Miguel wrote: > >> 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.
and should not, because it isn't the same molecule at a single time. > > > In some ways, this is related to multiple models and animations ... but > these things are not currently implemented properly. > OK, I agree it is not high priority; but the primitive discussion is. > > >> 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. > as I noted, at the same time and only with bonds inbetween one conformation but both with bonds to the connecting backbone border atoms. > > > 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? > *my* chime script did not contain ; for command separation. *my* Jmol script contains them, because I learned Jmol scripting from studying chime2jmol.pl output and this converted *my* chime scripts to semicolon containing lines. I recommend to make a list of all characters which are free in meaning in Jmol script which could serve as primitive punctuation and then we may vote, what character to take for what primitive. > > The fundamental problem is that the RasMol scripting language is > ambiguous. It was not formally defined and not well thought-out. The you are absolutely right > > 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 > and I didn't argue to make it more formal (my vote for returning the tokenization rather than the input command with the MessageCallBack method) > > 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 Take your schedule just as you like, but it is Christmas time and if someone here animates me I put my wishes on the list. With kind regards, Jan -- Snail to:Jan Reichert, IMB, D-07708 Jena, POB 100813. Voice:+49 3641 6562-05 (Fax:+49 3641 6562-10) :/i mailto:[EMAIL PROTECTED] ------------------------------------------------------- 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
