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If you run Chimera in nogui mode (i.e. with the command-line flag "--nogui") with no script file argument then standard input would be interpreted as Chimera commands. Alternatively, you could supply a script file (Chimera commands or Python) as an argument. This is basically described here:<div><br></div><div><a href="http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/options.html#nogui">http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/options.html#nogui</a></div><div><br></div><div>You could use a series of commands like:</div><div><br></div><div>open input.pdb</div><div>swapaa TYR :15.a</div><div>write output.pdb</div><div><br></div><div>to do the swapaa.</div><div><br></div><div>--Eric</div><div><br><div> <span class="Apple-style-span" style="border-collapse: separate; border-spacing: 0px 0px; color: rgb(0, 0, 0); font-family: Helvetica; font-size: 16px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; text-align: auto; -khtml-text-decorations-in-effect: none; text-indent: 0px; -apple-text-size-adjust: auto; text-transform: none; orphans: 2; white-space: normal; widows: 2; word-spacing: 0px; "><p style="margin: 0.0px 0.0px 0.0px 0.0px"><font face="Helvetica" size="5" style="font: 16.0px Helvetica"><span class="Apple-converted-space"> <span class="Apple-converted-space"> </span></span>Eric Pettersen</font></p><p style="margin: 0.0px 0.0px 0.0px 0.0px"><font face="Helvetica" size="5" style="font: 16.0px Helvetica"><span class="Apple-converted-space"> <span class="Apple-converted-space"> </span></span>UCSF Computer Graphics Lab</font></p><p style="margin: 0.0px 0.0px 0.0px 0.0px"><font face="Helvetica" size="5" style="font: 16.0px Helvetica"><span class="Apple-converted-space"> </span><a href="http://www.cgl.ucsf.edu">http://www.cgl.ucsf.edu</a></font></p><br class="Apple-interchange-newline"></span> </div><br><div><div>On Jun 9, 2008, at 1:14 PM, ProtEUS wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite"> <div><font face="Arial" size="2"> <div><font face="Arial" size="2">Hello all!</font></div> <div><font face="Arial" size="2"></font> </div> <div><font face="Arial" size="2">I am sorry if this is a dump question, but is it possible for swapaa to run fromJava server with Runtime.exec()?</font></div> <div><font face="Arial" size="2"></font> </div> <div><font face="Arial" size="2">Thank you very much!!</font></div> <div><font face="Arial" size="2"></font> </div> <div><font face="Arial" size="2">Andreas, Greece.</font></div></font></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">_______________________________________________</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">Chimera-users mailing list</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><a href="mailto:Chimera-users@cgl.ucsf.edu">Chimera-users@cgl.ucsf.edu</a></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><a href="http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users">http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users</a></div> </blockquote></div><br></div></body></html>