<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=""><div class=""><br class=""><div><blockquote type="cite" class=""><div class="">On 30 May 2017, at 23:06, 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=""><div class="">Hi Mike,</div><div class=""><br class=""></div><div class=""> We are working on making ChimeraX handle intergrative hybrid model format, an extension to mmCIF being developed by the wwPDB intended to handle coarse grain models.</div><div class=""><br class=""></div><div class=""><span class="Apple-tab-span" style="white-space:pre"> </span><a href="https://pdb-dev.rcsb.rutgers.edu/" class="">https://pdb-dev.rcsb.rutgers.edu</a></div><div class=""><br class=""></div><div class=""><span class="Apple-tab-span" style="white-space:pre"> </span><a href="https://github.com/ihmwg/IHM-dictionary" class="">https://github.com/ihmwg/IHM-dictionary</a></div><div class=""><br class=""></div><div class="">The Sali lab is working on this new file format and it is not clear if the IMP RMF format will continue to be used. There currently aren’t good standard formats for describing coarse-grain models. A recent (April 2017) Nature chromosome 3D structure article</div><div class=""><br class=""></div><div class=""><span class="Apple-tab-span" style="white-space:pre"> </span><a href="http://www.nature.com/nature/journal/v544/n7648/full/nature21429.html" class="">http://www.nature.com/nature/journal/v544/n7648/full/nature21429.html</a></div><div class=""><br class=""></div><div class="">has data at the NCBI GEO database with the chromosomes represented in PDB format:</div><div class=""><br class=""></div><div class=""><span class="Apple-tab-span" style="white-space:pre"> </span><a href="https://www.ncbi.nlm.nih.gov/gds/?term=GSE80280" class="">https://www.ncbi.nlm.nih.gov/gds/?term=GSE80280</a></div><div class=""><br class=""></div><div class=""> Tom</div><div class=""><br class=""></div><div class=""><br class=""></div><br class=""><div class=""><blockquote type="cite" class=""><div class="">On May 28, 2017, at 3:19 PM, Mike Goodstadt wrote:</div><br class="Apple-interchange-newline"><div class=""><div dir="auto" class="" 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; word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;">Hi Elaine,<div class="">Considering your reply further:</div><div class="">Will ChimeraX include a agnostic plain XYZ import option?</div><div class="">We work with non-atomistic chromatin confirmations and so are interested in this option.</div><div class="">What would be your recommendation for a format for non-atomistic particle (xyz) coordinates?</div><div class="">Also, I have been looking into IMP’s RMF format and comparing it to UMM (<a href="http://www.scalalife.eu/content/umm.html" class="">http://www.scalalife.eu/content/umm.html</a>).</div><div class="">Will RMF still receive official Chimera backing in ChimeraX?</div><div class="">Many thanks,</div><div class="">Mike</div><div class=""><br class=""></div><div class=""><div class=""><blockquote type="cite" class=""><div class="">On 26 May 2017, at 17:25, Elaine Meng wrote:</div><br class="Apple-interchange-newline"><div class=""><div class="">Hi Mike,<br class="">Not currently. You can use command “open formats” to list the current ChimeraX formats in the Log.<br class=""><br class="">The data formats are listed with a little more detail in the documentation for “open” (input) and “save” (output) commands. Input formats:<br class=""><<a href="http://rbvi.ucsf.edu/chimerax/docs/user/commands/open.html#local" class="">http://rbvi.ucsf.edu/chimerax/docs/user/commands/open.html#local</a>><br class=""><br class="">You may be able to use Chimera (not ChimeraX) to read XYZ and output PDB, if you don’t have any other converter handy.<br class="">I hope this helps,<br class="">Elaine<br class="">-----<br class="">Elaine C. Meng, Ph.D. <br class="">UCSF Chimera(X) team<br class="">Department of Pharmaceutical Chemistry<br class="">University of California, San Francisco<br class=""><br class=""><blockquote type="cite" class="">On May 25, 2017, at 4:10 PM, Mike Goodstadt wrote:<br class=""><br class="">Hi!<br class="">Many thanks for the great work on this new version.<br class="">Does ChimeraX support XYZ files?<br class="">Chimera did but I get an “unrecognized filetype” error in ChimeraX.<br class="">Best regards,<br class="">Mike Goodstadt<br class=""></blockquote><br class=""></div></div></blockquote></div><br class=""><div class=""><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="">Mike Goodstadt<br class=""><a href="mailto:mikegoodstadt@gmail.com" class="">mikegoodstadt@gmail.com</a><br class="">skype: mikegoodstadt<br class="">+34 653 756 614</div></div><br class=""></div></div><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><br 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=""><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="">ChimeraX-users mailing list</span><br 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=""><a href="mailto:ChimeraX-users@cgl.ucsf.edu" style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px;" class="">ChimeraX-users@cgl.ucsf.edu</a><br 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=""><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="">Manage subscription:</span><br 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=""><a href="http://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users" style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px;" class="">http://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users</a></div></blockquote></div><br class=""></div></div></blockquote></div><div class=""><br class="">
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