Hello Liu Wei-- > > I'm trying to calculate a structure ensemble of a di-domain protein using PRE > restrains. Since there is no example script for ensemble PRE calculation > (please > correct me if I am wrong), I wrote a script based on: > eginput/pre/refine/newRefine.py > The modified script can provide a back-calculated result based on a ensemble > structure. However, it cannot provide the correct ensemble structure when I > tested it using synthetic PREs from a known ensemble structure. A typical > result > is like this: > > REMARK ------------------------------------------------------------ REMARK > summary Name Energy RMS Violations REMARK summary total 6106.20 2258.0 REMARK > summary ANGL 211.84 0.354 0.0 REMARK summary BOND 3.74 0.001 0.0 REMARK > summary > IMPR 37.55 0.272 0.0 REMARK summary VDW 2631.49 2060.0 REMARK summary pre > 3221.57 > 14.020 198.0 REMARK > ------------------------------------------------------------ > REMARK REMARK Cross-validated terms: REMARK summary bbPre 3221.57 14.020 198.0 > REMARK ------------------------------------------------------------ REMARK > Paramagnetic Relaxation Enhancement Analysis REMARK PRE RMS Q-fac tau_c Viols > REMARK PRE Cysp107hn 19.112 0.713 6.000 51 REMARK PRE Cysp123hn 2.446 0.498 > 6.000 > 43 REMARK PRE Cysp148hn 18.198 0.744 6.000 46 REMARK PRE Cysp190hn 10.217 > 0.423 > 6.000 58 REMARK ------------------------------------------------------------ > > Is it because the high energy from VDW hinders further improvement > of PRE?
Is this a refinement, or calculation from randomly placed subunits? Are you starting with Ne=1? Do you have any data aside from PREs? A better starting script for docking may be eginput/diffTens/dock/dock.py in the Xplor-NIH distribution. > If so, here is another question. The .viols file shows that nonbonded > violations > mostly come from different spin labels, like this: > > ALT0 107 CYSP N ALT1 107 CYSP HN 0.98 1.83 0.85 > ALT0 107 CYSP N ALT1 107 CYSP CA 1.46 2.61 1.15 ALT0 107 CYSP N ALT1 107 CYSP > HA > 2.08 2.35 0.28 > > Below is the corresponding setting in the script: > Unfortunately, the VDW violation report does not honor the contraints interaction statement, so the presence of those violations is not a test of how well the setConstraints function is working. There is a new term repelPot, which does proper reporting. A (perhaps too) brief example of its use can be found in eginput/gb1_rdc/anneal2.py. best regards-- Charles _______________________________________________ Xplor-nih mailing list [email protected] https://dcb.cit.nih.gov/mailman/listinfo/xplor-nih
