Hi Brenton,
It seems 2HYY only has that one (type of) ligand present?
so:
fetch 2hyy
as cartoon
show sticks, organic
color black, elem c and organic
remove not chain a
gives me a cartoon representation of the protein, with a stick
representation of the ligand. There are 4 copies of the complex in the
asymmetric unit and they have chain ID's A-D, so the last command removes
all atoms except the ones in chain a.
I am personally more comfortable with this kind of selections, instead of
the 2hhy/something/something/something
In case you want to keep all molecules, but just select on of the ligands,
you could do something like:
select ligandA, organic and chain a and resname STI
Hope this helps,
Folmer
2015-01-06 9:40 GMT+01:00 Brenton Horne <brentonho...@ymail.com>:
> Hi,
>
> I know I must be getting annoying, although I must say this mailing list
> and its users have been very helpful for me so thank you all. My question
> this time is how do I select specific ligands? Like I am using PDB ID 2HYY
> and I'd like to set the imatinib (STI600) ligand as the only visible
> ligand, plus I'd like to colour it according to the CPK scheme, except with
> carbons coloured black. Now I've tried:
>
> select 2hyy/A/STI
>
> based on the Selection Algebra
> <http://pymolwiki.org/index.php/Selection_Algebra> page on PyMOL Wiki but
> this returned the result:
>
> Selector: selection "sele" defined with 0 atoms.
>
>
> ps. is there are any PDF document showing complete up-to-date command-line
> syntax for PyMOL because I think this will really help me. PyMOL Wiki I
> find generally only gives a snippet of the command-line syntax for a given
> topic. Plus I generally find the really general format of the syntax (e.g.,
>
> show reprentation [,object]
>
> ) with the square brackets PyMOL sometimes shows is confusing to me,
> unless it's accompanied by an example of how that code appears for a
> specific example.
>
> Thanks for your time,
> Brenton
>
>
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--
Folmer Fredslund
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look and join the conversation now. http://goparallel.sourceforge.net
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