xplor-nih-request at nmr.cit.nih.gov wrote: >Send Xplor-nih mailing list submissions to > xplor-nih at nmr.cit.nih.gov > >To subscribe or unsubscribe via the World Wide Web, visit > http://dcb.cit.nih.gov/mailman/listinfo/xplor-nih >or, via email, send a message with subject or body 'help' to > xplor-nih-request at nmr.cit.nih.gov > >You can reach the person managing the list at > xplor-nih-owner at nmr.cit.nih.gov > >When replying, please edit your Subject line so it is more specific >than "Re: Contents of Xplor-nih digest..." > > >Today's Topics: > > 1. Re: sge (Charles at Schwieters.org) > 2. Re: marvin example scripts (John Kuszewski) > > >---------------------------------------------------------------------- > >Message: 1 >Date: Tue, 15 May 2007 12:04:55 -0400 >From: Charles at Schwieters.org >Subject: Re: [Xplor-nih] sge >To: "Gary S. Thompson" <garyt at bmb.leeds.ac.uk> >Cc: xplor-nih at nmr.cit.nih.gov, Charles at Schwieters.org >Message-ID: <19035.1179245095 at khaki.cit.nih.gov> > >-----BEGIN PGP SIGNED MESSAGE----- >Hash: SHA1 > > >Hi Gary-- > > > > >>that would work but needs a bit more work as the file had info about >>threads etc but I can extemperize from here. Would you like me submit >>the pach back to you when i have finished? >> >> >> > >that would be great. > >thanks-- >Charles >-----BEGIN PGP SIGNATURE----- >Version: GnuPG v1.2.1 (GNU/Linux) >Comment: Processed by Mailcrypt 3.5.8+ <http://mailcrypt.sourceforge.net/> > >iD8DBQFGSdonPK2zrJwS/lYRAlxOAJoC42c0Ob4TploIIGnCH8L2wnpGGACfYeuj >AvVrFyaS2MGYemRbBuh+Ko0= >=IyIs >-----END PGP SIGNATURE----- > > >------------------------------ > >Message: 2 >Date: Tue, 15 May 2007 19:08:30 -0400 >From: John Kuszewski <johnk at mail.nih.gov> >Subject: Re: [Xplor-nih] marvin example scripts >To: "Gary S. Thompson" <garyt at bmb.leeds.ac.uk> >Cc: xplor-nih at nmr.cit.nih.gov >Message-ID: <AE99F858-CE8E-4F33-80A1-8C54813C9CD7 at mail.nih.gov> >Content-Type: text/plain; charset=US-ASCII; delsp=yes; format=flowed > >I got rid of the protG example, primarily because it wasn't useful >for showing people how to >use marvin to solve structures. > >The peak tables included in the CVN and IL-4 examples contain many >bad peaks. They were >generated by automatic peak picking using Dan Garrett's CAPP >program. After the initial matching >of peaks to shift assignments and filtering the resulting peak >assignments, about 10-15% of the >assigned peaks are completely wrong. More importantly, a very large >number of wrong peak assignments >are still attached to good peaks (i.e., peaks that have another, >correct, peak assignment). > >And as we showed in our 2005 JACS paper, adding wrong peak >assignments to otherwise-good peaks >is, for the behavior of marvin, entirely equivalent to adding >completely new, entirely wrong peaks. > >If you're really interested, the protG example is still available in >older versions of xplor-nih. > >--JK > >On May 15, 2007, at 11:04 AM, Gary S. Thompson wrote: > > >
Thanks John It just wqsn't clear from documentaion (at least to me ;-) that the data in these examples still contained bad peaks as the documentation (ehinput/README)only deals with protG regards gary n.b. the calculation of a fragments with runMarvinQuick is quite cool >>Dear all >> >>in the eginput directory it states in the readme >> >>(9) marvin >> contains an example of a method of weeding out incorrect NOEs. >>This >>example >> uses protein G and randomly-assigned NOEs as well as the >>experimental NOEs. >> This example uses the TCL scripting language. >> >>On a recently downloaded xplor nih distribution (2.17.0) marvin/ >>protg >>is empty except for a CVS directory. >> >>however, marvin does contain cvn and il4 and I have managed to get >>cvn/runMarvinQuick to run on our cluster and it did converge and >>produce >>a result. But, here is the question, does the cvn data dontain bogus >>nOes and if not where can I get the protG test data so as to test this >>feature? >> >> >>regards >>gary >> >> >>-- >>------------------------------------------------------------------- >>Dr Gary Thompson >>Astbury Centre for Structural Molecular Biology, >>University of Leeds, Astbury Building, >>Leeds, LS2 9JT, West-Yorkshire, UK Tel. +44-113-3433024 >>email: garyt at bmb.leeds.ac.uk Fax +44-113-2331407 >>------------------------------------------------------------------- >> >> >>_______________________________________________ >>Xplor-nih mailing list >>Xplor-nih at nmr.cit.nih.gov >>http://dcb.cit.nih.gov/mailman/listinfo/xplor-nih >> >> > > >------------------------------ > >_______________________________________________ >Xplor-nih mailing list >Xplor-nih at nmr.cit.nih.gov >http://dcb.cit.nih.gov/mailman/listinfo/xplor-nih > > >End of Xplor-nih Digest, Vol 51, Issue 10 >***************************************** > >. > > > -- ------------------------------------------------------------------- Dr Gary Thompson Astbury Centre for Structural Molecular Biology, University of Leeds, Astbury Building, Leeds, LS2 9JT, West-Yorkshire, UK Tel. +44-113-3433024 email: garyt at bmb.leeds.ac.uk Fax +44-113-2331407 -------------------------------------------------------------------
