<html><head><meta http-equiv="Content-Type" content="text/html; charset=us-ascii"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;" class=""><div class="">Hi Roden,</div><div class=""><br class=""></div>ChimeraX fitting works on volume data, also called "maps", 3d rectangular arrays of intensity values. The Amira SpatialGraph formats are I think vertices, edges and points and won't be of use for fitting in ChimeraX. File formats like an MRC map or Amira lattice data are the only kind that ChimeraX would do fitting in.<div class=""><br class=""></div><div class=""><span class="Apple-tab-span" style="white-space:pre"> </span>Tom<br class=""><div><br class=""><blockquote type="cite" class=""><div class="">On Oct 25, 2021, at 12:49 PM, Roden Deng Luo via ChimeraX-users <<a href="mailto:chimerax-users@cgl.ucsf.edu" class="">chimerax-users@cgl.ucsf.edu</a>> wrote:</div><br class="Apple-interchange-newline"><div class=""><meta charset="UTF-8" class=""><div dir="ltr" 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; text-decoration: none;" class="">Hi Tom, <div class=""><br class=""></div><div class="">Many thanks. I am very new to both ChimeraX and Amira. As shown in the screenshot on the right, it looks to me the data is a segmentation map. I initiated the original post because I wanted to use the functionality "Fit in map" in ChimeraX. Will there be a workaround that I can achieve this? As a first step, I would like to fit only a very small fragment of the segmentation map. </div><div class=""><br class=""></div><div class="">Best,</div><div class="">Roden</div><br class=""></div><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; text-decoration: none;" class=""><div class="gmail_quote" 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; text-decoration: none;"><div dir="ltr" class="gmail_attr">On Mon, Oct 25, 2021 at 10:29 PM Tom Goddard <<a href="mailto:goddard@sonic.net" target="_blank" class="">goddard@sonic.net</a>> wrote:<br class=""></div><blockquote class="gmail_quote" style="margin: 0px 0px 0px 0.8ex; border-left-width: 1px; border-left-style: solid; border-left-color: rgb(204, 204, 204); padding-left: 1ex;">Hi Roden,<br class=""><br class="">These 3 Amira files are vertex/edge/point data, not 3D lattices. The ChimeraX reader only handles 3D lattices Amira files. It does not look like our ChimeraX documentation explains this. I'll try to get this on our docs (3d lattice volume data, float, unsigned 16-bit, uncompressed only).<br class=""><br class=""> <span class="Apple-converted-space"> </span>Tom<br class=""><br class=""><br class="">> On Oct 25, 2021, at 12:20 PM, Roden Deng Luo <<a href="mailto:deng.luo@kaust.edu.sa" target="_blank" class="">deng.luo@kaust.edu.sa</a>> wrote:<br class="">><span class="Apple-converted-space"> </span><br class="">> Dear Tom and Andrea,<span class="Apple-converted-space"> </span><br class="">><span class="Apple-converted-space"> </span><br class="">> Thanks for the quick responses. Upon the kind approval from Andrea, I attached the .am file I received from Andrea (in the format of 2.0), as well as the other two that are exported from this file (in the format of 3.0, one is in ascii as revealed by the name).<span class="Apple-converted-space"> </span><br class="">><span class="Apple-converted-space"> </span><br class="">> Best regards,<span class="Apple-converted-space"> </span><br class="">> Roden<br class=""><br class=""></blockquote></div><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; text-decoration: none;" class=""><div 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; text-decoration: none;" class=""><hr class=""></div><font face="Arial" size="1" style="caret-color: rgb(0, 0, 0); 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;" class="">This message and its contents, including attachments are intended solely for the original recipient. 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