Henry - simple solution. On Sat, Aug 14, 2010 at 8:04 AM, Jakubowski, Henry <[email protected]>wrote:
> Hi, > > > > I’m trying to do a very simple thing, comparing the backbone of > dephosphoyrlated and phosphorylated Erk2. I used > Superpose<http://wishart.biology.ualberta.ca/SuperPose/> > Very nice.... > to align the structures of 1ERK (dephosphorylated Erk2) and 2ERK > (phosphorylated Erk2). I then separated the combined pdb files into two > files, file1.pdb and file2.pdb. I’ve created a very simple Jmol web page: > > > > > http://employees.csbsju.edu/hjakubowski/Jmol/phosphorylation/phosphoErk_2_nophosphoErk1.htm > > > > When I try to simultaneously load both files (see concantenated commands > below), I only see one of the traces of the backbone. I’ve gone to Jmol > help and this > site<http://www.bioinformatics.org/pipermail/molvis-list/2007q2/000427.html>with > no avail. I’m running Jmol 11.4 (haven’t had IT upgrade to 12 yet) but > I don’t think that is the problem. I’ve had a similar problem in the past. > Should be so simple. It seems to see only one file. I’ve tried: load > files “file1.pdb” “file2.pdb” and perturbations of it with no avail. When > I add the “” around the file name, the push button disappears in the web > page. > > > > Here is the set of commands I’m using. > > > > > > <p align="left"><font face="Arial, Helvetica, sans-serif" size="-1"> > > <script language="JavaScript" type="text/javascript"> > > jmolRadio("set frank off; background white; load file1.pdb > file2.pdb; rotate z 0; rotate y 60; rotate x -90; select all; spin off; > wireframe off; spacefill off; trace off; set ambient 40; set specpower 40; > slab off; ribbons off; cartoons off; label off; monitor off; model 0; select > 1.1; trace; color green; select 2.1; trace; color blue; move 0 360 0 0 0 0 0 > 0 6", "", false ); > > </script> > you need the keyword FILES and single or double quotes: jmolRadio("set frank off; background white; load FILES 'file1.pdb' 'file2.pdb';...") -- Robert M. Hanson Professor of Chemistry St. Olaf College 1520 St. Olaf Ave. Northfield, MN 55057 http://www.stolaf.edu/people/hansonr phone: 507-786-3107 If nature does not answer first what we want, it is better to take what answer we get. -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900
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