Frieda Reichsman wrote: > Hi, > > I am loading multiple pdb files into the applet, for example, > load "fileset" "file1.pdb" "file2.pdb" "file3.pdb" > > I am having trouble understanding the correct uses use of the commands > file and display. The documentation has not cleared it up completely > for me. > > So, for example, with this script: > > restrict none > select file=2 or file=3 > trace 0.2 > > select [fe] and file=2 > spacefill > > display file=2 or file=3 > > the traces appear, but the spacefilled [fe] does not appear. Why does > the rest of the structure in file2.pdb appear (in trace), and not the > iron atom (in spacefill) ? > Be sure you issue first
model 0 Otherwise you can only see the first model in the first file. Now when you select file=2 or file=3 trace 0.2 you will see all file data. What I think you are missing is that we might have three files and multiple models: -------File1---------|-----File2----------|----File3------------ --model--|---model---|------model---------|---model--|--model--- 1.1 1.2 2.1 3.1 3.2 When Jmol starts, the default is only to show the first model, numbered 1.1. The default is: select * model 1.1 display * Now, that select refers to ALL atoms in ALL models in ALL files, but only the first model is "displayable" and only its atoms are displayed. So whenever you need to display more than one model at the same time, you issue: model 0 # make all models displayable display 1.2 or 2.1 or display file=1 or file=2 or display file < 3 etc. What you are missing is the "model 0", or the equivalent in a context of animations, "frame 0". Those two commands are 100% synonymous. By the way, the reason [Fe] works here is that "Fe" is the PDB group. That's not a general method of showing iron, and if there were "Fe1" instead, it would not show it. I recommend instead: select _Fe That works for any file type, including PDB. Bob ------------------------------------------------------------------------- Take Surveys. Earn Cash. Influence the Future of IT Join SourceForge.net's Techsay panel and you'll get the chance to share your opinions on IT & business topics through brief surveys-and earn cash http://www.techsay.com/default.php?page=join.php&p=sourceforge&CID=DEVDEV _______________________________________________ Jmol-users mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/jmol-users
