Re: [PyMOL] seq_view and SD files

[Tomoko N. <tmk...@gm...>]

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 <m.s...@im...>:

> 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
>
>
>
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