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.
All the best,
Seok-Yong
Associate Professor of Biochemistry
Duke University School of Medicine
USA
