David wrote: > My personal opinion is that his failure reflects very > badly on that community, certain sections of which > have a history of selfishness in relation both to > structural data and computer algorithms.
Just to clarify (and give people the benefit of the doubt) ... My attempts were made 18 to 20 months ago. At the time Jmol had a much smaller following, and I did not have contacts who could approach these people, explain the situation, and 'make the pitch' on behalf of Jmol. > This is most unfortunate for Jmol as automatic secondary structure > prediction is one of the key Rasmol features (according to one of my > colleagues) that Jmol lacks. Did anyone ever try to approach Roger > Sayle, who presumably wrote devised the algorithm that handles this > in Rasmol? I exchanged a few email messages with Roger Sayle in Dec 2003. The RasMol source code had been released in the public domain up through version 2.6 beta 2 ... but I wanted to get his 'blessing' prior to looking at the source code. A copy of Roger's email response is in the Jmol cvs source code repository. Up to that point I had worked on Jmol independently. However, I felt the need to look at the RasMol source code because I was working on hydrogen bonding ... and I felt like I had reached a dead-end. (The problem is compounded by the fact that the hydrogen atoms are not present in most .pdb files). Looking at the RasMol source code was useful to me. It helped me understand how the 'classical' hydrogen bonds are supposed to work. From that, I was able to build an implementation that was appropriate for the Jmol data structures. I was able to extend it a bit ... and I think that Jmol does a marginally better job than RasMol at hydrogen bond identification in some situations. My attempts at protein secondary structure identification came shortly after this. In this case, I was unable to gain much insight from reading the RasMol source code ... I could not make the connection between the RasMol source and the text description of the algorithms listed in the Kabsch & Sander DSSP paper. After that I went looking for other implementations. At this point I suppose I could take another look at the RasMol source. Frankly, I had completely forgotten about it. But, as I said in my previous message, I believe it would be best if this effort was led by someone with a biochemistry background who has an interest in and understanding of the problem space. Miguel ------------------------------------------------------- This SF.Net email is sponsored by: Power Architecture Resource Center: Free content, downloads, discussions, and more. http://solutions.newsforge.com/ibmarch.tmpl _______________________________________________ Jmol-users mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/jmol-users
