Symmetry operators are used to produce copies of chains in biomolecular
assemblies. You can identify them with
select symop=1
select symop=2
etc.
so
display symop=2 and *:A
should work.
On Thu, Jun 19, 2014 at 1:14 PM, Rolf Huehne <[email protected]> wrote:
> On 06/19/2014 05:25 PM, Andreas Truszkowski wrote:
> > Hi,
> >
> > hiding protein chains with display *:chain or *:chain\modelnr is no
> > problem. But how can I hide a specific chain within a bilogical
> > assembly? The problem is that in biological assemblies the unit cell
> > (assymetric unit) is transformed n-times as described in the PDB REMARK
> > 350 section i.e. if I take the protein 4ins with two chains in the
> > assymetric unit and I apply the filter BIOMOLECULE 5 to it, the
> > resulting hexamere consists of three times chain A and B. Using
> > something like display *:Aleads to that every chain A is hidden.
> >
> > Is there a way to only show or hide a specific chain e.g. chain A in the
> > second unit cell?
> >
> I don't know about any simple way to achieve this (but I might be wrong).
>
> Unfortunately the BIOMOLECULE filter of Jmol was implemented different
> than what the PDB does with the biological unit files they provide.
> In these files each copy is placed into a new model so selecting each
> chain individually is rather easy. So maybe switching to use these
> biological unit files might be the easiest way to solve your problem.
>
> If that is not an option you might be able to solve the problem by using
> the 'atomindex' property (see
> http://jena3d.fli-leibniz.de/doc/jmol_scripting/index.htm#atomproperties)
> in
> combination with the atom selector function 'within(POLYMER,
> atomindex=n' (see
> http://jena3d.fli-leibniz.de/doc/jmol_scripting/index.htm#atomexpressions
> ).
>
> If you would only need to do this for a small set of predefined PDB
> entries you might collect the necessary data rather easily.
> If you would need it for any PDB structure it might require quite some
> Jmol script programming.
>
> The general idea is like this:
>
> 1) Each atom has an individual index number assigned, starting with
> zero. It can be used for atom selection by using for example 'atomindex=0'.
>
> 2) You should be able to select all atoms belonging to the same chain by
> using the atom expression 'within(POLYMER, atomindex=0)'.
>
> 3) Identify the atomindex for the first atom of each chain (manually or
> programmatically) and build the proper atom expression from 2).
>
> I don't know if 2) will work in all cases. I just tried it for PDB entry
> 4INS and it worked.
>
> The order of the chains you will get by 'atomindex' might not be the
> same as you might expect. It will depend on the way how the atoms for
> the copies are created. To solve this programmatically might be difficult.
>
> One way to achieve 3) might be to go like this:
> a) Use atomindex=0 to identify the atoms of the first chain.
> b) Select the first chain and determine the maximum atomindex.
> c) Add one to the maximum atomindex and use it in a) to find the next
> chain.
> d) Repeat this until the maximum atomindex of the whole structure is
> reached.
> This will of course not work, if the atomindex numbers within each chain
> are not sequential. You would have to check this first.
>
> Good luck,
> Rolf
> --
>
> Rolf Huehne
> Postdoc
>
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--
Robert M. Hanson
Larson-Anderson Professor of Chemistry
Chair, Department 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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