Thanks to everybody who sent advice on this (John K., Tingting, John V., David H., hope i didn't miss anybody). The renaming worked, using John K's script (see below).
Tom Pochapsky On Sep 13, 2008, at 4:06 PM, John Kuszewski wrote: > Ah. Then the problem is almost certainly spaces in the names of > your segids. You could save yourself a lot of hassle by correcting > the psf and starting pdb files: > > Struct @file.psf end > coor @file.pdb > > Vector do (segid = "a") (segid " a ") > Write struct output=file2.psf end > Write coor output=file2.pdb end > Stop > > --JK > > On Sep 12, 2008, at 3:40 PM, Thomas Pochapsky > <pochapsk at brandeis.edu> wrote: > >> Hi, >> >> I generated a multimeric protein structure from a model built in >> PyMOL (painfully, so I don't want to have to do it again!), and >> generated a .psf file with the subunits each generated with the >> segment subroutine: >> >> segment >> name=" A" >> chain >> @toppar:toph19.pep >> coordinates @tet1.pdb >> end >> end >> coor @tet1.pdb >> end >> >> and each subunit specified with the segment names " A", " B" >> etc. The PDB file I generated has lines in it like: >> >> ATOM 1 N MET 2 20.811 62.100 33.497 1.00 >> 0.00 A >> >> with the label at the end being the chain specifier, and these are >> all appropriate throughout the PDB file. >> >> >> The PSF file shows the following for the same entry: >> >> 1 A 2 MET N NH3 -0.100000 >> 14.0070 0 >> >> Again, each atom appears to have the appropriate label (A or B or >> whatever) immediately preceding the residue number in the psf file. >> >> However, when I try to assign NOEs to atoms in the structure using >> the form shown in eginput mef_dna, (as) >> >> assign ( segid A and resid 48 and name hn ) (segid A and resid 49 >> and name hn ) 3.0 0.5 0.5 >> >> no atoms are picked and i get an error message: >> >> %NOE-ERR PROBLEM AT 1 -999.000 -999.000 -999.000 -999.000 >> SELRPN: 0 atoms have been selected out of 5322 >> SELRPN: 0 atoms have been selected out of 5322 >> >> Clearly, my selection statement isn't working, but I have tried every >> variation I can think of of how segid might be constructed, I still >> get the error. Anybody have any insights? >> >> Thanks, >> Tom Pochapsky >> >> _______________________________________________ >> Xplor-nih mailing list >> Xplor-nih at nmr.cit.nih.gov >> http://dcb.cit.nih.gov/mailman/listinfo/xplor-nih
