<html><head><meta http-equiv="Content-Type" content="text/html; charset=utf-8"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;" class="">Hi Vincent,<div class=""><br class=""></div><div class=""> I'm glad to hear from all of you about this need. I get how mseries or the Chimera next/prev/skip buttons allows you flip through maps or class average images. Oliver wants some finer control than mseries allows and the Chimera user interface is cumbersome (rows of checkbuttons for every model) and I am missing the fine details of how the comparisons are done in practice that would allow an improved capability. For instance astronomers will quickly flip back and forth between two perfectly aligned images of the sky to see if anything changed (e.g. a supernova) -- the comparison requires fast aligned flipping repeated many times. I don't understand the precise kinds of comparisons you, Guillaume and Oliver are talking about, so it is hard to develop anything to help.</div><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 Feb 3, 2022, at 12:20 AM, vincent Chaptal <<a href="mailto:vincent.chaptal@ibcp.fr" class="">vincent.chaptal@ibcp.fr</a>> wrote:</div><br class="Apple-interchange-newline"><div class=""><font size="4" style="caret-color: rgb(0, 0, 0); font-family: Helvetica; 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=""><font face="monospace" class="">Hi,<span class="Apple-converted-space"> </span><br class=""><br class="">we use the mseries a lot to compare maps and create movies.<span class="Apple-converted-space"> </span><br class="">It is really great and allows for preliminary observations. Now that we are now moving in more detailed examinations, I can see where Oliver's query goes and is interesting. I also think it's not a niche but the future of cryoEM observations.<span class="Apple-converted-space"> </span><br class=""><br class="">More tools along these lines could only be an asset.<span class="Apple-converted-space"> </span><br class="">Best<br class="">Vincent<br class=""></font></font><br style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 18px; 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="moz-cite-prefix" style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 18px; 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;">Le 02/02/2022 à 21:58, Tom Goddard via ChimeraX-users a écrit :<br class=""></div><blockquote type="cite" cite="mid:DE346E73-FA40-4803-BCF6-6005F2A84267@sonic.net" style="font-family: Helvetica; font-size: 18px; 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; text-decoration: none;" class=""><div class="">Hi Guillaume,</div><div class=""><br class=""></div><div class="">The row of checkbuttons (default 10 buttons one for each model) will not handle 50 maps unless you have an extremely wide screen (about two normal screens wide) with Chimera shown full width. I don't understand how it is useful for comparing many maps since I have not used it. Of course often we have dozens of data sets open and compare them. For example the tile command can show them all in a rectangular grid, and there are many many other ways.</div><div class=""><br class=""></div><div class="">Have you used the Chimera "displayed models" and "skip models" check buttons below the command-line?</div><div class=""><br class=""></div><div class=""><span class="Apple-tab-span" style="white-space: pre;"> </span>Tom</div><div class=""><br class=""><blockquote type="cite" class=""><div class="">On Feb 2, 2022, at 12:42 PM, Guillaume Gaullier <<a href="mailto:guillaume.gaullier@icm.uu.se" class="moz-txt-link-freetext" moz-do-not-send="true">guillaume.gaullier@icm.uu.se</a>> wrote:</div><br class="Apple-interchange-newline"><div class=""><div class="" style="word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;">Hi,<div class=""><br class=""></div><div class="">Just to confirm that this is also my experience with cryoEM. For very straightforward projects, you can get away with only a handful of maps (I typically request 4 from normal 3D classification). But once you’re using advanced methods to analyze heterogeneity (like cryoSPARC 3DVA or cryoDRGN), it is very common to have to examine 50 maps or more every time you get results from a new job, and you rarely run a single job. Having more ways to navigate multiple maps can only help!</div><div class=""><br class=""></div><div class="">Cheers,<br class=""><div class=""><div dir="auto" class="" style="caret-color: rgb(0, 0, 0); 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; word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;"><div dir="auto" class="" style="caret-color: rgb(0, 0, 0); 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; word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;"><div dir="auto" class="" style="caret-color: rgb(0, 0, 0); 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; word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;"><div dir="auto" class="" style="caret-color: rgb(0, 0, 0); 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; word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;"><div dir="auto" class="" style="caret-color: rgb(0, 0, 0); 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; word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;"><div class="" style="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; line-break: after-white-space;"><div class="" style="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; line-break: after-white-space;"><div 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; line-break: after-white-space;"><div class="" style="word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;"><div 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;"><br class="Apple-interchange-newline">Guillaume</div><div 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;"><br class=""></div></div></div></div></div></div></div></div></div></div></div><div class=""><br class=""><blockquote type="cite" class=""><div class="">On 2 Feb 2022, at 20:37, Oliver Clarke via ChimeraX-users <<a href="mailto:chimerax-users@cgl.ucsf.edu" class="moz-txt-link-freetext" moz-do-not-send="true">chimerax-users@cgl.ucsf.edu</a>> wrote:</div><br class="Apple-interchange-newline"><div class=""><div class="" style="word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;"><div class="">Hi Tom,</div><div class=""><br class=""></div>It is increasingly not niche at least for single particle cryo-EM folks - pretty much all of us deal with the issue of comparing many classes, or sets of classes, in the context of one or more atomic models. Anything that facilitates that is useful to most of us in the field these days in my experience. Believe me if I had the faintest idea how to add it in I would do so! :)<div class=""><br class=""></div><div class="">Cheers</div><div class="">Oli<br class=""><div class=""><br class=""><blockquote type="cite" class=""><div class="">On Feb 2, 2022, at 2:34 PM, Tom Goddard <<a href="mailto:goddard@sonic.net" class="moz-txt-link-freetext" moz-do-not-send="true">goddard@sonic.net</a>> wrote:</div><br class="Apple-interchange-newline"><div class=""><div class="" style="word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;">Got it. Never knew about that "skip in previous/next" row in the Chimera daily build. Seems really like a niche feature but I understand it is useful to you. This is the kind of feature that is so special purpose that it would be good candidate for someone who really benefits from it to implement it as a ChimeraX plugin.<div class=""><br class=""></div><div class=""><span class="Apple-tab-span" style="white-space: pre;"></span>Tom</div><div class=""><br class=""><div class=""><br class=""><blockquote type="cite" class=""><div class="">On Feb 2, 2022, at 11:20 AM, Oliver Clarke via ChimeraX-users <<a href="mailto:chimerax-users@cgl.ucsf.edu" class="moz-txt-link-freetext" moz-do-not-send="true">chimerax-users@cgl.ucsf.edu</a>> wrote:</div><br class="Apple-interchange-newline"><div class=""><div class="" style="word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;">Hi Tom, right - in recent-ish nightly builds of Chimera Eric added another row - "skip in previous/next" which allows one to control which models are excluded from the sequence. <div class=""><br class=""></div><div class="">So in the attached picture, models 3&4 would be excluded from the sequence - #3 would always be displayed, while #4 would always be hidden. This is very useful to be able to do on the fly, when one is comparing lots of different models & 3D classes that are aligned to one another.<div class=""><br class=""></div><div class="">Cheers</div><div class="">Oli</div><div class=""><div class=""><br class=""></div><div class=""><span id="cid:7F759D57-DE4D-480E-B57B-A0128F079CCF" class=""><PastedGraphic-1.png></span><br class=""><div class=""><br class=""><blockquote type="cite" class=""><div class="">On Feb 2, 2022, at 2:11 PM, Tom Goddard <<a href="mailto:goddard@sonic.net" class="moz-txt-link-freetext" moz-do-not-send="true">goddard@sonic.net</a>> wrote:</div><br class="Apple-interchange-newline"><div class=""><div class="" style="word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;">Hi Oliver,<div class=""><br class=""></div><div class=""> <span class="Apple-converted-space"> </span>You are right the ChimeraX mseries command does not allow you to easily remove or add models to the sequence if models that the slider displays. Could you explain how that works in Chimera? I guess you are referring to the optional row of "Displayed model" checkbuttons below the command line in Chimera that can be shown using command-line preferences and has Next and Previous buttons. But I don't understand how that lets you change which models you cycle through -- doesn't it always cycle through all models in model number order? Eric implemented that Chimera feature and maybe I just don't understand how it works.</div><div class=""><br class=""></div><div class=""><span class="Apple-tab-span" style="white-space: pre;"></span>Tom<br class=""><div class=""><br class=""><blockquote type="cite" class=""><div class="">On Feb 2, 2022, at 8:43 AM, Oliver Clarke via ChimeraX-users <<a href="mailto:chimerax-users@cgl.ucsf.edu" class="moz-txt-link-freetext" moz-do-not-send="true">chimerax-users@cgl.ucsf.edu</a>> wrote:</div><br class="Apple-interchange-newline"><div class=""><div class="" style="word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;">I've played with this a bit now Tom and I still think the Chimera implementation is superior for some use cases, as it is more flexible - it is easy to remove or add volumes or models to the series "on the fly", whereas in ChimeraX this needs to be done when creating the series (unless I am missing something which is entirely possible!). <div class=""><br class=""></div><div class="">It would be great to have at some point an implementation of a "default" model/volume series as exists in Chimera, where one can click next/prev or have an option to temporarily add/remove each model from the series.<div class=""><br class=""></div><div class="">Cheers</div><div class="">Oli<br class=""><div class=""><br class=""><blockquote type="cite" class=""><div class="">On Sep 29, 2021, at 3:30 PM, Tom Goddard <<a href="mailto:goddard@sonic.net" class="moz-txt-link-freetext" moz-do-not-send="true">goddard@sonic.net</a>> wrote:</div><br class="Apple-interchange-newline"><div class=""><div class="" style="word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;">Hi Oli,<div class=""><br class=""></div><div class=""> <span class="Apple-converted-space"> </span>The "mseries slider" command in ChimeraX provides a related capability to flip through several models using a slider, for example,</div><div class=""><br class=""></div><div class=""><span class="Apple-tab-span" style="white-space: pre;"></span>mseries slider #1-5,7-12</div><div class=""><br class=""></div><div class="">allows displaying one of the specified models without effecting the display of models that are not listed in the command.</div><div class=""><br class=""></div><div class=""><span class="Apple-tab-span" style="white-space: pre;"></span><a href="https://www.cgl.ucsf.edu/chimerax/docs/user/commands/mseries.html" class="moz-txt-link-freetext" moz-do-not-send="true">https://www.cgl.ucsf.edu/chimerax/docs/user/commands/mseries.html</a></div><div class=""><br class=""></div><div class=""> <span class="Apple-converted-space"> </span>Tom</div><div class=""><br class=""></div><div class=""><br class=""><div class=""><br class=""><blockquote type="cite" class=""><div class="">On Sep 29, 2021, at 9:42 AM, Oliver Clarke via ChimeraX-users <<a href="mailto:chimerax-users@cgl.ucsf.edu" class="moz-txt-link-freetext" moz-do-not-send="true">chimerax-users@cgl.ucsf.edu</a>> wrote:</div><br class="Apple-interchange-newline"><div class=""><div class="" style="word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;">Hi,<div class=""><br class=""></div><div class="">The Next/Previous buttons in original Chimera, combined with the capacity to lock the display status of one model (using the "Skip") checkboxes, are really useful when comparing multiple maps (particularly multiple aligned maps with a single atomic model), and I really miss this functionality in ChimeraX... would it be possible to add it to the (diminishing!) list of features to port over?</div><div class=""><br class=""></div><div class="">Cheers</div><div class="">Oli</div><div class=""><div class=""><br class=""></div><div class="">PS My mind was blown yesterday when I found out that ChimeraX has (universal?) undo/redo bound to hotkeys! Would it be possible to add the option of user defined hotkeys...? E.g. for invoking a custom function, style, lighting etc?</div><div class=""><span id="cid:E3D075A9-FAF1-4BDC-98AF-9F9BE5B23C66" class=""><PastedGraphic-1.png></span></div></div></div>_______________________________________________<br class="">ChimeraX-users mailing list<br class=""><a href="mailto:ChimeraX-users@cgl.ucsf.edu" class="moz-txt-link-freetext" moz-do-not-send="true">ChimeraX-users@cgl.ucsf.edu</a><br class="">Manage subscription:<br class=""><a href="https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users" class="moz-txt-link-freetext" moz-do-not-send="true">https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users</a><br class=""></div></blockquote></div><br class=""></div></div></div></blockquote></div><br class=""></div></div></div>_______________________________________________<br class="">ChimeraX-users mailing list<br class=""><a href="mailto:ChimeraX-users@cgl.ucsf.edu" class="moz-txt-link-freetext" moz-do-not-send="true">ChimeraX-users@cgl.ucsf.edu</a><br class="">Manage subscription:<br class=""><a href="https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users" class="moz-txt-link-freetext" moz-do-not-send="true">https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users</a><br class=""></div></blockquote></div><br class=""></div></div></div></blockquote></div><br class=""></div></div></div></div>_______________________________________________<br class="">ChimeraX-users mailing list<br class=""><a href="mailto:ChimeraX-users@cgl.ucsf.edu" class="moz-txt-link-freetext" moz-do-not-send="true">ChimeraX-users@cgl.ucsf.edu</a><br class="">Manage subscription:<br class=""><a href="https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users" class="moz-txt-link-freetext" moz-do-not-send="true">https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users</a><br class=""></div></blockquote></div><br class=""></div></div></div></blockquote></div><br class=""></div></div>_______________________________________________<br class="">ChimeraX-users mailing list<br class=""><a href="mailto:ChimeraX-users@cgl.ucsf.edu" class="moz-txt-link-freetext" moz-do-not-send="true">ChimeraX-users@cgl.ucsf.edu</a><br class="">Manage subscription:<br class=""><a href="https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users" class="moz-txt-link-freetext" moz-do-not-send="true">https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users</a><br class=""></div></blockquote></div><br class=""></div><br class=""><br class=""><br class=""><br class=""><br class=""><br class=""><br class=""><br class="">När du har kontakt med oss på Uppsala universitet med e-post så innebär det att vi behandlar dina personuppgifter. 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</pre></blockquote><br style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 18px; 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="moz-signature" style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 18px; 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;">--<span class="Apple-converted-space"> </span><br class=""><div style="margin: 0px; font-style: normal; font-variant-caps: normal; font-weight: normal; font-stretch: normal; font-size: 12px; line-height: normal; font-family: Helvetica; -webkit-text-stroke-width: initial; -webkit-text-stroke-color: rgb(0, 0, 0);" class=""><span class="s1" style="-webkit-font-kerning: none;">Vincent Chaptal, PhD</span></div><div style="margin: 0px; font-style: normal; font-variant-caps: normal; font-weight: normal; font-stretch: normal; font-size: 12px; line-height: normal; font-family: Helvetica; -webkit-text-stroke-width: initial; -webkit-text-stroke-color: rgb(0, 0, 0);" class=""><span class="s1" style="-webkit-font-kerning: none;">Director of GdR APPICOM</span></div><div style="margin: 0px; font-style: normal; font-variant-caps: normal; font-weight: normal; font-stretch: normal; font-size: 12px; line-height: normal; font-family: Helvetica; -webkit-text-stroke-width: initial; -webkit-text-stroke-color: rgb(0, 0, 0);" class=""><span class="s1" style="-webkit-font-kerning: none;">Drug Resistance and Membrane Proteins Lab</span></div><div style="margin: 0px; font-style: normal; font-variant-caps: normal; font-weight: normal; font-stretch: normal; font-size: 12px; line-height: normal; font-family: Helvetica; -webkit-text-stroke-width: initial; -webkit-text-stroke-color: rgb(0, 0, 0); min-height: 14px;" class=""><span class="s1" style="-webkit-font-kerning: none;"></span><br class=""></div><div style="margin: 0px; font-style: normal; font-variant-caps: normal; font-weight: normal; font-stretch: normal; font-size: 12px; line-height: normal; font-family: Helvetica; -webkit-text-stroke-width: initial; -webkit-text-stroke-color: rgb(0, 0, 0);" class=""><span class="s1" style="-webkit-font-kerning: none;">MMSB -UMR5086</span></div><div style="margin: 0px; font-style: normal; font-variant-caps: normal; font-weight: normal; font-stretch: normal; font-size: 12px; line-height: normal; font-family: Helvetica; -webkit-text-stroke-width: initial; -webkit-text-stroke-color: rgb(0, 0, 0);" class=""><span class="s1" style="-webkit-font-kerning: none;">7 passage du Vercors<span class="Apple-converted-space"> </span></span></div><div style="margin: 0px; font-style: normal; font-variant-caps: normal; font-weight: normal; font-stretch: normal; font-size: 12px; line-height: normal; font-family: Helvetica; -webkit-text-stroke-width: initial; -webkit-text-stroke-color: rgb(0, 0, 0);" class=""><span class="s1" style="-webkit-font-kerning: none;">69007 LYON</span></div><div style="margin: 0px; font-style: normal; font-variant-caps: normal; font-weight: normal; font-stretch: normal; font-size: 12px; line-height: normal; font-family: Helvetica; -webkit-text-stroke-width: initial; -webkit-text-stroke-color: rgb(0, 0, 0);" class=""><span class="s1" style="-webkit-font-kerning: none;">FRANCE</span></div><div style="margin: 0px; font-style: normal; font-variant-caps: normal; font-weight: normal; font-stretch: normal; font-size: 12px; line-height: normal; font-family: Helvetica; -webkit-text-stroke-width: initial; -webkit-text-stroke-color: rgb(0, 0, 0);" class=""><span class="s1" style="-webkit-font-kerning: none;">+33 4 37 65 29 01</span></div><div style="margin: 0px; font-style: normal; font-variant-caps: normal; font-weight: normal; font-stretch: normal; font-size: 12px; line-height: normal; font-family: Helvetica; -webkit-text-stroke-width: initial; -webkit-text-stroke-color: rgb(0, 0, 0);" class=""><span class="s1" style="-webkit-font-kerning: none;"><a class="moz-txt-link-freetext" href="http://www.appicom.cnrs.fr/">http://www.appicom.cnrs.fr</a></span></div><div style="margin: 0px; font-style: normal; font-variant-caps: normal; font-weight: normal; font-stretch: normal; font-size: 12px; line-height: normal; font-family: Helvetica; -webkit-text-stroke-width: initial; -webkit-text-stroke-color: rgb(0, 0, 0);" class=""><span class="s1" style="-webkit-font-kerning: none;"><a class="moz-txt-link-freetext" href="http://mmsb.cnrs.fr/en/">http://mmsb.cnrs.fr/en/</a></span></div></div></div></blockquote></div><br class=""></div></body></html>