There are some new syntaxes that also make this particular task very easy.
By the way, see the RCSB beta site, which has a new "Ligand in pocket"
view. For example, the Ligand tab below the applet at
http://ccnightly.rcsb.org/pdb/explore/jmol.do?structureId=1eve&bionumber=1
This utilizes the CONTACT command along with several other options.
In particular, the SELECT, DISPLAY and HIDE commands all have two optional
initial parameters:
display GROUP ....
display ADD/REMOVE ....
which are just shortcuts for
display within(group,.....)
and
display displayed OR .....
display displayed AND NOT (....)
Bob
On Thu, Jan 9, 2014 at 8:40 AM, Glen van Ginkel <g...@ebi.ac.uk> wrote:
> Thanks Maciek,
>
> That worked a treat!
>
> Glen
>
>
>
> On 09/01/14 12:01, Maciek Wójcikowski wrote:
>
> Hi Glen,
>
> Have you tried double within function? I use following command to
> display residues within 10A from any ligand:
>
> display within(groups,within(10,TRUE,*/2))
>
> Note: receptor is model #1 and multiple ligands are in model 2 as
> frames. Change "*/2" to your ligand selection.
>
> ----
> Pozdrawiam, | Best regards,
> Maciek Wójcikowski
> mac...@wojcikowski.pl
>
>
> 2014/1/9 Glen van Ginkel <g...@ebi.ac.uk>
>
>> Hi all,
>>
>> After loading a PDB file I'm trying to restrict the view to the
>> environment (surrounding residues) of a specific ligand. I'm able to
>> select atoms within a given distance, but for amino acids that are
>> truncated due to the distance cut-off I'd like to show the whole
>> residue. Put another way, I want to display complete residues (Nucleic
>> or Protein monomers, interacting heterogens and co-factors) within a
>> given distance of a ligand.
>>
>> I've looked through much documentation and many website but I can't seem
>> to find the necessary commands to do this.
>>
>>
>> If any of you have suggestions I'd be most eager to hear from you.
>>
>> Kind regards,
>>
>> Glen
>>
>>
>> --
>> Protein Data Bank in Europe (PDBe: http://pdbe.org)
>> EMBL-EBI
>> Wellcome Trust Genome Campus
>> Hinxton, Cambridge
>> CB10 1SD
>>
>> Tel: 01223 492529
>> http://www.facebook.com/proteindatabank
>> http://twitter.com/PDBeurope
>>
>>
>>
>>
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--
Robert M. Hanson
Larson-Anderson Professor of Chemistry
St. Olaf College
Northfield, MN
http://www.stolaf.edu/people/hansonr
If nature does not answer first what we want,
it is better to take what answer we get.
-- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900
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