Re: [Jmol-users] Jmol load FILTER "SELECT *.CA; BIOMOLECULE n; APPLY SYMMETRY"

[Bob H. <ha...@st...>]

Mauricio Carrillo Tripp wrote:

>     The different sets of atoms
>     created by individual BIOMT transformations are selectable using the
>     "symop" selection option:
>
>     select symop=3
>     select symop<6
>
>     etc. (There is a bug there -- symop=1 specifically is not
>     selectable in
>     11.5.32)
>
>
> OK, so for example, if I want to display 1/2 capsid, I will have to load
> the PDB file 30 times, each time using a different select in the 
> loading filter.

heavens, no. You just load it once, then display only the parts of the 
capsid you want (if you can settle for just *.CA atoms). If you want all 
the atoms, I think you probably can't load 1/2 the capsid anyway.

> By using the append option in the load command, all 30 biomolecules
> will 'live' on different frames, which can be independently selected by
> frame, OR the symop operator. correct?

you just select and display them in the sets you want. Maybe

display symop=2 or symop=3 or ....

and that would display whatever part of the capsid you want to display.

>  
>
>
>
>     > 2) have the option to apply symmetry to any number of chains in the
>     > ASU (many capsids have more than one chain in the ASU), I
>     believe one
>     > can do that with the filter as is, right? I'm thinking of the option
>     > to show chain A of biomol 1 and chain C of biomol 7 (or any
>     > combination), again, to present an specific interface.
>     >
>     So tell me more about what it means when there are multiple
>     biomolecules. What would that indicate? 
>
>
> The spherical virus capsid (biounit) is made up of 60 identical copies 
> of the ASU (biomol 1).
> The ASU in itself can be made up of one or more independent chains, 
> which in general
> terms corresponds to the triangulation number value (T). So for 
> example, a T=3 capsid has
> 3 independent chains (A,B,C) forming the ASU, which in turn will give 
> 180 (3x60) chains forming the
> full capsid.

I understand.

> The PDB file contains coordinates for the first copy of the ASU, and 
> also the 60
> transformations (biomat 1...60) that need to be applied to those 
> coordinates in order to generate the full
> capsid (usually the first transformation is the identity). So each PDB 
> file, in essence, contains a full
> capsid (functional biounit), in a very reduced space (file size).

Yes.

> In addition to the intra-unit interfaces (protein-protein interactions 
> between the chains that form the
> ASU), one is also interested in seeing/studying the inter-unit 
> interfaces (protein-protein interactions
> between the chains of different copies of the ASU). Some of these 
> inter-unit interfaces are formed by
> up to six copies of the ASU, all sharing a common symmetry axis (in 
> this case, a 6-fold symmetry axis).
>  

Right, so probably what we want to add to the filter is the capability 
of selecting specific BIOMT records.

>
> In most cases there is no need to generate a full capsid (it looks 
> pretty awesome
> though ;). Because of symmetry, ~1/4 capsid contains all interfaces of 
> interest.

Still a lot of atoms if you want all of them.

-- 
Robert M. Hanson
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