<html><head><meta http-equiv="Content-Type" content="text/html; charset=utf-8"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;" class=""><meta http-equiv="Content-Type" content="text/html; charset=utf-8" class=""><div style="word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;" class="">Hi Austin,<div class=""><br class=""></div><div class=""> Of course I remember you, it was a great trip to Rocky Mountain Laboratories. Thanks for your hospitality! And I see your SARS-Cov-2 images in the media -- very nice.</div><div class=""><br class=""></div><div class=""> Here's the ChimeraX voodoo to save all your objs in one command</div><div class=""><br class=""></div><div class=""><span class="Apple-tab-span" style="white-space:pre"> </span>perframe "save ~/Desktop/objs/model$1.obj model #1.$1" frames 23</div><div class=""><br class=""></div><div class="">It uses the perframe command that runs another command once each frame (usually used for recording an animation video). The $1 gets the frame number substituted in 1, 2, 3 and the frames tells it how many frames, in your case use 100 to get the 100 models. Here are the perframe docs</div><div class=""><br class=""></div><div class=""><span class="Apple-tab-span" style="white-space:pre"> </span><a href="https://www.cgl.ucsf.edu/chimerax/docs/user/commands/perframe.html" class="">https://www.cgl.ucsf.edu/chimerax/docs/user/commands/perframe.html</a><br class=""><div class=""><br class=""></div><div class="">if you need more info.</div><div class=""><br class=""></div><div class=""><span class="Apple-tab-span" style="white-space:pre"> </span>Tom</div><div class=""><br class=""></div><div class=""><br class=""><blockquote type="cite" class=""><div class="">On Jul 29, 2020, at 10:19 PM, Athman, Austin (NIH/NIAID) [E] <<a href="mailto:austin.athman@nih.gov" class="">austin.athman@nih.gov</a>> wrote:</div><br class="Apple-interchange-newline"><div class=""><div class="WordSection1" style="page: WordSection1; caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none;"><div style="margin: 0in 0in 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">Tom,<o:p class=""></o:p></div><div style="margin: 0in 0in 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><o:p class=""> </o:p></div><div style="margin: 0in 0in 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">I’m Austin Athman, from the NIAID Rocky Mountain Laboratories Visual Arts Department. I took some of your sessions on ChimeraX when you were out to Hamilton MT in the past, and I believe you assisted my colleague Ryan Kissinger on some ChimeraX questions he had. I have one for you I hope you can help.<o:p class=""></o:p></div><div style="margin: 0in 0in 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><o:p class=""> </o:p></div><div style="margin: 0in 0in 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">I have received a morphing model of the spike protein on RSV for an animation project we are working on for Barney Graham and Jason McLellan. The morph is in 100 steps, and I have 2 different morphs (one for attachment, and another for fusion), making 200 steps total. I am exporting the surface model of each step to an OBJ file for use in our animation software. I have managed to write a single command line that I copy/paste in over and over, changing just the id and file number for export to get the files I need.<span class="Apple-converted-space"> </span><o:p class=""></o:p></div><div style="margin: 0in 0in 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><o:p class=""> </o:p></div><div style="margin: 0in 0in 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">Is there a way I can automate this further, so that ChimeraX will iterate through each id and export to individual files for me without copy/pasting the command each time and modifying it? It would save me hours of time.<o:p class=""></o:p></div><div style="margin: 0in 0in 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><o:p class=""> </o:p></div><div style="margin: 0in 0in 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">Unfortunately, I am very new to ChimeraX, and know only enough to get me into trouble, specifically, how to show/hide surfaces, and export!<o:p class=""></o:p></div><div style="margin: 0in 0in 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><o:p class=""> </o:p></div><div style="margin: 0in 0in 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">Here is a screenshot of my model, and also the Excel doc I use to keep track and build my command for each file export, just so you can see what I am doing at the moment. It takes some time for each to save as well, so I don’t know if that delay will make it difficult for the command line to wait and continue each time for each export. There may be some additional commands I can just add between each line in the excel, and I can just copy and past the entire thing and let it run, but that is where I hope you might be able to tell me what I am missing.<o:p class=""></o:p></div><div style="margin: 0in 0in 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><o:p class=""> </o:p></div><div style="margin: 0in 0in 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">Hope you are well in these times. Also, thank you for your work and videos on coronavirus. Good informative stuff.<o:p class=""></o:p></div><div style="margin: 0in 0in 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><o:p class=""> </o:p></div><div style="margin: 0in 0in 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">-Austin Athman<o:p class=""></o:p></div><div style="margin: 0in 0in 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><o:p class=""> </o:p></div><div style="margin: 0in 0in 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><o:p class=""> </o:p></div><div style="margin: 0in 0in 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><o:p class=""> </o:p></div><div style="margin: 0in 0in 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><span id="cid:image006.jpg@01D665FE.A9B5F0A0" class=""><image006.jpg></span><o:p class=""></o:p></div><div style="margin: 0in 0in 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><o:p class=""> </o:p></div><div style="margin: 0in 0in 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><span id="cid:image008.jpg@01D665FE.A9B5F0A0" class=""><image008.jpg></span><o:p class=""></o:p></div><div style="margin: 0in 0in 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><o:p class=""> </o:p></div><div style="margin: 0in 0in 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><o:p class=""> </o:p></div><div style="margin: 0in 0in 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><o:p class=""> </o:p></div><div style="margin: 0in 0in 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><span style="color: rgb(31, 73, 125);" class=""><o:p class=""> </o:p></span></div><div style="margin: 0in 0in 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><b class=""><span style="font-size: 8pt; font-family: Cambria, serif; color: white;" class="">--<o:p class=""></o:p></span></b></div><div style="margin: 0in 0in 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><b class=""><span style="font-size: 16pt; font-family: Cambria, serif; color: rgb(31, 73, 125);" class=""><span id="cid:image009.png@01D665FE.A9B5F0A0" class=""><image009.png></span></span></b><span style="font-size: 12pt; font-family: Cambria, serif; color: rgb(31, 73, 125);" class=""><o:p class=""></o:p></span></div><div style="margin: 0in 0in 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><span style="font-size: 14pt; font-family: Cambria, serif; color: rgb(31, 73, 125);" class="">.....................................................................<o:p class=""></o:p></span></div><div style="margin: 0in 0in 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><span style="font-family: Cambria, serif; color: rgb(31, 73, 125);" class="">Rocky Mountain Laboratories NIH/NIAID<o:p class=""></o:p></span></div><div style="margin: 0in 0in 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><a href="http://myrtb.nih.gov/" class=""><span style="font-family: Cambria, serif; color: rgb(5, 99, 193);" class="">Research Technologies Branch</span></a><span style="font-family: Cambria, serif; color: rgb(31, 73, 125);" class=""><o:p class=""></o:p></span></div><div style="margin: 0in 0in 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><span style="font-family: Cambria, serif; color: rgb(31, 73, 125);" class="">903 South 4th Street<o:p class=""></o:p></span></div><div style="margin: 0in 0in 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><span style="font-family: Cambria, serif; color: rgb(31, 73, 125);" class="">Hamilton MT 59840<o:p class=""></o:p></span></div><div style="margin: 0in 0in 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><span style="font-family: Cambria, serif; color: rgb(31, 73, 125);" class="">Phone: (406) 375-7480<o:p class=""></o:p></span></div><div style="margin: 0in 0in 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><span style="font-family: "Adobe Garamond Pro Bold", serif; color: rgb(31, 73, 125);" class=""><o:p class=""> </o:p></span></div><div style="margin: 0in 0in 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><span style="font-size: 8pt; color: rgb(31, 73, 125);" class="">DISCLAIMER: The information in this e-mail and any of its attachments is confidential and may contain sensitive information. It should not be used by anyone who is not the original intended recipient. If you have received this e-mail in error please inform the sender and delete it from your mailbox or any other storage devices. National Institute of Allergy and Infectious Diseases shall not accept liability for any statements made that are sender's own and not expressly made on behalf of the NIAID by one of its representatives. <span class="Apple-converted-space"> </span></span></div></div></div></blockquote></div><br class=""></div></div></body></html>