<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="">I have fixed the bug where opening a map in ChimeraX in nogui mode raises an error. It was trying to show the volume viewer gui interface. This does not fix the problem that offscreen rendering is not working in nogui mode noted in this bug report<div class=""><br class=""></div><div class=""><span class="Apple-tab-span" style="white-space:pre"> </span><a href="https://plato.cgl.ucsf.edu/trac/ChimeraX/ticket/1427" class="">https://plato.cgl.ucsf.edu/trac/ChimeraX/ticket/1427</a></div><div class=""><br class=""></div><div class=""> Tom</div><div class=""><br class=""><div><br class=""><blockquote type="cite" class=""><div class="">On Nov 7, 2018, at 10:09 AM, Greg Couch <<a href="mailto:gregc@cgl.ucsf.edu" class="">gregc@cgl.ucsf.edu</a>> wrote:</div><br class="Apple-interchange-newline"><div class=""><p style="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; background-color: rgb(255, 255, 255); text-decoration: none;" class="">To save images in nogui mode, you need to start up ChimeraX with the --offscreen flag. However, that code isn't working right now, so I've filed a bug report on your behalf.</p><p style="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; background-color: rgb(255, 255, 255); text-decoration: none;" class=""> -- Greg<br class=""></p><div class="moz-cite-prefix" style="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; background-color: rgb(255, 255, 255); text-decoration: none;">On 11/7/18 8:07 AM, Lukas Pravda wrote:<br class=""></div><blockquote type="cite" cite="mid:05836905-514E-49EC-8405-5AB4A4AFB771@ebi.ac.uk" style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; background-color: rgb(255, 255, 255); text-decoration: none;" class=""><div class="WordSection1" style="page: WordSection1;"><div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: Calibri, sans-serif;" class=""><span style="font-size: 11pt;" class="">Hi all,<o:p class=""></o:p></span></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: Calibri, sans-serif;" class=""><span style="font-size: 11pt;" class=""><o:p class=""> </o:p></span></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: Calibri, sans-serif;" class=""><span style="font-size: 11pt;" class="">I was wondering if there is a way how to generate images from linux terminal. I’ve come across a couple of very old posts in the mailing list stating that this was not possible at that time. So, I wonder if anything has changed.<o:p class=""></o:p></span></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: Calibri, sans-serif;" class=""><span style="font-size: 11pt;" class=""><o:p class=""> </o:p></span></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: Calibri, sans-serif;" class=""><span style="font-size: 11pt;" class="">If I use cif files only, chimerax gives “Unable to render images to save them” message. If I try to include volumetric data from cryo-EM overlaid on the structure I get an exception during opening a *.map file. Please see the script below. The exception is in the attachment<o:p class=""></o:p></span></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: Calibri, sans-serif;" class=""><span style="font-size: 11pt;" class=""><o:p class=""> </o:p></span></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: Calibri, sans-serif;" class=""><span style="font-size: 11pt;" class="">Best,<o:p class=""></o:p></span></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: Calibri, sans-serif;" class=""><span style="font-size: 11pt;" class="">Lukas<o:p class=""></o:p></span></div><div style="border-style: none none solid; border-bottom-width: 1pt; border-bottom-color: windowtext; padding: 0cm 0cm 1pt;" class=""><div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: Calibri, sans-serif; border: none; padding: 0cm;" class=""><span style="font-size: 11pt;" class=""><o:p class=""> </o:p></span></div></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: Calibri, sans-serif;" class=""><span style="font-size: 11pt;" class=""><o:p class=""> </o:p></span></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: Calibri, sans-serif;" class=""><span style="font-size: 11pt;" class="">open emd_8909.map<o:p class=""></o:p></span></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: Calibri, sans-serif;" class=""><span style="font-size: 11pt;" class="">volume #1 color white transparency 0.7 level 0.1 step 1<o:p class=""></o:p></span></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: Calibri, sans-serif;" class=""><span style="font-size: 11pt;" class="">zoom 1.2<o:p class=""></o:p></span></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: Calibri, sans-serif;" class=""><span style="font-size: 11pt;" class="">open 6ds5.cif<o:p class=""></o:p></span></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: Calibri, sans-serif;" class=""><span style="font-size: 11pt;" class="">set bgColor white<o:p class=""></o:p></span></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: Calibri, sans-serif;" class=""><span style="font-size: 11pt;" class="">hide selAtoms<o:p class=""></o:p></span></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: Calibri, sans-serif;" class=""><span style="font-size: 11pt;" class="">show selAtoms ribbons<o:p class=""></o:p></span></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: Calibri, sans-serif;" class=""><span style="font-size: 11pt;" class="">color bychain ribbons<o:p class=""></o:p></span></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: Calibri, sans-serif;" class=""><span style="font-size: 11pt;" class="">light full<o:p class=""></o:p></span></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: Calibri, sans-serif;" class=""><span style="font-size: 11pt;" class="">light shadow true<o:p class=""></o:p></span></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: Calibri, sans-serif;" class=""><span style="font-size: 11pt;" class="">save image default.png width 1600 height 1600 supersample 5 transparentBackground true<o:p class=""></o:p></span></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: Calibri, sans-serif;" class=""><span style="font-size: 11pt;" class="">turn y 90<o:p class=""></o:p></span></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: Calibri, sans-serif;" class=""><span style="font-size: 11pt;" class="">save image y.png width 1600 height 1600 supersample 5 transparentBackground true<o:p class=""></o:p></span></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: Calibri, sans-serif;" class=""><span style="font-size: 11pt;" class="">turn z 90<o:p class=""></o:p></span></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: Calibri, sans-serif;" class=""><span style="font-size: 11pt;" class="">save image z.png width 1600 height 1600 supersample 5 transparentBackground true<o:p class=""></o:p></span></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: Calibri, sans-serif;" class=""><span style="font-size: 11pt;" class=""><o:p class=""> </o:p></span></div></div><br class=""><fieldset class="mimeAttachmentHeader"></fieldset><pre class="moz-quote-pre" wrap="">_______________________________________________
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</pre></blockquote><span style="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; background-color: rgb(255, 255, 255); text-decoration: none; float: none; display: inline !important;" class="">_______________________________________________</span><br style="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; background-color: rgb(255, 255, 255); text-decoration: none;" class=""><span style="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; background-color: rgb(255, 255, 255); text-decoration: none; float: none; display: inline !important;" class="">ChimeraX-users mailing list</span><br style="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; background-color: rgb(255, 255, 255); text-decoration: none;" class=""><a href="mailto:ChimeraX-users@cgl.ucsf.edu" style="color: rgb(149, 79, 114); text-decoration: underline; font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; background-color: rgb(255, 255, 255);" class="">ChimeraX-users@cgl.ucsf.edu</a><br style="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; background-color: rgb(255, 255, 255); text-decoration: none;" class=""><span style="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; background-color: rgb(255, 255, 255); text-decoration: none; float: none; display: inline !important;" class="">Manage subscription:</span><br style="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; background-color: rgb(255, 255, 255); text-decoration: none;" class=""><a href="http://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users" style="color: rgb(149, 79, 114); text-decoration: underline; font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; background-color: rgb(255, 255, 255);" class="">http://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users</a><br style="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; background-color: rgb(255, 255, 255); text-decoration: none;" class=""></div></blockquote></div><br class=""></div></body></html>