<html xmlns:v="urn:schemas-microsoft-com:vml" xmlns:o="urn:schemas-microsoft-com:office:office" xmlns:w="urn:schemas-microsoft-com:office:word" xmlns:m="http://schemas.microsoft.com/office/2004/12/omml" xmlns="http://www.w3.org/TR/REC-html40">
<head>
<meta http-equiv="Content-Type" content="text/html; charset=utf-8">
<meta name="Generator" content="Microsoft Word 15 (filtered medium)">
<!--[if !mso]><style>v\:* {behavior:url(#default#VML);}
o\:* {behavior:url(#default#VML);}
w\:* {behavior:url(#default#VML);}
.shape {behavior:url(#default#VML);}
</style><![endif]--><style><!--
/* Font Definitions */
@font-face
{font-family:"Cambria Math";
panose-1:2 4 5 3 5 4 6 3 2 4;}
@font-face
{font-family:Calibri;
panose-1:2 15 5 2 2 2 4 3 2 4;}
/* Style Definitions */
p.MsoNormal, li.MsoNormal, div.MsoNormal
{margin:0cm;
font-size:11.0pt;
font-family:"Calibri",sans-serif;}
a:link, span.MsoHyperlink
{mso-style-priority:99;
color:blue;
text-decoration:underline;}
span.apple-tab-span
{mso-style-name:apple-tab-span;}
span.EmailStyle19
{mso-style-type:personal-reply;
font-family:"Times New Roman",serif;
color:windowtext;
text-decoration:none none;}
.MsoChpDefault
{mso-style-type:export-only;
font-size:10.0pt;}
@page WordSection1
{size:612.0pt 792.0pt;
margin:72.0pt 72.0pt 72.0pt 72.0pt;}
div.WordSection1
{page:WordSection1;}
--></style><!--[if gte mso 9]><xml>
<o:shapedefaults v:ext="edit" spidmax="1026" />
</xml><![endif]--><!--[if gte mso 9]><xml>
<o:shapelayout v:ext="edit">
<o:idmap v:ext="edit" data="1" />
</o:shapelayout></xml><![endif]-->
</head>
<body lang="EN-US" link="blue" vlink="purple" style="word-wrap:break-word">
<div class="WordSection1">
<p class="MsoNormal"><span style="font-family:"Times New Roman",serif">Hi Tom,<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-family:"Times New Roman",serif"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-family:"Times New Roman",serif">Thank you for your quick answer.<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-family:"Times New Roman",serif"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-family:"Times New Roman",serif">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></o:p></span></p>
<p class="MsoNormal"><span style="font-family:"Times New Roman",serif">My tomogram is about 8 Gb and therefore it should all fit.<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-family:"Times New Roman",serif"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-family:"Times New Roman",serif">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></o:p></span></p>
<p class="MsoNormal"><span style="font-family:"Times New Roman",serif"><o:p> </o:p></span></p>
<div>
<p class="MsoNormal"><span style="font-family:"Times New Roman",serif">Thank you and all best…<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-family:"Times New Roman",serif">Andrea Fera<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Times New Roman",serif"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:8.0pt;font-family:"Times New Roman",serif">--<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:8.0pt;font-family:"Times New Roman",serif">Andrea Fera, PhD<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:8.0pt;font-family:"Times New Roman",serif">Senior Data Scientist<o:p></o:p></span></p>
<p class="MsoNormal"><img width="190" height="74" style="width:1.9791in;height:.7708in" id="Picture_x0020_1" src="cid:image002.jpg@01D71038.31AE79D0"><o:p></o:p></p>
</div>
<p class="MsoNormal"><span style="font-family:"Times New Roman",serif"><o:p> </o:p></span></p>
<div>
<div style="border:none;border-top:solid #E1E1E1 1.0pt;padding:3.0pt 0cm 0cm 0cm">
<p class="MsoNormal"><b>From:</b> Tom Goddard <goddard@sonic.net> <br>
<b>Sent:</b> Wednesday, March 3, 2021 12:33 PM<br>
<b>To:</b> Andrea Fera <andrea.fera@revealgc.com><br>
<b>Cc:</b> ChimeraX Users Help <chimerax-users@cgl.ucsf.edu><br>
<b>Subject:</b> Re: How to expand the RAN in ChimeraX?<o:p></o:p></p>
</div>
</div>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">Hi Andrea,<o:p></o:p></p>
<div>
<p class="MsoNormal"><o:p> </o:p></p>
</div>
<div>
<p class="MsoNormal">The volume command dataCacheSize option will do this. For example for 32 Gbytes of memory cache for volume data use command<o:p></o:p></p>
<div>
<p class="MsoNormal"><o:p> </o:p></p>
</div>
<div>
<p class="MsoNormal"><span class="apple-tab-span"> </span>volume dataCacheSize 32000<o:p></o:p></p>
</div>
<div>
<p class="MsoNormal"><o:p> </o:p></p>
</div>
<div>
<p class="MsoNormal">The default is to set it to half the physical memory of the computer. <o:p></o:p></p>
</div>
<div>
<p class="MsoNormal"><o:p> </o:p></p>
</div>
<div>
<p class="MsoNormal"><a href="https://www.rbvi.ucsf.edu/chimerax/docs/user/commands/volume.html#sampling">https://www.rbvi.ucsf.edu/chimerax/docs/user/commands/volume.html#sampling</a><o:p></o:p></p>
</div>
<div>
<p class="MsoNormal"><o:p> </o:p></p>
</div>
<div>
<p class="MsoNormal">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></o:p></p>
</div>
<div>
<p class="MsoNormal"><o:p> </o:p></p>
</div>
<div>
<p class="MsoNormal"><span class="apple-tab-span"> </span>Tom<o:p></o:p></p>
</div>
<div>
<p class="MsoNormal"><o:p> </o:p></p>
</div>
<div>
<p class="MsoNormal"><o:p> </o:p></p>
</div>
<div>
<p class="MsoNormal"><o:p> </o:p></p>
<div>
<p class="MsoNormal"><br>
<br>
<o:p></o:p></p>
<blockquote style="margin-top:5.0pt;margin-bottom:5.0pt">
<div>
<p class="MsoNormal">On Mar 3, 2021, at 9:04 AM, Andrea Fera <<a href="mailto:andrea.fera@revealgc.com">andrea.fera@revealgc.com</a>> wrote:<o:p></o:p></p>
</div>
<p class="MsoNormal"><o:p> </o:p></p>
<div>
<div>
<p class="MsoNormal"><span style="font-family:"Times New Roman",serif">Dear Mr. Goddard,</span><o:p></o:p></p>
</div>
<div>
<p class="MsoNormal"><span style="font-family:"Times New Roman",serif"> </span><o:p></o:p></p>
</div>
<div>
<p class="MsoNormal"><span style="font-family:"Times New Roman",serif">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></o:p></p>
</div>
<div>
<p class="MsoNormal"><span style="font-family:"Times New Roman",serif"> </span><o:p></o:p></p>
</div>
<div>
<p class="MsoNormal"><span style="font-family:"Times New Roman",serif">I am a strenuous fan of your software! Especially for volume rendering of cryo-type tomograms.</span><o:p></o:p></p>
</div>
<div>
<p class="MsoNormal"><span style="font-family:"Times New Roman",serif">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></o:p></p>
</div>
<div>
<p class="MsoNormal"><span style="font-family:"Times New Roman",serif"> </span><o:p></o:p></p>
</div>
<div>
<p class="MsoNormal"><span style="font-family:"Times New Roman",serif">Thank you and all best…</span><o:p></o:p></p>
</div>
<div>
<p class="MsoNormal"><span style="font-family:"Times New Roman",serif">Andrea Fera</span><o:p></o:p></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Times New Roman",serif"> </span><o:p></o:p></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:8.0pt;font-family:"Times New Roman",serif">--</span><o:p></o:p></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:8.0pt;font-family:"Times New Roman",serif">Andrea Fera, PhD</span><o:p></o:p></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:8.0pt;font-family:"Times New Roman",serif">Senior Data Scientist</span><o:p></o:p></p>
</div>
<div>
<p class="MsoNormal"><image003.jpg><o:p></o:p></p>
</div>
</div>
</blockquote>
</div>
<p class="MsoNormal"><o:p> </o:p></p>
</div>
</div>
</div>
</body>
</html>