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Hi Tom--
Since John dealt with the other question, it seems fair that I give
this one a crack:
>
> We are trying to use RDCs for the first time in our structure
> calculations, and would appreciate any examples of how one goes about
> implementing them in simulated annealing calculations on globular
> proteins. We have only the raw data (deltas from bicelle alignments).
> In particular, it would be nice if we could simultaneously get Da and Dr
> as in JMR 131, 159-162 (1998) Clore et al. I have looked at some of the
> example files we got with XPLOR-NIH, but I still haven't made sense of
> them.
>
A stopgap possibility would be to extract the rdc protocol from the
eginputs/mef_dna/sa_internal_mef.inp. Assuming you have data from a
single experiment (one set of values for Da, rhombicity), just focus
on the JNHp class.
A new, simple example is in the works, but is not quite yet ready. Sorry.
A summary of the necessary steps is:
1) initial setup
evaluate ($ini_sani = 0.01) evaluate ($fin_sani = 1.0)
evaluate ($ksani = $ini_sani)
sani
nres=1600
class JNHp
force $ksani
potential harmonic
{====>}
coeff 0.0 -20.0 0.39
@mef_dip_nh.tbl {* dipolar coupling restraints for protein amide NH. *}
end
evaluate ($sani_fac = ($fin_sani/$ini_sani)^(1/$ncycle))
2) then during cooling (at each step), adjust the associated force constant.
evaluate ($ksani = $ksani*$sani_fac)
sani class JNHp force $ksani end
3) final analysis:
sani print threshold=0.0 class JNHp end
evaluate ($rms_sani_JNH_prot=$result)
evaluate ($viol_sani_JNH_prot=$violations)
evaluate ($R_JNH_prot=$result/26.7)
I hope to have a complete example in the next release of xplor-nih.
best regards--
Charles
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