Hello Diego--
> I would like to use a refinement protocol against ensembles of different
> sizes (2, 4 ,6, 8, 10) for a multidomain protein (a tandem of SH2s
> domains, one SH3 and one splitPH domain separated by flexible linkers).
> I'm using restraints from SAXS intensities and chemical shift
> perturbations for the interaction surface between the splitPH and one of
> the SH2 domains.
> When I run the script below, which has been adapted from SAXS_EI
> protocol in the eginput xplor-nih2.29 directory, XPLOR crashes at
> different stages of the protocol generating a number of error messages
> (such as : /dms/prog/src/xplor-nih/bin/xplor: line 525: 1401
> Segmentation fault).
First, let's fix up the NOE setup:
>
> # set up NOE potential
> noe=PotList('NOE')
> potList.append(noe)
> from noePotTools import create_NOEPot
> for (name,scale,file) in [('inte',1,"interface.tbl"),
> ]:
> pot = AvePot(create_NOEPot(name,file))
This should be
pot = AvePot(create_NOEPot(name,file,sim=esim.member()))
This so that the distance restraints are satisfied for each ensmeble
member.
Also note that The Rgyr setup will restrain each ensemble member to
have the target Rgyr.
>
> # Ratio of gyration potential
> protocol.initCollapse("resid 488:933",
> Rtarget=32) # approximate value from Guinier analysis
> rgyr = AvePot(XplorPot, 'COLL')
> potList.append(rgyr)
>
Let's focus on getting rid of the segfaults, and then work on getting
the ivm setup correct. If you still get segfaults with the above fix,
please send the last 30 lines or so of a log file.
thanks--
Charles
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--
Charles Schwieters email: Charles at Schwieters.org
www: http://schwieters.org/cds
phone: (301) 402-4914 PGP key: http://schwieters.org/cds/pgp.txt
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