Re: [Jmol-users] Sidechain H-bonds?

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

Thank you, David. Yes, I agree completely.

An interesting aspect of Jmol is that it is a mix of implementing what 
others have successfully done elsewhere and innovating totally new ways 
of doing things that either haven't ever been done or haven't ever been 
done effectively. In every case what we try to do is find out (a) 
whether a problem has already been satisfactorily solved,  (b) if so, if 
that algorithm is freely available and useable within the GNU Lesser 
Public License, and (c) if it is reasonable to implement within Jmol.  
If any one of these answers is "no" as, for example, was the case with 
translucency (not c) or JVXL format (not a) then the real fun begins. 
But if (a-c) are yes, then we can still get to work.

Code size is not necessarily an issue anymore. The really nice thing 
about Jmol 11 is that it doesn't so much matter any more if something 
takes space -- we'll just isolate it in a JAR file that only gets 
downloaded if the capability is needed. This new feature of Jmol will be 
particularly useful for just such situations.

So, regarding the mainchain-sidechain hydrogen bond, you can help by 
finding out about (a) and (b). What is HBPLUS? Is the algorithm 
published? Is the code available for checking? Is it reasonably 
efficient? Please enter this as a feature request with as much 
background information as you can find -- URLs, personal experience, 
suggestions -- so that we can continue a thread specifically in relation 
to it. It's possible, for example, that we would expand upon it and 
produce a Jmol that can calculate reasonable hydrogen bonds for ANY 
situation, not just PDB files.

Bob



David Leader wrote:

>Thanks, Bob, for specific suggestions for using the H-bond data in 
>our database to display sidechain mainchain H-bonds in motifs. I'll 
>have to consider the best way to proceed within the constraints of 
>our setup.
>
>As a general comment, however, I would say that I appreciate that 
>Jmol is in a different phase at the moment from what it was when 
>Miguel was doing most of the work. At that time the emphasis was to 
>reproduce the RasMol/Chime capabilities, which were especially 
>directed towards representing proteins. Miguel did an incredible job, 
>to the extent that Chime can now be considered to have been replaced 
>completely by Jmol. However, given that one of the features of Rasmol 
>introduced in Jmol is the automatic calculation of 
>mainchain-mainchain H-bonds, which is obviously of interest to some 
>protein chemist, if it had been possible to introduce 
>mainchain-sidechain calculations this would have been of similar 
>benefit. It may be worth bearing in mind, should the wheel ever turn 
>again and the protein features are ever subject to reexamination. 
>Clearly, at the moment the emphasis - and interest of the people that 
>are doing the work - is in other areas which will extend the 
>usefulness of Jmol to a larger section of the scientific community. I 
>appreciate that and am grateful for it.
>
>David
>  
>