<html><head><meta http-equiv="Content-Type" content="text/html; charset=us-ascii"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;" class="">Hi Yong Liu,<div class=""><br class=""></div><div class=""> First start by figuring out the ChimeraX commands to do what you want. For example, the commands to save an image of chain A shown as atoms could be</div><div class=""><br class=""></div><div class=""><span class="Apple-tab-span" style="white-space:pre"> </span>open 2bbv</div><div class=""><br class=""></div><div class=""><span class="Apple-tab-span" style="white-space:pre"> </span>show #1/A only</div><div class=""><span class="Apple-tab-span" style="white-space:pre"> </span>view</div><div class=""><span class="Apple-tab-span" style="white-space:pre"> </span>save ~/Desktop/2bbv_chain_A.png</div><div class=""><br class=""></div><div class="">Now the trick is we want to do that for all chains. The ChimeraX command language has not looping methods so we have to use some Python. Also you wanted to create a new command that does the 3 commands above with the right chain id and model number substituted in. I've attached some Python code chain_images.py that does that makes the command. If you open that Python file in ChimeraX it will define the command then type</div><div class=""><br class=""></div><div class=""><span class="Apple-tab-span" style="white-space:pre"> </span>chainimages #1</div><div class=""><br class=""></div><div class="">to make the images. I've put this example Python code on the ChimeraX Recipes web site</div><div class=""><br class=""></div><div class=""><span class="Apple-tab-span" style="white-space:pre"> </span><a href="https://rbvi.github.io/chimerax-recipes/chain_images/chain_images.html" class="">https://rbvi.github.io/chimerax-recipes/chain_images/chain_images.html</a></div><div class=""><br class=""></div><div class="">If you want ChimeraX to define this command each time you start you can put command "open ~/scripts/chain_images.py" in ChimeraX startup preferences.</div><div class=""><br class=""></div><div class=""> Tom</div><div class=""><br class=""></div><div class=""></div></body></html>