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Hi Elaine,</div>
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<div><font size="2"><span style="font-size:11pt">> rainbow #1.5-23 structures palette blue:orange
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<div><font size="2"><span style="font-size:11pt">This is exactly what I was looking for! Thank you very much for your help.
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<div><font size="2"><span style="font-size:11pt">The ligand positions are a part of a trajectory but were (for analysis reasons) saved in a .pdb file, which is why ChimeraX read it as submodels instead of trajectories.<br>
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<div><font size="2"><span style="font-size:11pt">Cheers,</span></font></div>
<div><font size="2"><span style="font-size:11pt">Lorena<br>
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<div id="divRplyFwdMsg" dir="ltr"><font face="Calibri, sans-serif" style="font-size:11pt" color="#000000"><b>From:</b> Elaine Meng <meng@cgl.ucsf.edu><br>
<b>Sent:</b> 23 May 2022 18:19<br>
<b>To:</b> Lorena Zuzic <lorena.zuzic@chem.au.dk><br>
<b>Cc:</b> chimerax-users@cgl.ucsf.edu <chimerax-users@cgl.ucsf.edu><br>
<b>Subject:</b> Re: [chimerax-users] Colouring submodels using a palette</font>
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<div class="PlainText">Hi Lorena,<br>
Atomic models, regardless of whether they are models, submodels, subsubmodels ... are "structures" -- you just need to specify which ones to color, if there are other models also present that you don't want to color. E.g. if you have models #1-3 but only want
to color submodels of #1, something like:<br>
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rainbow #1 structures palette blue:orange<br>
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...or to act on specific submodels #1.5 to #1.23 only, something like:<br>
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rainbow #1.5-23 structures palette blue:orange<br>
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See rainbow documentation:<br>
<<a href="https://rbvi.ucsf.edu/chimerax/docs/user/commands/color.html#sequential">https://rbvi.ucsf.edu/chimerax/docs/user/commands/color.html#sequential</a>><br>
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I'm going from your description that these ligand positions are really submodels. If this was opened as a trajectory in ChimeraX, the commands above would not work since the time steps are not different models (or submodels).<br>
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I hope this helps,<br>
Elaine<br>
-----<br>
Elaine C. Meng, Ph.D. <br>
UCSF Chimera(X) team<br>
Department of Pharmaceutical Chemistry<br>
University of California, San Francisco<br>
<br>
> On May 23, 2022, at 6:04 AM, Lorena Zuzic via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:<br>
> <br>
> Hi all,<br>
> <br>
> I have a model that contains 256 submodels of a ligand across trajectory frames. I would like to colour the individual models using a palette (e.g., blue:orange) so that the time progression across frames is depicted in colour. Is there a way to assign palette
range to submodels?<br>
> <br>
> Best wishes,<br>
> Lorena <br>
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