<html><head><meta http-equiv="Content-Type" content="text/html charset=utf-8"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class="">Hi Matt,<div class=""><br class=""></div><div class=""> The threshold and subtract operations each create a new copy of the data in memory and the original will be have all its data loaded. So the operations I suggested would take 3 times 64 Gbytes or 192 Gbytes. Unless your machine has at least 128 Gbytes (plus virtual memory which is usually ~3x physical memory), it won’t work the way I suggest. If you have 128 Gbytes of memory or more I think what I suggest will be as fast as the disk speed will allow (probably take tens of minutes). If you have less memory then Python could do it just using 64 Gbytes for the one copy of the data in memory, or if you used fancy Python it could be done one plane at a time, so any small amount of memory would suffice.</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><blockquote type="cite" class=""><div class="">On May 12, 2017, at 10:23 AM, Dougherty, Matthew T wrote:</div><br class="Apple-interchange-newline"><div class=""><div id="divtagdefaultwrapper" dir="ltr" style="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; font-size: 12pt; font-family: Calibri, Arial, Helvetica, sans-serif;" class=""><div style="margin-top: 0px; margin-bottom: 0px;" class="">Considering the files are 64GB in size, what would be more efficient, <span style="font-size: 12pt;" class="">chimera script or python?</span></div><div style="margin-top: 0px; margin-bottom: 0px;" class="">10% difference, 10x, 100x, etc</div><div style="margin-top: 0px; margin-bottom: 0px;" class=""><br class=""></div><div id="Signature" class=""><div id="divtagdefaultwrapper" style="font-size: 12pt; background-color: rgb(255, 255, 255); font-family: Calibri, Arial, Helvetica, sans-serif, EmojiFont, 'Apple Color Emoji', 'Segoe UI Emoji', NotoColorEmoji, 'Segoe UI Symbol', 'Android Emoji', EmojiSymbols;" class=""><div class="BodyFragment"><font size="2" class=""><div class="PlainText">Matthew Dougherty<br class="">National Center for Macromolecular Imaging<br class="">Baylor College of Medicine<br class=""><span style="font-size: 13pt; font-family: Calibri;" class="">=================================================</span><br class=""></div><div class="PlainText"><span style="font-size: 13pt; font-family: Calibri;" class="">=================================================</span><span style="font-size: 13pt; font-family: Calibri;" class=""><br class=""></span></div></font></div></div></div></div><hr tabindex="-1" style="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; display: inline-block; width: 743.8125px;" class=""><span style="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; float: none; display: inline !important;" class=""></span><div id="divRplyFwdMsg" dir="ltr" style="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;" class=""><font face="Calibri, sans-serif" style="font-size: 11pt;" class=""><b class="">From:</b><span class="Apple-converted-space"> </span>Tom Goddard<br class=""><b class="">Sent:</b><span class="Apple-converted-space"> </span>Friday, May 12, 2017 12:07:47 PM<br class=""><b class="">To:</b><span class="Apple-converted-space"> </span>Dougherty, Matthew T<br class=""><b class="">Cc:</b><span class="Apple-converted-space"> </span><a href="mailto:chimera-users@cgl.ucsf.edu" class="">chimera-users@cgl.ucsf.edu</a><br class=""><b class="">Subject:</b><span class="Apple-converted-space"> </span>Re: [Chimera-users] scripting & density</font><div class=""> </div></div><div style="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;" class=""><font size="2" class=""><b class="">***CAUTION:*** This email is not from a BCM Source. Only click links or open attachments you know are safe.</b></font><hr class="">Hi Matt,<div class=""><br class=""></div><div class=""> You would use vop threshold to make a map that has only the values 50-74 and then subtract it from the original map, and repeat with the range 90-110.</div><div class=""><br class=""></div><div class=""><span class="Apple-tab-span" style="white-space: pre;"></span>vop thresh #0 min 50 set 0 max 74 setmax 0</div><div class=""><span class="Apple-tab-span" style="white-space: pre;"></span>vop subtract #0 #1</div><div class=""><br class=""></div><div class=""> Tom</div><div class=""><br class=""><div class=""><blockquote type="cite" class=""><div class="">On May 12, 2017, at 8:42 AM, Dougherty, Matthew T wrote:</div><br class="Apple-interchange-newline"><div class=""><div id="divtagdefaultwrapper" dir="ltr" class="" style="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; font-size: 12pt; font-family: Calibri, Arial, Helvetica, sans-serif;"><div class="" style="margin-top: 0px; margin-bottom: 0px;">Hi,</div><div class="" style="margin-top: 0px; margin-bottom: 0px;"><br class=""></div><div class="" style="margin-top: 0px; margin-bottom: 0px;">I have a dataset, its values are 1-255. I would like to modify the density values using a script.</div><div class="" style="margin-top: 0px; margin-bottom: 0px;">Specifically, I would like to set density values 50-74 & 90-110 to the value of zero.</div><div class="" style="margin-top: 0px; margin-bottom: 0px;">Is there a way to do that using scripting, or do I need to do that using python?</div><div class="" style="margin-top: 0px; margin-bottom: 0px;"><br class=""></div><div id="Signature" class=""><div id="divtagdefaultwrapper" class="" style="font-size: 12pt; background-color: rgb(255, 255, 255); font-family: Calibri, Arial, Helvetica, sans-serif, EmojiFont, 'Apple Color Emoji', 'Segoe UI Emoji', NotoColorEmoji, 'Segoe UI Symbol', 'Android Emoji', EmojiSymbols;"><div class="BodyFragment"><font size="2" class=""><div class="PlainText">Matthew Dougherty<br class="">National Center for Macromolecular Imaging<br class="">Baylor College of Medicine<br class=""><span class="" style="font-size: 13pt; font-family: Calibri;">=================================================</span><br class=""></div><div class="PlainText"><span class="" style="font-size: 13pt; 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