<html><head><meta http-equiv="Content-Type" content="text/html charset=windows-1252"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;">Hi Alex,<div><br></div><div> The “measure distance” code is the measure() function in</div><div><br></div><div><span class="Apple-tab-span" style="white-space:pre"> </span>chimera/share/Measure/measure.py</div><div><br></div><div>It handles distances between atoms and also surfaces and can handle multiple distance calculations and prints the result but unfortunately does not return it as a Python value. I’ve attached some Python code to find the minimum distance between two sets of atoms.</div><div><br></div><div> Unfortunately the Chimera Python programming interface is not documented. The programmer’s guide on the Chimera web side documentation page may be of some use, especially the examples, </div><div><br></div><div><span class="Apple-tab-span" style="white-space:pre"> </span><a href="http://www.cgl.ucsf.edu/chimera/docs/ProgrammersGuide/index.html">http://www.cgl.ucsf.edu/chimera/docs/ProgrammersGuide/index.html</a></div><div><br></div><div>and also the Chimera Python scripts on the Chimera developer web site can be of some use</div><div><br></div><div><span class="Apple-tab-span" style="white-space:pre"> </span><a href="http://plato.cgl.ucsf.edu/trac/chimera/wiki/Scripts">http://plato.cgl.ucsf.edu/trac/chimera/wiki/Scripts</a></div><div><br></div><div>Many of the simpler Chimera commands are in</div><div><br></div><div><span class="Apple-tab-span" style="white-space:pre"> </span>chimera/share/Midas/__init__.py</div><div><br></div><div>To find others you can search all the Python under chimera/share for “addCommand(“ (for example on Linux or Mac shell command find . -type f -exec grep -nH -e "addCommand(" {} +) giving the attached file of command names and modules where the code is located.</div><div><br></div><div> In our next generation Chimera we are making full reference documentation for Python programming.</div><div><br></div><div><span class="Apple-tab-span" style="white-space: pre;"> </span>Tom</div><div><br></div><div></div></body></html>