Dear Martin If you wish to add names at the top of each record, a short python program is available in http://www.redbrick.dcu.ie/~noel/talks/PythonForChemistry.pdf.
hope this helps Tomoko 2008/5/24 Martin Stoermer <[email protected]>: > Hi folks, > we often use Pymol to visualize SD files overlayed on protein structures > usually coming out of docking and other VS runs. I've noticed that when > using the seq_view window, some SD files which have the names of individual > ligands at the very top of each record in the SDF have these names usefully > displayed in seq_view, but if the names are in a <name> field, they don't > displayed, we just get '' '' type entries for each ligand. Whilst I > understand that seq-view is primarily for looking at and manipulating > portions of the protein sequence, is there some way to view the name fields > in Pymol? > e.g. the following type of entry would have ZINC09999999_0 displayed in the > seq_view window: > > $$$$ > ZINC09999999_0 > -OEChem-05230802443D > > 50 54 0 0 0 0 0 0 0999 V2000 > 40.7619 54.6488 8.1176 C 0 0 0 0 0 0 0 0 0 0 0 0 > 40.1173 55.8601 8.2935 C 0 0 0 0 0 0 0 0 0 0 0 0 > 41.2285 54.2825 6.8679 C 0 0 0 0 0 0 0 0 0 0 0 0 > > but the following would just display " or sometimes UNK > > > csCF1100/05020817022D > > 9 8 0 0 0 0 0 0 0 0999 V2000 > 10.9319 -19.1708 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 > 12.2508 -19.9323 0.0000 C 0 0 3 0 0 0 0 0 0 0 0 0 > 13.5698 -19.1708 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 > 14.8887 -19.9323 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 > 16.2077 -19.1708 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 > 17.5266 -19.9323 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 > 10.9319 -17.6478 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 > 9.6129 -19.9323 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 > 12.2508 -21.4553 0.0000 Br 0 0 0 0 0 0 0 0 0 0 0 0 > 1 2 1 0 0 > 2 3 1 0 0 > 3 4 1 0 0 > 4 5 1 0 0 > 5 6 1 0 0 > 1 7 2 0 0 > 1 8 1 0 0 > 2 9 1 0 0 > M END > > <Name> (1) > (+/-)2-BROMOHEXANOIC ACID (2-BROMOCAPROIC ACID) > > > <Amount> (1) > 25G > > > <Supplier catalogue number> (1) > 24,283-7 > > > <Location> (1) > STORE > > > <CAS_Number> (1) > 2681-83-6 > > > <MW> (1) > 195.0449 > > $$$$ > > > thanks, > Martin > > Dr. Martin Stoermer > Institute For Molecular Bioscience > University of Queensland > > > > ------------------------------------------------------------------------- > This SF.net email is sponsored by: Microsoft > Defy all challenges. Microsoft(R) Visual Studio 2008. > http://clk.atdmt.com/MRT/go/vse0120000070mrt/direct/01/ > _______________________________________________ > PyMOL-users mailing list > [email protected] > https://lists.sourceforge.net/lists/listinfo/pymol-users > >
