<html><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><br><div><div>Am 05.03.2009 um 07:44 schrieb Dechang Li:</div><div><br></div><div>Not sure about VMD, but you can write a short script for pymol in python:</div><div><br></div><div>1: reading velocities from gro</div><div>2: converting gro2pdb</div><div>3: read in pdb into pymol</div><div>4: create cgo object containing arrow (search in the list archives or on the wiki page of pymol)</div><div><br></div><div>Best</div><div><span class="Apple-tab-span" style="white-space:pre"> </span>Martin<br></div><div><br></div><div>Snippet for step 2 and 3:</div><div><br></div><div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font: normal normal normal 11px/normal Monaco; "><span style="color: #0000ff">def</span> gro( fnm , name=<span style="color: #0000ff">None</span>,state=<span style="color: #800000">1</span>):</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font: normal normal normal 11px/normal Monaco; "> <span style="color: #00aa00">'''</span></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font: normal normal normal 11px/normal Monaco; color: rgb(0, 170, 0); "> Loads a <span style="text-decoration: underline">gro</span> <span style="text-decoration: underline">gromacs</span> File</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font: normal normal normal 11px/normal Monaco; color: rgb(0, 170, 0); "> @param fnm: filename to load</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font: normal normal normal 11px/normal Monaco; color: rgb(0, 170, 0); "> @param name: Name of object</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font: normal normal normal 11px/normal Monaco; color: rgb(0, 170, 0); "> @param state: state to load to</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font: normal normal normal 11px/normal Monaco; color: rgb(0, 170, 0); "> '''</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font: normal normal normal 11px/normal Monaco; "> tmpfile=mktemp(<span style="color: #00aa00">".</span><span style="text-decoration: underline ; color: #00aa00">pdb</span><span style="color: #00aa00">"</span>)</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font: normal normal normal 11px/normal Monaco; "> comd=<span style="color: #00aa00">"</span><span style="text-decoration: underline ; color: #00aa00">editconf</span><span style="color: #00aa00"> -f %s -o %s"</span> % (fnm,tmpfile) </div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font: normal normal normal 11px/normal Monaco; "> <span style="color: #0000ff">if</span> os.system(comd):</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font: normal normal normal 11px/normal Monaco; color: rgb(0, 170, 0); "><span style="color: #000000"> </span><span style="color: #0000ff">print</span><span style="color: #000000"> </span>"Running command %s failed"<span style="color: #000000">%comd</span></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font: normal normal normal 11px/normal Monaco; color: rgb(0, 0, 255); "><span style="color: #000000"> </span>return<span style="color: #000000"> </span>False</div><p style="margin: 0.0px 0.0px 0.0px 0.0px; font: 11.0px Monaco; min-height: 15.0px"> <br class="webkit-block-placeholder"></p><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font: normal normal normal 11px/normal Monaco; "> <span style="color: #0000ff">if</span> name ==<span style="color: #0000ff">None</span>:</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font: normal normal normal 11px/normal Monaco; "> cmd.load(tmpfile, fnm[:-<span style="color: #800000">4</span>] ,state=state)</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font: normal normal normal 11px/normal Monaco; "> <span style="color: #0000ff">else</span>:</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font: normal normal normal 11px/normal Monaco; "> cmd.load(tmpfile,name,state=state)</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font: normal normal normal 11px/normal Monaco; "> os.remove(tmpfile)</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font: normal normal normal 11px/normal Monaco; color: rgb(0, 0, 255); "><span style="color: #000000"> </span>return<span style="color: #000000"> </span>True</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font: normal normal normal 11px/normal Monaco; color: rgb(0, 0, 255); "><br></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font: normal normal normal 11px/normal Monaco; color: rgb(0, 0, 255); "><br></div></div></div></body></html>