Re: [Jmol-users] Hydrogens in pentose: sidechain or backbone?

[Timothy D. <mol...@ma...>]

On May 31, 2006, at 12:05 p, Angel Herraez wrote:

>> so this is also a problem with the protein set as well? I'll have to
>> go back and see what we did here.
>
> Maybe not. As I recall, it was something like my expectation to
> select one out of two H atoms from Gly alphaC; Miguel argued that
> they were backbone where I expected sidechain, or the other way
> round. Anyway, I agreed on the rationale, and solved my problem with
> a trick as usual (I was translating a Chime version that stopped
> working the same way in Jmol).
>
hi Angel,

as I recall the rationale: there is no way to distinguish glycine's  
"backbone" hydrogen from it's "side chain" hydrogen, either  
chemically or by atom id, so Jmol calls them both backbone.


> If you (and/or somebody else)  go back and find the criteria being
> used, I could help on compiling a doc page explaining these sets, and
> put it on the Wiki for others.
>

inclusion in the backbone set is determined by atom id; from  
JmolConstants.java:

     // Terminal nuclic acid
     "H5T", // 45 - 5' terminus hydrogen which replaces P + O1P + O2P

     // nucleic acid backbone hydrogens
     //
     "1H5'", // 51 - first  equivalent H on sugar 5' carbon
     "2H5'", // 52 - second  equivalent H on sugar 5' carbon
     "H4'",  // 53 - H on sugar ring 4' carbon
     "H3'",  // 54 - H on sugar ring 3' carbon
     "1H2'", // 55 - first equivalent H on sugar ring 2' carbon
     "2H2'", // 56 - second equivalent H on sugar ring 2' carbon
     "2HO'", // 57 - H on sugar 2' oxygen, unique to RNA
     "H1'",  // 58 - H on sugar ring 1' carbon
     //
     "H3T",  // 59 - 3' terminus hydrogen



so all of these hydrogens should be selected if you say

select nucleic and backbone

protein backbone Hs are determined in similar fashion.  is it  
possible that your pdb file did not use these atom identifiers?


tim
-- 
Timothy Driscoll                                em: mol...@ma...
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