at 11:22 am EDT on (Tuesday) 4 November 2003 Sebastian Lisken said:
> Hi again, the recent discussion I joined was about .pdb files and > the "set connect" script command. Miguel said that when there is > bond information in a file, Jmol should stick to it, and I wonder > if this would apply to all formats. Back in the days of CaGe > development, the suggestion was made to indicate in a molecule > convention that the data should be taken "as is", even in the > case of "unchemical" molecules. >
In CML we feel strongly that what the author specifies is what the content is. There are certain obvious errors (bonds referring to non-existent atoms or negative hydrogenCount) but everything else is "valid". One reason for this is that it could be an *example* of an unacceptable or unstable molecule.
Many program "add" information - Jmol will add bonds if atoms are within a certain distance or will relocate atoms within a crystallographic unit cell. I personally argue against this as there may be good reasons not to. At least there need to be controls that the user can set so that these default actions do not occur. I think Jmol may have some of those but I can't find them on the menu.
We are trying to work towards a system in CML where programs actively add metadata on the information it has added. Then a consumer could decide what had been changed and whether they wish to reverse it.
P.
BTW I see nothing wrong in the CML files attached.
> I got a colleague who is still working with CaGe to send me two > samples of the CML format that I made our program send to the Jmol > applet. Note the "convention" in the third lines.
This is perfectly acceptable. However software need not take any action on this. We hope that an agreed set of conventions will arise. In this case I don't think it's necessary as the molecule is CML-valid.
I wonder what a > current version of the applet would make of them? What the display > should be with the "unchemical" file I don't know, I'm afraid - this > is not a question of the "what do you see" style but rather one > for the developers: what would Jmol make of the data in these > files, and would you be willing to make it adhere strictly to the > bonds and atom positions? > > Sebastian
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