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Dear Charles,
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?
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:
def setConstraints(): #number of conformers (support up to 10 conformers) scaleVdw = 1.0 / float( nconf ) xplor.command(""" constraints ! interaction (all) (all) inter = (segid " ") (segid " ") inter = (resid "107"
and segid "ALT0") (resid "107" and segid "ALT0") inter = (resid "123" and segid "ALT0") (resid "123" and segid "ALT0") inter = (resid "148" and segid "ALT0") (resid "148" and segid "ALT0") inter = (resid "190" and segid "ALT0") (resid "190" and segid "ALT0")
inter = (resid "107" and segid "ALT1") (resid "107" and segid "ALT1") inter = (resid "123" and segid "ALT1") (resid "123" and segid "ALT1") inter = (resid "148" and segid "ALT1") (resid "148" and segid "ALT1") inter = (resid "190" and segid "ALT1") (resid
"190" and segid "ALT1") inter = (resid "107" and segid "ALT2") (resid "107" and segid "ALT2") inter = (resid "123" and segid "ALT2") (resid "123" and segid "ALT2") inter = (resid "148" and segid "ALT2") (resid "148" and segid "ALT2") inter = (resid "190" and
segid "ALT2") (resid "190" and segid "ALT2") weights * 1 end inter = (segid " ") (segid "ALT0") inter = (segid " ") (segid "ALT1") inter = (segid " ") (segid "ALT2") weights * 1 vdw %f end end""" % scaleVdw ) return
Looks the setting is not working. Is there something wrong? Thanks & regards,
Liu Wei
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