<html><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">Hi Divya,<div><span class="Apple-tab-span" style="white-space:pre"> </span>In the 1.2422 release that you are using there is no "nsteps" keyword. In that version it was called "steps". The documentation that corresponds to your version is bundled with you version (use your Chimera's Help menu or type "help <i>command-name</i>" in its command line). Documentation on the web corresponds (depending on where you look) either to the current production release [1.5.3] or the current daily build [1.6].</div><div><span class="Apple-tab-span" style="white-space:pre"> </span>I would highly recommend that you upgrade to a current version of Chimera since <i>many</i> improvements have been made to the minimization code (and everything else really) since the 1.2422 build (which is more than 4 years old after all).</div><div><br></div><div>--Eric</div><div><br></div><div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font-size: 16px; "><font face="Helvetica" size="5" style="font: normal normal normal 16px/normal Helvetica; "> Eric Pettersen</font></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font-size: 16px; "><font face="Helvetica" size="5" style="font: normal normal normal 16px/normal Helvetica; "> UCSF Computer Graphics Lab</font></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font-size: 16px; "><font face="Helvetica" size="5" style="font: normal normal normal 16px/normal Helvetica; "> <a href="http://www.cgl.ucsf.edu">http://www.cgl.ucsf.edu</a></font></div><div><font face="Helvetica" size="5" style="font: normal normal normal 16px/normal Helvetica; "><br></font></div><div><div>On Dec 1, 2011, at 11:09 AM, divya neelagiri wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite"><div class="gmail_quote">Hello,<br><br>I got this error when I was trying to minimize a structure. please tell me what went wrong.<br><br><br>Executing testchim.py...Opening test1_chimera.mol2...1 model opened<br><br>Traceback (most recent call last):<br> File "/data/pgm/chimera/chimera_1.2422/share/__main__.py", line 59, in ?<br> value = chimeraInit.init(sys.argv)<br> File "CHIMERA/share/chimeraInit.py", line 298, in init<br> chimera.openModels.open(a, prefixableType=1)<br> File "CHIMERA/share/chimera/__init__.py", line 1253, in open<br> File "CHIMERA/share/chimera/__init__.py", line 746, in _openPython<br> File "testchim.py", line 10, in ?<br> rc("minimize nsteps 70000 stepsize 0.001 interval 100 freeze none nogui true")<br> File "CHIMERA/share/chimera/__init__.py", line 1912, in runCommand<br> File "CHIMERA/share/Midas/midas_text.py", line 60, in makeCommand<br> File "CHIMERA/share/MMMD/ChimeraExtension.py", line 29, in cmdMMMD<br> File "CHIMERA/share/Midas/midas_text.py", line 281, in doExtensionFunc<br> File "CHIMERA/share/Midas/midas_text.py", line 1885, in _getRealKw<br>MidasError: Keyword 'nsteps' doesn't match any known keywords<br> Error while processing testchim.py:<br>MidasError: Keyword 'nsteps' doesn't match any known keywords<br>(see reply log for Python traceback info)<br><br><br><br><br>This is my program. I tried to execute it from command line using<br> chimera --nogui testchim.py<br><br>import os<br>import chimera<br><br>from chimera import runCommand as rc<br>from chimera import replyobj<br><br>os.chdir("/data2/di/database_build/outputs/outputs_mol2_sdf")<br> fn = "test1_chimera.mol2"<br>rc("open " + fn)<br>rc("minimize nsteps 70000 stepsize 0.001 interval 100 freeze none nogui true")<br>rc("write format mol2 0 min/" + fn)<br>rc("close all")<br> rc("stop now")<br><br><br> </div><br> _______________________________________________<br>Chimera-users mailing list<br><a href="mailto:Chimera-users@cgl.ucsf.edu">Chimera-users@cgl.ucsf.edu</a><br>http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users<br></blockquote></div><br></div><br><br><div apple-content-edited="true"> </div><br></body></html>