<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="">Thanks Tom,<div class="">I knew you’d have a good suggestion — I’ll try it out!</div><div class="">Cathy</div><div class=""><br class=""><div class=""><div><blockquote type="cite" class=""><div class="">On Oct 3, 2016, at 2:02 PM, Tom Goddard <<a href="mailto:goddard@sonic.net" class="">goddard@sonic.net</a>> wrote:</div><br class="Apple-interchange-newline"><div class=""><meta http-equiv="Content-Type" content="text/html charset=utf-8" class=""><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class="">Hi Cathy,<div class=""><br class=""></div><div class=""> I think you should use the fit atomic structure to do the alignment. Here’s how. Open a copy of the atomic structure in and put it in the orientation you want for the maps, I’ll call this the reference structure (#0). Now open your first map (#1) with its fit structure (#2). Align the fit atomic structure with the reference atomic structure</div><div class=""><br class=""></div><div class=""><span class="Apple-tab-span" style="white-space:pre"> </span>match #2 #0</div><div class=""><br class=""></div><div class="">Then move the map so it aligns with its fit atomic structure.</div><div class=""><br class=""></div><div class=""><span class="Apple-tab-span" style="white-space:pre"> </span>matrixcopy #2 #1</div><div class=""><br class=""></div><div class="">The reference structure need not be displayed to do this. Now save an image</div><div class=""><br class=""></div><div class=""><span class="Apple-tab-span" style="white-space:pre"> </span>copy some/directory/map1.png supersample 3</div><div class=""><br class=""></div><div class="">Then close the first map and model and load the second map and model and repeat.</div><div class=""><br class=""></div><div class=""><span class="Apple-tab-span" style="white-space:pre"> </span>close #1,2</div><div class=""><br class=""></div><div class="">You could make a command script that has repetitions of these command plus two open commands before the map to open the map and fit model, and then run that script in Chimera (just use File / Open, and script file with suffix *.cmd), and that will produce all the images. You might want to save the reference model in the desired orientation as a Chimera session file so you can rerun with exactly the same orientation at a later date if you decide to change something (e.g. image size, background color).</div><div class=""><br class=""></div><div class=""> Tom</div><div class=""><br class=""></div><div class=""><br class=""><div class=""><blockquote type="cite" class=""><div class="">On Oct 3, 2016, at 7:58 AM, Cathy Lawson wrote:</div><br class="Apple-interchange-newline"><div class=""><meta http-equiv="Content-Type" content="text/html charset=utf-8" class=""><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class="">Dear USCF Chimera Team,<br class=""><div class=""><br class=""></div><div class="">I’m looking for suggestions on how to go about the following:</div><div class="">For the EMDataBank map challenge we have sets of EM maps of the same molecule that have been submitted in different orientations.</div><div class="">We’d like to automate production of images for each set of maps with a common orientation/scale so that they can be readily compared.</div><div class="">Models fitted to each map are in principle available, so this could be part the process if needed (e.g., to define transformations between map positions/orientations).</div><div class=""><br class=""></div><div class="">Many thanks,</div><div class=""><br class=""></div><div class="">Cathy</div><div class=""><br class=""></div><div class=""><br class=""></div><br class=""><div class="">
<div style="font-family: Helvetica; font-style: normal; font-variant-ligatures: normal; font-variant-position: normal; font-variant-caps: normal; font-variant-numeric: normal; font-variant-alternates: normal; font-variant-east-asian: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-align: -webkit-auto; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-text-stroke-width: 0px; word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class=""><div style="font-family: Helvetica; font-style: normal; font-variant-ligatures: normal; font-variant-position: normal; font-variant-caps: normal; font-variant-numeric: normal; font-variant-alternates: normal; font-variant-east-asian: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-align: -webkit-auto; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-text-stroke-width: 0px; word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class=""><div style="font-family: Helvetica; font-style: normal; font-variant-ligatures: normal; font-variant-position: normal; font-variant-caps: normal; font-variant-numeric: normal; font-variant-alternates: normal; font-variant-east-asian: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-align: -webkit-auto; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-text-stroke-width: 0px; word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class=""><div style="font-family: Helvetica; font-style: normal; font-variant-ligatures: normal; font-variant-position: normal; font-variant-caps: normal; font-variant-numeric: normal; font-variant-alternates: normal; font-variant-east-asian: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-align: -webkit-auto; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-text-stroke-width: 0px; word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class=""><div style="font-family: Helvetica; font-style: normal; font-variant-ligatures: normal; font-variant-position: normal; font-variant-caps: normal; font-variant-numeric: normal; font-variant-alternates: normal; font-variant-east-asian: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-align: -webkit-auto; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-text-stroke-width: 0px; word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class=""><div style="font-family: Helvetica; font-style: normal; font-variant-ligatures: normal; font-variant-position: normal; font-variant-caps: normal; font-variant-numeric: normal; font-variant-alternates: normal; font-variant-east-asian: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-align: -webkit-auto; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-text-stroke-width: 0px; word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class=""><div style="font-family: Helvetica; font-style: normal; font-variant-ligatures: normal; font-variant-position: normal; font-variant-caps: normal; font-variant-numeric: normal; font-variant-alternates: normal; font-variant-east-asian: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-align: -webkit-auto; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-text-stroke-width: 0px; word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class="">******************<br class="">Catherine Lawson, Ph.D.</div><div style="font-family: Helvetica; font-style: normal; font-variant-ligatures: normal; font-variant-position: normal; font-variant-caps: normal; font-variant-numeric: normal; font-variant-alternates: normal; font-variant-east-asian: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-align: -webkit-auto; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-text-stroke-width: 0px; word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class="">EMDataBank, RCSB PDB</div><div style="font-family: Helvetica; font-style: normal; font-variant-ligatures: normal; font-variant-position: normal; font-variant-caps: normal; font-variant-numeric: normal; font-variant-alternates: normal; font-variant-east-asian: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-align: -webkit-auto; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-text-stroke-width: 0px; word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class="">Center for Integrative Proteomics Research</div><div style="font-family: Helvetica; font-style: normal; font-variant-ligatures: normal; font-variant-position: normal; font-variant-caps: normal; font-variant-numeric: normal; font-variant-alternates: normal; font-variant-east-asian: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-align: -webkit-auto; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-text-stroke-width: 0px; word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class="">Rutgers University</div><div style="font-family: Helvetica; font-style: normal; font-variant-ligatures: normal; font-variant-position: normal; font-variant-caps: normal; font-variant-numeric: normal; font-variant-alternates: normal; font-variant-east-asian: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-align: -webkit-auto; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-text-stroke-width: 0px; word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class=""><div class=""><a href="http://emdatabank.org/" class="">http://emdatabank.org</a><br class=""><br class=""><br class=""><br class=""><br class=""><br class=""><br class=""><br class=""><br class=""><br class=""><br class=""><br class=""></div></div></div></div></div></div></div></div>
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