Dear Charles and others,
I am refining a structure of a protein that has several flexible residues
(defined as residues for which {1H}-15N NOEs are < 0.6).
I would like to make sure that I am taking this flexibility into account
correctly during the RDC-driven refinement.
In brief, I have created two separate RDC potential classes, 'rdc_rig' and
'rdc_flx' and two separate types of *.tbl files: one containing the "flexible"
residues and the other containing the "rigid" residues. I then set the rdc_flx
potential type to square:
rdc_flx.setPotType("square")
and left the default settings for the rdc_rig.
In the *.tbl files for "flexible" residues, I set the max error field to a
large number (40 Hz) and the min error value to 0 Hz for residues with positive
RDCs, and min to 40 Hz and max to 0 Hz for residues with negative RDCs. Here
is an example:
assign
( resid 600 and name OO)
( resid 600 and name Z)
( resid 600 and name X)
( resid 600 and name Y)
( resid 5 and name HA)
( resid 5 and name CA) -3.6200 40.0 0.0
assign
( resid 600 and name OO)
( resid 600 and name Z)
( resid 600 and name X)
( resid 600 and name Y)
( resid 48 and name HA)
( resid 48 and name CA) 19.3800 0.0 40.0
My questions are:
-- Is this a correct way to set up a half-open square well potential in XPLOR
(and deal with flexible residues)?
-- Should I be using different k(dipolar) values for "rigid" and "flexible"
potentials?
Thank you,
Tatyana
Tatyana I. Igumenova, Ph.D.
Assistant Professor
Department of Biochemistry and Biophysics
Texas A & M University
300 Olsen Boulevard
Biochemistry Building, Rm. N118A
TAMU 2128 | College Station, TX 77843-2128
http://coda.tamu.edu/Igumenova/
Tel.(office) 979.845.6312 | Tel.(lab) 979.845.6313
Fax 979.845.4946
