[Molvis-list] pdb-l: working with a file with two models superimposed

Angel Herraez angel.herraez at uah.es
Wed Jun 18 12:44:08 EDT 2008

Kevin Karplus wrote:

> What I've never gotten to work is 
> 	select 10-13.CB
> or 	select 10.CB
> which the documentation implies should work.  I always have to do
> 	select 10-13 and *.CB

It doesn't work with intervals (only available for residue numbers, 
btw). But it should work for single atoms:

select 10.CB

for the other:
select 10-13 and *.CB

> That is, it would be nice to have
> 	select atom 114 and */1
> to get 
> Atom: CB 114  Group: TYR 16  Chain: A  Model: 1

As has been said:
select atomno=114 and */1

> As I hardly ever handle biomolecules, I am not sure if atom numbers  
> in them are global or per chain.

In pdb format, atom numbers are specified in the file, so Rasmol will 
use those. They are usually global (in properly formatted pdb files 
like those from PDB).

> Now, here's what really would rock:  arithmetic expressions based on  
> coordinates, e.g.:
> 	x + y > 0

You can do that  in Jmol, although you have to learn how to do it ;)  
"Molecular math" is the name Bob Hanson coined for it.
Make sure to get the latest prerelease for that sort of things, and 
select @{ select(j; {*}; j.x+j.y>0) } 

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