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<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>
<DIV><FONT face=Arial size=2></FONT> </DIV>
<DIV><FONT face=Arial size=2>I also tried to use the script mode with simple
commands, but i am getting back error like:</FONT></DIV>
<DIV><FONT face=Arial size=2></FONT> </DIV>
<DIV><FONT face=Arial size=2>cannot execute 'gzip'...</FONT></DIV>
<DIV><FONT face=Arial size=2></FONT> </DIV>
<DIV><FONT face=Arial size=2>and a series of other errors of
python.</FONT></DIV>
<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">
<P style="MARGIN: 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></P>
<P style="MARGIN: 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></P>
<P style="MARGIN: 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></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>
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