Charles,
First, I should point out that that command probably doesn't do what you
think it does. This is more for structures that have bond order defined.
Jmol does not calculate protein-specific hydrogen valences when bonds are
all single bonds, as in PDB files. This is more for files that have bond
order specified.
The answer is that the hydrogen atoms do not automatically become part of a
group. So you need to specify:
calculate hydrogens {4}
select 4 or hydrogen and connected({4})
(Note that {4} is necessary at the end there, because "connected(4)" means
"connected to four atoms".)
Also:
selectHydrogen TRUE
is an anachronism. You shouldn't ever need it. I don't know why exactly that
was a Rasmol command. We certainly don't need it in Jmol. If ever you don't
want to select hydrogens, just use
select ..... and not hydrogen
Bob
On Thu, Mar 10, 2011 at 11:30 AM, Charles Harrison Shubert <[email protected]
> wrote:
> Script:
>
> load 1crn.pdb;
> calculate HYDROGENS 4; set selectHydrogen TRUE; select 4; spacefill 0.5;
>
> Results: 4's atoms spacefill, but the calculated hydrogens don't.
>
> Question: How do I get the calculated hydrogens to spacefill?
>
> Thanks,
>
> --Chuck
>
> Charles Shubert
> Senior Architect and Program Leader,
> Software Tools for Academics and Researchers (STAR)
>
> Office of Educational Innovation and Technology (OEIT), DUE
> Massachusetts Institute of Technology
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>
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>
>
>
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