as
obtained from the data processing and post-processing suite in the PDB
header records. And I am not the reviewer BTW.
Fred.
--
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