<html><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><div><div>On Jun 10, 2008, at 10:25 AM, ProtEUS wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite"> <div><font face="Arial" size="2">Hello again!</font></div> <div><font face="Arial" size="2"></font> </div> <div><font face="Arial" size="2">I tried the way you explained me, but it doesn't seem to work.</font></div></blockquote><div><br></div>I think I need more detail than "doesn't seem to work". Did you get an error message? Was the output wrong? What specifically happened?</div><div><br><blockquote type="cite"> <div><font face="Arial" size="2"></font> <span class="Apple-style-span" style="-webkit-text-stroke-width: -1; ">I also tried to use the script mode with simple commands, but i am getting back error like:</span></div> <div><font face="Arial" size="2"></font> </div> <div><font face="Arial" size="2">cannot execute 'gzip'...</font></div></blockquote><div><br></div>That's just a warning that files compressed with 'compress' (i.e. ending in '.Z') won't be openable in Chimera because no gzip executable could be found. You can ignore it assuming that none of the files you're using are compressed that way.</div><div><br><blockquote type="cite"> <div><font face="Arial" size="2"></font> </div> <div><font face="Arial" size="2">and a series of other errors of python.</font></div></blockquote><div><br></div><div>The text of the script you used and the contents of the error messages would be helpful.</div><div><br></div><div>--Eric</div><div><br></div><blockquote type="cite"> <div><font face="Arial" size="2"></font> </div> <div><font face="Arial" size="2">Could you please help me with this situation?</font></div> <div><font face="Arial" size="2"></font> </div> <div><font face="Arial" size="2">Thank you so much in advance...</font></div> <div><font face="Arial" size="2"></font> </div> <div><font face="Arial" size="2">Andreas.</font></div> <blockquote dir="ltr" style="PADDING-RIGHT: 0px; PADDING-LEFT: 5px; MARGIN-LEFT: 5px; BORDER-LEFT: #000000 2px solid; MARGIN-RIGHT: 0px"> <div style="FONT: 10pt arial">----- Original Message ----- </div> <div style="BACKGROUND: #e4e4e4; FONT: 10pt arial; font-color: black"><b>From:</b> <a title="pett@cgl.ucsf.edu" href="mailto:pett@cgl.ucsf.edu">Eric Pettersen</a> </div> <div style="FONT: 10pt arial"><b>To:</b> <a title="proteus.support@gmail.com" href="mailto:proteus.support@gmail.com">ProtEUS</a> </div> <div style="FONT: 10pt arial"><b>Cc:</b> <a title="chimera-users@cgl.ucsf.edu" href="mailto:chimera-users@cgl.ucsf.edu">chimera-users@cgl.ucsf.edu</a> </div> <div style="FONT: 10pt arial"><b>Sent:</b> Tuesday, June 10, 2008 1:31 AM</div> <div style="FONT: 10pt arial"><b>Subject:</b> Re: [Chimera-users] Swapaa from Java Runtime.exec</div> <div><br></div>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="WORD-SPACING: 0px; FONT: 16px Helvetica; TEXT-TRANSFORM: none; COLOR: rgb(0,0,0); TEXT-INDENT: 0px; WHITE-SPACE: normal; LETTER-SPACING: normal; BORDER-COLLAPSE: separate; border-spacing: 0px 0px; -khtml-text-decorations-in-effect: none; -apple-text-size-adjust: auto; orphans: 2; widows: 2"><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><font style="FONT: 16px Helvetica" face="Helvetica" size="5"><span class="Apple-converted-space"> <span class="Apple-converted-space"> </span></span>Eric Pettersen</font></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><font style="FONT: 16px Helvetica" face="Helvetica" size="5"><span class="Apple-converted-space"> <span class="Apple-converted-space"> </span></span>UCSF Computer Graphics Lab</font></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><font style="FONT: 16px Helvetica" face="Helvetica" size="5"><span class="Apple-converted-space"> </span><a href="http://www.cgl.ucsf.edu">http://www.cgl.ucsf.edu</a></font></div><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: 0px">_______________________________________________</div> <div style="MARGIN: 0px">Chimera-users mailing list</div> <div style="MARGIN: 0px"><a href="mailto:Chimera-users@cgl.ucsf.edu">Chimera-users@cgl.ucsf.edu</a></div> <div style="MARGIN: 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></blockquote><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></body></html>