<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="">Hi Andrea,<div class=""><br class=""></div><div class=""> I saw from your bug report that your "out of memory" error is from the OpenGL graphics trying to create an OpenGL texture of about 20 Gbytes for a 10 Gbyte tiff image stack (graphics is twice as large to handle brightness and transparency in image style).</div><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/4316" class="">https://plato.cgl.ucsf.edu/trac/ChimeraX/ticket/4316</a></div><div class=""><br class=""></div><div class="">Your graphics driver is Mesa, software rendering. I don't know what controls how big a 3D texture the Mesa driver will allow. The machine has 1.5 Tbytes memory so it has plenty. I suspect the driver simply won't allow a single large 3D texture, probably limited to 8 Gbytes. By switching ChimeraX to use multiple 2D textures it may be able to render. To use 2D texture rendering for volume model #1 use ChimeraX command</div><div class=""><br class=""></div><div class=""><span class="Apple-tab-span" style="white-space:pre"> </span>volume #1 projectionMode 2d-z</div><div class=""><br class=""></div><div class="">documentation here</div><div class=""><br class=""></div><div class=""><span class="Apple-tab-span" style="white-space:pre"> </span><a href="https://www.rbvi.ucsf.edu/chimerax/docs/user/commands/volume.html#dispsolid" class="">https://www.rbvi.ucsf.edu/chimerax/docs/user/commands/volume.html#dispsolid</a></div><div class=""><br class=""></div><div class=""> Tom</div><div class=""><form method="post" id="propertyform" action="https://plato.cgl.ucsf.edu/trac/ChimeraX/ticket/4316#trac-add-comment" style="clear: both; margin-bottom: 2em;" class=""><div style="font-family: Verdana, Arial, "Bitstream Vera Sans", Helvetica, sans-serif; font-size: 13px;" class=""></div><div class="collapsed" style="font-family: Verdana, Arial, "Bitstream Vera Sans", Helvetica, sans-serif; font-size: 13px;"></div></form><div><br class=""><blockquote type="cite" class=""><div class="">On Mar 3, 2021, at 11:19 AM, Andrea Fera <<a href="mailto:andrea.fera@revealgc.com" class="">andrea.fera@revealgc.com</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: 0cm; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><span style="font-family: "Times New Roman", serif;" class="">Hi Tom,<o:p class=""></o:p></span></div><div style="margin: 0cm; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><span style="font-family: "Times New Roman", serif;" class=""><o:p class=""> </o:p></span></div><div style="margin: 0cm; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><span style="font-family: "Times New Roman", serif;" class="">Thank you for your quick answer.<o:p class=""></o:p></span></div><div style="margin: 0cm; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><span style="font-family: "Times New Roman", serif;" class=""><o:p class=""> </o:p></span></div><div style="margin: 0cm; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><span style="font-family: "Times New Roman", serif;" class="">If the default value is 50% of the physical RAM of the computer, in my case in this server (Lynux) it should be a few hundreds Gb then.<o:p class=""></o:p></span></div><div style="margin: 0cm; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><span style="font-family: "Times New Roman", serif;" class="">My tomogram is about 8 Gb and therefore it should all fit.<o:p class=""></o:p></span></div><div style="margin: 0cm; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><span style="font-family: "Times New Roman", serif;" class=""><o:p class=""> </o:p></span></div><div style="margin: 0cm; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><span style="font-family: "Times New Roman", serif;" class="">I knew that you had set it up in a great way but since I have had such problems in the past, and my first run of t he rendering failed… I was just checking. Thank you!<o:p class=""></o:p></span></div><div style="margin: 0cm; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><span style="font-family: "Times New Roman", serif;" class=""><o:p class=""> </o:p></span></div><div class=""><div style="margin: 0cm; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><span style="font-family: "Times New Roman", serif;" class="">Thank you and all best…<o:p class=""></o:p></span></div><div style="margin: 0cm; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><span style="font-family: "Times New Roman", serif;" class="">Andrea Fera<o:p class=""></o:p></span></div><div style="margin: 0cm; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><span style="font-size: 10pt; font-family: "Times New Roman", serif;" class=""><o:p class=""> </o:p></span></div><div style="margin: 0cm; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><span style="font-size: 8pt; font-family: "Times New Roman", serif;" class="">--<o:p class=""></o:p></span></div><div style="margin: 0cm; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><span style="font-size: 8pt; font-family: "Times New Roman", serif;" class="">Andrea Fera, PhD<o:p class=""></o:p></span></div><div style="margin: 0cm; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><span style="font-size: 8pt; font-family: "Times New Roman", serif;" class="">Senior Data Scientist<o:p class=""></o:p></span></div><div style="margin: 0cm; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><span id="cid:image002.jpg@01D71038.31AE79D0"><image002.jpg></span><o:p class=""></o:p></div></div><div style="margin: 0cm; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><span style="font-family: "Times New Roman", serif;" class=""><o:p class=""> </o:p></span></div><div class=""><div style="border-style: solid none none; border-top-width: 1pt; border-top-color: rgb(225, 225, 225); padding: 3pt 0cm 0cm;" class=""><div style="margin: 0cm; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><b class="">From:</b><span class="Apple-converted-space"> </span>Tom Goddard <<a href="mailto:goddard@sonic.net" class="">goddard@sonic.net</a>><span class="Apple-converted-space"> </span><br class=""><b class="">Sent:</b><span class="Apple-converted-space"> </span>Wednesday, March 3, 2021 12:33 PM<br class=""><b class="">To:</b><span class="Apple-converted-space"> </span>Andrea Fera <<a href="mailto:andrea.fera@revealgc.com" class="">andrea.fera@revealgc.com</a>><br class=""><b class="">Cc:</b><span class="Apple-converted-space"> </span>ChimeraX Users Help <<a href="mailto:chimerax-users@cgl.ucsf.edu" class="">chimerax-users@cgl.ucsf.edu</a>><br class=""><b class="">Subject:</b><span class="Apple-converted-space"> </span>Re: How to expand the RAN in ChimeraX?<o:p class=""></o:p></div></div></div><div style="margin: 0cm; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><o:p class=""> </o:p></div><div style="margin: 0cm; font-size: 11pt; font-family: Calibri, sans-serif;" class="">Hi Andrea,<o:p class=""></o:p></div><div class=""><div style="margin: 0cm; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><o:p class=""> </o:p></div></div><div class=""><div style="margin: 0cm; font-size: 11pt; font-family: Calibri, sans-serif;" class="">The volume command dataCacheSize option will do this. For example for 32 Gbytes of memory cache for volume data use command<o:p class=""></o:p></div><div class=""><div style="margin: 0cm; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><o:p class=""> </o:p></div></div><div class=""><div style="margin: 0cm; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><span class="apple-tab-span"> <span class="Apple-converted-space"> </span></span>volume dataCacheSize 32000<o:p class=""></o:p></div></div><div class=""><div style="margin: 0cm; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><o:p class=""> </o:p></div></div><div class=""><div style="margin: 0cm; font-size: 11pt; font-family: Calibri, sans-serif;" class="">The default is to set it to half the physical memory of the computer. <o:p class=""></o:p></div></div><div class=""><div style="margin: 0cm; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><o:p class=""> </o:p></div></div><div class=""><div style="margin: 0cm; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><a href="https://www.rbvi.ucsf.edu/chimerax/docs/user/commands/volume.html#sampling" style="color: blue; text-decoration: underline;" class="">https://www.rbvi.ucsf.edu/chimerax/docs/user/commands/volume.html#sampling</a><o:p class=""></o:p></div></div><div class=""><div style="margin: 0cm; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><o:p class=""> </o:p></div></div><div class=""><div style="margin: 0cm; font-size: 11pt; font-family: Calibri, sans-serif;" class="">I would not suggest changing it because surface and image rendering typically use an amount memory for the graphics similar to the data size. The cache is only for the volume data, so with graphics, the current setting can utilize all your memory. Increasing it can cause data to be paged out to disk with horrible performance. The above setting is not saved. If you did want to change it for every ChimeraX session you would use Preferences / Startup / Execute these commands at startup.<o:p class=""></o:p></div></div><div class=""><div style="margin: 0cm; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><o:p class=""> </o:p></div></div><div class=""><div style="margin: 0cm; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><span class="apple-tab-span"> <span class="Apple-converted-space"> </span></span>Tom<o:p class=""></o:p></div></div><div class=""><div style="margin: 0cm; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><o:p class=""> </o:p></div></div><div class=""><div style="margin: 0cm; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><o:p class=""> </o:p></div></div><div class=""><div style="margin: 0cm; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><o:p class=""> </o:p></div><div class=""><div style="margin: 0cm; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><br class=""><br class=""><o:p class=""></o:p></div><blockquote style="margin-top: 5pt; margin-bottom: 5pt;" class=""><div class=""><div style="margin: 0cm; font-size: 11pt; font-family: Calibri, sans-serif;" class="">On Mar 3, 2021, at 9:04 AM, Andrea Fera <<a href="mailto:andrea.fera@revealgc.com" style="color: blue; text-decoration: underline;" class="">andrea.fera@revealgc.com</a>> wrote:<o:p class=""></o:p></div></div><div style="margin: 0cm; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><o:p class=""> </o:p></div><div class=""><div class=""><div style="margin: 0cm; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><span style="font-family: "Times New Roman", serif;" class="">Dear Mr. Goddard,</span><o:p class=""></o:p></div></div><div class=""><div style="margin: 0cm; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><span style="font-family: "Times New Roman", serif;" class=""> </span><o:p class=""></o:p></div></div><div class=""><div style="margin: 0cm; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><span style="font-family: "Times New Roman", serif;" class="">This is Andrea. I am not sure that you remember me, but we met in 2013 or so in S. Francisco and Berkeley.</span><o:p class=""></o:p></div></div><div class=""><div style="margin: 0cm; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><span style="font-family: "Times New Roman", serif;" class=""> </span><o:p class=""></o:p></div></div><div class=""><div style="margin: 0cm; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><span style="font-family: "Times New Roman", serif;" class="">I am a strenuous fan of your software! Especially for volume rendering of cryo-type tomograms.</span><o:p class=""></o:p></div></div><div class=""><div style="margin: 0cm; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><span style="font-family: "Times New Roman", serif;" class="">I do have a tomogram pf a few Gb that I would like to render with your software. I use a Lynux server with LOTS of RAM. How can I increase the RAM allocated by ChimeraX?</span><o:p class=""></o:p></div></div><div class=""><div style="margin: 0cm; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><span style="font-family: "Times New Roman", serif;" class=""> </span><o:p class=""></o:p></div></div><div class=""><div style="margin: 0cm; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><span style="font-family: "Times New Roman", serif;" class="">Thank you and all best…</span><o:p class=""></o:p></div></div><div class=""><div style="margin: 0cm; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><span style="font-family: "Times New Roman", serif;" class="">Andrea Fera</span><o:p class=""></o:p></div></div><div class=""><div style="margin: 0cm; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><span style="font-size: 10pt; font-family: "Times New Roman", serif;" class=""> </span><o:p class=""></o:p></div></div><div class=""><div style="margin: 0cm; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><span style="font-size: 8pt; font-family: "Times New Roman", serif;" class="">--</span><o:p class=""></o:p></div></div><div class=""><div style="margin: 0cm; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><span style="font-size: 8pt; font-family: "Times New Roman", serif;" class="">Andrea Fera, PhD</span><o:p class=""></o:p></div></div><div class=""><div style="margin: 0cm; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><span style="font-size: 8pt; font-family: "Times New Roman", serif;" class="">Senior Data Scientist</span><o:p class=""></o:p></div></div><div class=""><div style="margin: 0cm; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><image003.jpg><o:p class=""></o:p></div></div></div></blockquote></div><div style="margin: 0cm; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><o:p class=""> </o:p></div></div></div></div><span style="caret-color: rgb(0, 0, 0); font-family: Helvetica; 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