Hello,
I'm either mis-understanding the format of the rdc constraint tables, or
having trouble getting xplor-nih (python) to make use of the error
entry. One of our NMR experiments was run at lower digital resolution, so
we wanted to increase the "tolerance" in the rdc evaluation for that
table. Changing the number following the residual dipolar coupling
values over quite a wide range didn't make any difference at
all in the rdc energy reported during the simulation or in the final
summary table. (the value I'm changing is the "0.2" below - have
varied it from 0.1 to 10.0 with absolutely no difference in the reported
energies of the rdc term using xplor-nih 2.11 and 2.12):
assign ( resid 500 and name OO )
( resid 500 and name Z )
( resid 500 and name X )
( resid 500 and name Y )
( resid 7 and name N )
( resid 7 and name HN ) -14.5 0.2
In the create_RDCPot function of rdcPotTools.py there's a line:
# default threshold value
rdc.setThreshold( 0.5 )
Is this possibly not being changed to the value in the table (or is this
just for reporting # of violations in the final analysis)?
Any ideas, suggestions, or corrections of my mis-interpretations would
be most appreciated.
Thanks,
- Mark
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Mark Girvin
Biochemistry Department [email protected]
Albert Einstein College of Medicine Tel:(718) 430-2025/2021
1300 Morris Park Ave. FAX:(718) 430-8565
Bronx, NY 10461 http://www.bioc.aecom.yu.edu/labs/girvlab
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