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
