Good to know Bob. I must check them out.
----
Pozdrawiam, | Best regards,
Maciek Wójcikowski
[email protected]
2014/1/10 Robert Hanson <[email protected]>
> 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 <[email protected]> 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
>> [email protected]
>>
>>
>> 2014/1/9 Glen van Ginkel <[email protected]>
>>
>>> 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
>>>
>>>
>>>
>>>
>>> ------------------------------------------------------------------------------
>>> CenturyLink Cloud: The Leader in Enterprise Cloud Services.
>>> Learn Why More Businesses Are Choosing CenturyLink Cloud For
>>> Critical Workloads, Development Environments & Everything In Between.
>>> Get a Quote or Start a Free Trial Today.
>>>
>>> http://pubads.g.doubleclick.net/gampad/clk?id=119420431&iu=/4140/ostg.clktrk
>>> _______________________________________________
>>> Jmol-users mailing list
>>> [email protected]
>>> https://lists.sourceforge.net/lists/listinfo/jmol-users
>>>
>>
>>
>>
>> ------------------------------------------------------------------------------
>> CenturyLink Cloud: The Leader in Enterprise Cloud Services.
>> Learn Why More Businesses Are Choosing CenturyLink Cloud For
>> Critical Workloads, Development Environments & Everything In Between.
>> Get a Quote or Start a Free Trial Today.
>> http://pubads.g.doubleclick.net/gampad/clk?id=119420431&iu=/4140/ostg.clktrk
>>
>>
>>
>> _______________________________________________
>> Jmol-users mailing
>> [email protected]https://lists.sourceforge.net/lists/listinfo/jmol-users
>>
>>
>>
>>
>> ------------------------------------------------------------------------------
>> CenturyLink Cloud: The Leader in Enterprise Cloud Services.
>> Learn Why More Businesses Are Choosing CenturyLink Cloud For
>> Critical Workloads, Development Environments & Everything In Between.
>> Get a Quote or Start a Free Trial Today.
>>
>> http://pubads.g.doubleclick.net/gampad/clk?id=119420431&iu=/4140/ostg.clktrk
>> _______________________________________________
>> Jmol-users mailing list
>> [email protected]
>> https://lists.sourceforge.net/lists/listinfo/jmol-users
>>
>>
>
>
> --
> 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
>
>
>
> ------------------------------------------------------------------------------
> CenturyLink Cloud: The Leader in Enterprise Cloud Services.
> Learn Why More Businesses Are Choosing CenturyLink Cloud For
> Critical Workloads, Development Environments & Everything In Between.
> Get a Quote or Start a Free Trial Today.
>
> http://pubads.g.doubleclick.net/gampad/clk?id=119420431&iu=/4140/ostg.clktrk
> _______________________________________________
> Jmol-users mailing list
> [email protected]
> https://lists.sourceforge.net/lists/listinfo/jmol-users
>
>
------------------------------------------------------------------------------
CenturyLink Cloud: The Leader in Enterprise Cloud Services.
Learn Why More Businesses Are Choosing CenturyLink Cloud For
Critical Workloads, Development Environments & Everything In Between.
Get a Quote or Start a Free Trial Today.
http://pubads.g.doubleclick.net/gampad/clk?id=119420431&iu=/4140/ostg.clktrk
_______________________________________________
Jmol-users mailing list
[email protected]
https://lists.sourceforge.net/lists/listinfo/jmol-users
