>> if you simply reduce data you don't get compatible with RasMol script >> language. I appreciate your honest feedback
>> And I am very unhappy with such a decision and I think all >> the biomacromolecular structure people dealing with PDB files are. > > I don't think Micheal said that Jmol is not going to support it at > all... but only not on short terms... That is correct. We will solve this problem, but we cannot do it in the short term. The Jmol architecture did not anticipate multiple instances of the same atom at different locations. This represents a significant change and cannot be easily squeezed-in. In some ways, this is related to multiple models and animations ... but these things are not currently implemented properly. >> Parsing a >> PDB header is a pain and not really necessary for a molecule display >> applet, but parsing the structure data is prerequisite, so all >> features of an ATOM or HETATM (CONECT, TER) should be represented in >> the Jmol atom object, and they all should be addressable by script >> selection commands. I agree, but currently we have a growing list of more basic features which are 'missing' ... alternate conformations will have to wait a while. > How are the alternative conformations displayed in Rasmol? Not at the > same time, or are they? Very good question ... I have no idea. > If not, we could have Jmol read the > alternatives into separate frames, so that one can select one > conformation by selecting a specific frame... I don't see how this would work for the applet. >> > > restrict [Glu]71;A >> > > would in RasMol select only one of them and not [Glu]71;B, but on >> the command line, the ";" is not interpreted as alternative >> conformation separator. >> > ... >> > This, of course, conflicts with Chime's use of ; as the statement >> separator character. > > This is a problem. We have to make a choice here what we want to > support... Rasmol 2.7.2 or Chime... I guess this cannot be done in a > universal way... Jan, *your* chime scripts are using ; as a statement separator ... what do you recommend we do? The fundamental problem is that the RasMol scripting language is ambiguous. It was not formally defined and not well thought-out. The behavior is context-dependent. For example, if you define a set name which corresponds to a residue name, the behavior changes: define val arg select val Presumably, we would hope to define some rules that would allow the parser to unambiguously distinguish between a ; that is a statement separator and a ; that is an alternate-location specifier. For me, the right time to address this issue and continue this discussion is after I have had a chance to think about it a little more think about how to modify the Jmol data structures to support alternate conformations. Miguel ------------------------------------------------------- This SF.net email is sponsored by: SF.net Giveback Program. Does SourceForge.net help you be more productive? Does it help you create better code? SHARE THE LOVE, and help us help YOU! Click Here: http://sourceforge.net/donate/ _______________________________________________ Jmol-users mailing list [EMAIL PROTECTED] https://lists.sourceforge.net/lists/listinfo/jmol-users
