<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="">Hi Yanhe,<div class=""><br class=""></div><div class=""> The fit sequential mode which fits each atomic model after subtracting the density occupied by other atomic models appears to be working find in ChimeraX 1.4 in my tests. So I think it has something to do with your map and models and their initial placement.</div><div class=""><br class=""></div><div class=""> Here is an test example I just tried. I opened a dimer atomic model, made a 10A map from it, split the dimer into two monomer models, move one of the monomers so it collides with the other, then fit the two monomers.</div><div class=""><br class=""></div><div class=""><span class="Apple-tab-span" style="white-space:pre"> </span>open 7ej3</div><div class=""><span class="Apple-tab-span" style="white-space:pre"> </span>molmap #1 10</div><div class=""><span class="Apple-tab-span" style="white-space:pre"> </span>split #1</div><div class=""><span class="Apple-tab-span" style="white-space:pre"> </span>color #1.2 lightblue</div><div class=""><span class="Apple-tab-span" style="white-space:pre"> </span>move x 10 model #1.1 coord #1.1</div><div class=""><span class="Apple-tab-span" style="white-space: pre;"> </span>fit #1.1-2 in #2 seq 2 res 10</div><div class=""><br class=""></div><div class="">It worked as expected pushing the monomers apart so they fit nicely without clashing.</div><div class=""><br class=""></div><div class=""> To debug what is going wrong in your specific case you can do the sequential fitting steps by hand. Make a simulated map from your second monomer with the molmap command, subtract it from your map using volume subtract with the "minrms true" option so the simulated map is first scaled to match the experimental map, then fit the first monomer in that difference map. Now make a molmap simulated map of the new first monomer position, subtract it from the original experimental map and fit the second monomer into the result. This is exactly the process that the fitmap command with the sequential option is using. Doing it step by step will probably reveal your problem. A simpler approach could be to use "fit #2,3 in #1 seq 1 res 3.7" to see just the first step (fitting only model #2 after subtracting the density occupied by #3), judge whether the result makes sense, then use "fit #3,2 in #1 seq 1 res 3.7" to take one more step fitting only model #3 after subtracting the density occupied by #2.</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><div class="">Sequential fitting resulting from example commands on 7ej3</div><div class=""><img apple-inline="yes" id="1549C2F4-4DB7-4C0C-99AA-6744DF89ACCB" width="571" height="543" src="cid:CA15AB8A-D398-4379-B4D9-88B5ED769A2A" class=""><br class=""><div><br class=""><blockquote type="cite" class=""><div class="">On Sep 21, 2022, at 8:17 AM, Yanhe Zhao 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=""><div dir="ltr" class="">Greeting there developer,<div class=""><br class=""><div class="">I am using fitmap command of chimerax to fit pdb to map, the command as below:</div><div class="">fitmap #2,3 inMap #1 seq 2 res 3.7</div><div class="">#2 and #3 are copy of each other and I manually placed them in different positions in map,</div><div class="">#2 and #3 come to same position after the command running, I had shift option false, but come to same result.</div><div class="">I remember it works in chimera.</div><div class="">Could you please point me out?</div><div class=""><br class=""></div><div class="">Thanks and have a nice day,</div><div class="">Yanhe</div><div class=""><br class=""></div></div></div>
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