Peter,
As you know, .pdb files normally don't contain either hydrogens or bond order.
Yes. NMR structures sometimes contain *some* hydrogens. XRay ones normally don.
Therefore, when you see a C-O you don't know if it is a C=O or a C-O-H
Yes. It's an adventure
Can the code currently in CDK deal with this?
In general only the author and god know what the actual structures are (often only god). The protein backbone is usually OK. The side chain amino acids/bases may/mayNot be protonated. For many ligands it is impossible to tell what the stuff is at all, let alone where the H atoms are.
This is over drastic for many structures but the real work should be done by data depositors and not viewing programs. And better formats.
> If not I suggest this shouldn't be a Jmol > function but a CDK plugin (e.g. addMissingH with CDK) In general, I agree.
RasMol/Chime includes some simple H-bond detection for a few special cases (protein backbones & 'classic' DNA)
So we have been looking for something 'simple' to put in Jmol to support existing scripts that use the 'hbonds on' command.
Any complicated hbond calculations should certainly happen in the context of CDK.
Or elsewhere.
> There are two main strategies: > - a write a tool to calculate H-bonds from geometry. This will solve 80% > of the problems quickly and you'll spend the next 5 years chasing down > the rest. > > - borrow someone else's algorithms (or better provide more than one). > > I suggest the latter if it's easy to do. That sounds like the right approach.
> I'd ask on CCL if anyone has an > opensource tool to calculate H-bonds and what are the most widely used > approaches. What is CCL?
Computational Chemistry List ccl.net. Ask something like:
What programs are there which can either/or (a) add missing hydrogens in PDB files (b) calculate HBonds.
and offer to post the replies to the list.
P.
Miguel
>
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