Re: [Jmol-users] How do I select ...

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

Annemarie,

I think this is just a bug in those older versions. (10.9 is just this 
past week available)

With 10.9 I get:

load 1ale.pdb
select *.?H
  15 atoms selected
select 1.2H
  5 atoms selected
select *.2H
  5 atoms selected

So that seems to be working correctly. See 
http://www.stolaf.edu/academics/jmol for the latest files.

Bob Hanson

Annemarie Honegger wrote:

> I am using Jmol 10.3 .1 or 10.2
>
> In a PDB file, If hydrogens are present, the hydrogens on the same 
> atom are distinguished 
> by a number preceeding the  atom label, e.g.
>
> ATOM      1  N   ALA     1       0.039  -0.028   0.000  1.00  0.00    
>          
> ATOM      2  CA  ALA     1       1.499  -0.043   0.000  1.00  0.00    
>          
> ATOM      3  C   ALA     1       2.055   1.361   0.000  1.00  0.00    
>          
> ATOM      4  O   ALA     1       1.301   2.383   0.012  1.00  0.00    
>          
> ATOM      5  CB  ALA     1       1.956  -0.866  -1.217  1.00  0.00    
>          
> ATOM      6  OXT ALA     1       3.314   1.524  -0.012  1.00  0.00    
>          
> ATOM      7 1H   ALA     1      -0.315  -0.995   0.000  1.00  0.00    
>          
> ATOM      8 2H   ALA     1      -0.300   0.461   0.841  1.00  0.00    
>          
> ATOM      9 3H   ALA     1      -0.300   0.461  -0.841  1.00  0.00    
>          
> ATOM     10  HA  ALA     1       1.847  -0.534   0.928  1.00  0.00    
>          
> ATOM     11 1HB  ALA     1       3.058  -0.939  -1.274  1.00  0.00    
>          
> ATOM     12 2HB  ALA     1       1.571  -1.903  -1.181  1.00  0.00    
>          
> ATOM     13 3HB  ALA     1       1.610  -0.425  -2.172  1.00  0.00    
>          
> TER                                                                    
>         
>
> When I click on one of these hydrogens, the identifier is returned 
> correctly, e.g
> [ALA]1.1H #7
>
> The "atom expressions" documentation does not specify a valid way to 
> address
> these hydrogens.  If I try to specify this hydrogen in a "select" 
> command, e.g.
>
> select 1.1H
> or 
> select *.1H
>
> I get an error message,
> "unrecognized expression token: 1.1 : select 1.1H"
> in the first case,
> " end of expression expected : select *.1H"
> in the second case
>
> Funnily, 
>
> select *.?H
> does find the three hydrogens on the nitrogen atom
>
> How can I  select a particular one of these hydrogens? I cannot use 
> the atom number, since
> I need my script to work on different structures.
>
> Thank you for your help
>
>                                                                 
>  Annemarie Honegger
>
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