Hi everyone,
I'm trying to run PASD in xplor version 2.18 on my data. I have 4
spectra (recorded with different mixing times) that I'm putting in;
initial matching scripts (one for each spectrum) ran fine, logfiles look
promising in terms of assignments found. I then rewrote jointFilter.tcl
to read in shiftAssignments and peaks from all spectra (since in
eginput/marvin/cvn there's also only one jointFilter script that reads
in both 3dC and 3dN), but once running, it stays at the netFilter step
forever. The last entry in the logfile shows that netFilter was started,
but nothing else is logged; my calculation was then aborted by the
queueing system after 48h (!). Is it just too much for the netFilter to
handle data from 4 spectra? (Each spectrum has ~300-500 peaks, there are
~350 shiftAssignments.) Would it help to split jointFilter in two or
four to only handle two spectra or one spectrum each? Or have I
overlooked something?
I'm attaching the jointFilter script I'm using up to the netFilter step.
Any help would be greatly appreciated. Thanks very much in advance!
Best greetings,
--robert.
package require aeneas
#
# this entire example takes about 12 hours to run on a 60-processor cluster.
# If you just want to verify that things run, run all the scripts with
# the flag -quick
#
set quickMode [flagExists $argv -quick]
#
# initialization
#
initParamPsfPdb \
-psfFileName ./prot.psf \
-randomCoords
#
# quick mode will only calculate the structure of the first 36 residues
of cyanovirin
#
if {$quickMode} {
XplorCommand "delete sele (not (resid 1:36)) end"
}
#
# make sure the initial coords have good covalent geometry
#
cleanCovalentGeom
#
# set up the 3dC NOEs
#
XplorCommand "set message off echo off end"
set noe_3dc1 [create_MarvinNOEPotential 3dC]
readShiftAssignments \
-fileName "prot_3dc1_pass1.shiftAssignments" \
-pot $noe_3dc1
readMarvinPeaks \
-fileName "prot_3dc1_pass1.peaks" \
-pot $noe_3dc1
XplorCommand "set message off echo off end"
set noe_3dc2 [create_MarvinNOEPotential 3dC]
readShiftAssignments \
-fileName "prot_3dc2_pass1.shiftAssignments" \
-pot $noe_3dc2
readMarvinPeaks \
-fileName "prot_3dc2_pass1.peaks" \
-pot $noe_3dc2
XplorCommand "set message off echo off end"
set noe_3dc3 [create_MarvinNOEPotential 3dC]
readShiftAssignments \
-fileName "prot_3dc3_pass1.shiftAssignments" \
-pot $noe_3dc3
readMarvinPeaks \
-fileName "prot_3dc3_pass1.peaks" \
-pot $noe_3dc3
XplorCommand "set message off echo off end"
set noe_3dc4 [create_MarvinNOEPotential 3dC]
readShiftAssignments \
-fileName "prot_3dc4_pass1.shiftAssignments" \
-pot $noe_3dc4
readMarvinPeaks \
-fileName "prot_3dc4_pass1.peaks" \
-pot $noe_3dc4
set peakRemarks3dC1 [list]
set saRemarks3dC1 [list]
set peakRemarks3dC2 [list]
set saRemarks3dC2 [list]
set peakRemarks3dC3 [list]
set saRemarks3dC3 [list]
set peakRemarks3dC4 [list]
set saRemarks3dC4 [list]
set peakRemarksJoint [list]
initializePeakAssignmentNumFiltersFailed -pot $noe_3dc1
initializePeakAssignmentNumFiltersFailed -pot $noe_3dc2
initializePeakAssignmentNumFiltersFailed -pot $noe_3dc3
initializePeakAssignmentNumFiltersFailed -pot $noe_3dc4
currentFilterSummary $noe_3dc1
currentFilterSummary $noe_3dc2
currentFilterSummary $noe_3dc3
currentFilterSummary $noe_3dc4
netFilter \
-pot [list $noe_3dc1 $noe_3dc2 $noe_3dc3 $noe_3dc4] \
-intraresidueNeighborhoods \
-extendNeighborhoodsWithHighScoringPeakAssignments \
-failedFiltersCutoff 0 \
-numIterations 5 \
-expectedContactsPerShiftAssignment [list 10 10 10 10] \
-createInverseExceptions \
-preferIntra \
-resetNumFailedFilters \
-remarksVariableName peakRemarksJoint
