johngrant wrote:Is there a site showing how to use JMOL, for example, how to select and view a particular chain? This does not appear to work with the GUI within the JMOL tool.
A presenter showing the tool said "restrict" when she was keying in data on a scioly JMOL tutorial, but there wasn't any depth to this. Outlining the syntax and basic command structure would be helpful.An old manual guidance led me to believe Restrict[*b] would work but the JMOL app rejected this command.
Thanks!
If you go to
http://cbm.msoe.edu/stupro/so/index.html and open the "2010 Pre-build Competition Environment" in the sidebar on the left, right above the screen showing the protein should be a link to a "Jmol Quick Reference Sheet", or something to that effect. It's a PDF that outlines the basic commands used in Jmol. That might be what you're looking for.
The "restrict" command is in fact what you want if you're trying to select and view only a particular subset of the protein, but the brackets are unnecessary. Just "restrict*b" or "restrict *b" (the space has no effect) will show only chain B.
The asterisk refers to a chain. To restrict your view even further, you would use, for example, "restrict*b and 1-160", where "1-160" refers to the range of numbers of amino acid residues within chain B you want to show.
If you wanted to show multiple chains or multiple ranges of residues, you would use "or", as in "restrict*b or *d".
If you're using an "and" and an "or" in the same command, you might need parentheses (not brackets) to specify which goes with what; e.g., "restrict(*b or *d) and 1-160" would show you residues 1-160 of chain B and residues 1-160 of chain D, while "restrict*b or (*d and 1-160)" would show you all of chain B and residues 1-160 of chain D.
Another tip: after restricting your view to any subset of the protein, I recommend using the "center" command to avoid wrestling with the small peripheral part of the PDB file you're viewing.
The default is for the center of rotation of the file to be the center of mass of the whole thing, but if you're only looking at a part of it on one edge, you don't really want it rotating around that point, because then in order to see the other side of your little part, you have to swing it all the way around that center. Some angles of viewing aren't even possible that way, because your part would be off-screen when you've got it sufficiently zoomed in to see the details.
Therefore, it can be very useful to add "center*b" if you're viewing chain B, or "center*b and 1-160" if you just restricted it to chain B and 1-160 (i.e., whatever you just put in the "restrict" command, use the same thing in the "center" command). This will save you a lot of annoyance.