On Monday, 21 November 2016 11:53:22 PM Seok-Yong Lee wrote:
> Hi All,
>
> We have recently solved several structures of a membrane protein in slightly
> different conformations at low resolutions (3.9-4.2 A). We would like to see
> that these structures reflect truly different conformations and to what
> extent these structures are discernible. To answer this question, we would
> need to estimate local and global coordinate uncertainty of these structures
> to see if the local/global conformational differences of the structures are
> bigger than the local/global coordinate uncertainty.
>
> I am wondering if there is any good way/program to show local coordinate
> uncertainty. I found that using SFCHECK I can get (i) amplitude of
> displacement of atom from electron density and (ii) correlation coefficient
> per residue. I have following questions.
>
> 1)Can we use this amplitude of displacement as local
> coordinate uncertainly? If not, is there a way to use as this displacement
> amplitude to get an estimate of the local coordinate error?
>
> 2)The output regarding this plot in SFCHECK is somewhat difficult
> to understand, as it shows a bar graph with multiples of sigma per residue.
> What does it mean by those residues with no sigma? Do these residues have too
> much or too less errors?
>
> 3)Is there a way to convert the output as a text file so that I can
> plot it myself?
>
> 4)Any recommendation with other programs that can produce local
> coordinate uncertainty per residue?
>
> Any advice would be greatly appreciated. Thank you in advance.
I don't think that the uncertainty/error in individual coordinates is a good
way to
describe or quantify the existence of "truly different conformations", unless
what
you really meant is "different rotamers" or some other very local property.
Nevertheless, if you want to estimate coordinate error from the available
refined
quantities, I suggest looking at
Cruickshank, D. W. J. (1999). Acta Cryst. D55, 583–601.
This paper describes an empirical estimate DPI that seems close to what you
are asking for. A further empirical simplification was suggest by David Blow
Acta Cryst. (2002). D58, 792-797
https://doi.org/10.1107/S0907444902003931
If the intent is to ask whether a conformation resulting from final refinement
against
data from one crystal is compatible with the data from a different crystal, I
suspect
the most powerful and convincing test is to simply try it. Transfer the
relevant
piece of the model from crystal A into your working model for crystal B, refine
a bit
(maybe only B factors or TLS), and see whether the resulting R/Rfree value are
different
from those you previously had for the crystal B model. You could then try the
complementary excercise by placing the original model from crystal B into the
context of the current model and data from crystal A.
Ethan Merritt
--
mail: Biomolecular Structure Center, K-428 Health Sciences Bldg
MS 357742, University of Washington, Seattle 98195-7742
