> does anyone know why in the labels for atoms we are pulling in > something called the "modelTagNumber"?
My recollection (which may well be mistaken) is that model numbers are only displayed in the default label if there is more than one model loaded. > My guess is that in PDB files you have > > MODEL 3 > > in a PDB file, then the idea is to indicate that number instead of the > sequential number in the file (1, 2, 3, ....). Model numbers in a PDB file need not be sequential. > For example, if you label an atom with %M (the model number) or you > click on an atom and look at the status line, if there are multiple > models you will see: > > whatever /[THIS NUMBER] > > But that's not the number you actually need to access that model (I > don't think). It should be the same number that one would use to access the model. > Furthermore, with XYZ files, what's happening is that the second line > of XYZ files is going into that same variable. So, if you have a > MULTIPLE model file that has, say, at the top: > > 23 > this is my information > <atom definitions here> > > and then you load that model and click on an atom, you see something like: > > C 1/this is my information I vaguely recall that ... > My questions: > > 1) Is it intentional that the number after the / in an atom > description in a PDB file identifies the number in the MODEL record > instead of 1+m, where m is the index of the model in the file, 0, 1, > 2, ...? Yes > 2) Is it important that it do so? Yes. The RasMol syntax for specifying model number uses the model number in the PDB file. > 3) Why is the information in the second line of an XYZ file being put > in this same variable? At one point I was trying to make the model 'number' be a text tag. This was part of my effort to have a consistent view of molecular data files. I have seen multi-model .xyz files that have some type of model-identification information on the second line. If you look at some other file types (like gaussian) I think that you will find that the 'modelTag' is set to the energy ... but maybe I never implemented that. > 4) I want to fix this. What do you recommend I do about it? We must leave PDB files alone. For all other file types it might be better to make the model number become a 1-based integer sequence. This is essentially what we do for atom numbers. PDBs get their own atom numbers ... everyone else is sequential starting from 1. I suspect that you could make that change without breaking anything. It would be interesting to look at Compiler.java and see what it will accept after the '/'. If it will only accept integers then you can *definitely* make the change for the other file types. Miguel ------------------------------------------------------- This SF.net email is sponsored by: Splunk Inc. Do you grep through log files for problems? Stop! Download the new AJAX search engine that makes searching your log files as easy as surfing the web. DOWNLOAD SPLUNK! http://sel.as-us.falkag.net/sel?cmd=lnk&kid3432&bid#0486&dat1642 _______________________________________________ Jmol-developers mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/jmol-developers
