<html><head></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">It was pretty much a design decision since the superposition functionality of MAV doesn't make any sense if you have multiple chains of the same structure associated with the alignment. I can imagine some ways of dealing with the superposition issue, but at this stage of MAV's development I'd say the one-chain-per-structure association limitation is pretty much baked in and is unlikely to change.<div><br></div><div>You can work around the limitation by using the "split" command to break the chains into separate models, which can then all be associated with a single sequence of the alignment.</div><div><br></div><div>--Eric</div><div><br><div><span class="Apple-style-span" style="border-collapse: separate; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; color: rgb(0, 0, 0); font-family: Helvetica; font-size: 16px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; -webkit-text-decorations-in-effect: none; text-indent: 0px; -webkit-text-size-adjust: auto; text-transform: none; orphans: 2; white-space: normal; widows: 2; word-spacing: 0px; "><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><font face="Helvetica" size="5" style="font: normal normal normal 16px/normal Helvetica; "> Eric Pettersen</font></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><font face="Helvetica" size="5" style="font: normal normal normal 16px/normal Helvetica; "> UCSF Computer Graphics Lab</font></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><font face="Helvetica" size="5" style="font: normal normal normal 16px/normal Helvetica; "> <a href="http://www.cgl.ucsf.edu">http://www.cgl.ucsf.edu</a></font></div><br class="Apple-interchange-newline"></span></div></div><div><div><div>On Oct 17, 2012, at 1:08 PM, Tom Goddard wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite">
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<div class="moz-cite-prefix">Hi Ed,<br>
<br>
I don't know if more than one chain can be associated with a
sequence in Multalign Viewer. The documentation says<br>
<br>
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A structure (even if it has multiple chains) cannot be associated
with more
than one sequence, but a single sequence can be associated with
more than one structure."<br>
<br>
<a class="moz-txt-link-freetext" href="http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/multalignviewer/multalignviewer.html#association">http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/multalignviewer/multalignviewer.html#association</a><br>
<br>
That doesn't really say whether multiple chains of a single
structure can associate with a sequence, only that multiple
structures (different PDB models) can associate with the same
sequence. So I tried it as I'm sure you did and I was not able to
make it associate more than one chain (I used groel 1grl) with the
same sequence in a multiple alignment. When I load the structure
it associates chain A but not any of the other chains. Then if I
use MultAlign Viewer menu Structure / Associations... to associate
chain B with the same sequence then it seems to lose the
association of chain A. At least when I select residues on the
sequence, only chain B on the structure has residues selected.<br>
<br>
I'm forwarding this to the Chimera list since Elaine Meng or
Eric Pettersen will have a better answer.<br>
<br>
Tom<br>
<br>
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Hi,<br>
I am wondering if this is a bug or limitation in Chimera, or if
I am missing something. I have a molecular model of F-actin, with
many identical chains. Using the Multialign Viewer, it appears
that I can only do a 1 to 1 mapping of a single chain to a single
sequence. How can I map 10 identical chains to one sequence?<br>
Regards,<br>
Ed<br>
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