<div dir="ltr"><div dir="ltr"><div dir="ltr"><div><div>Thanks, Elaine! <br></div>You command "rainbow structures" works beautifully. <br>There is "a Mg ion" and "a water molecule" in the two conformations.<br></div><div>(1) If the two conformations have exactly the same compositions (by shifting the structure), the "Mg ion" and the "water molecule" do not follow the same path as the protein. They move but separate from the protein.<br></div><div>(2) If the two conformations have slightly different compositions, the "Mg ion" and the "water molecule" do not show up in the morphed pdb ensemble.<br></div><div>Is there a way to morph the specific components properly?<br></div><div>Steve<br></div><div><br></div></div><div dir="ltr"><div><div><br></div></div></div></div></div><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">On Thu, Feb 14, 2019 at 3:25 PM Elaine Meng <<a href="mailto:meng@cgl.ucsf.edu">meng@cgl.ucsf.edu</a>> wrote:<br></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">Hi Steve,<br>
You want “rainbow structures”:<br>
<br>
<<a href="http://rbvi.ucsf.edu/chimerax/docs/user/commands/color.html#sequential" rel="noreferrer" target="_blank">http://rbvi.ucsf.edu/chimerax/docs/user/commands/color.html#sequential</a>><br>
<br>
Best,<br>
Elaine<br>
<br>
> On Feb 14, 2019, at 12:21 PM, Steve Chou <<a href="mailto:stevezchou@gmail.com" target="_blank">stevezchou@gmail.com</a>> wrote:<br>
> <br>
> Dear Elaine,<br>
> Thanks for your fast reply.<br>
> I (1) saved the trajectory as a multi-model PDB file (11 models, like an NMR ensemble), <br>
> (2) loaded the ensemble PDB back to ChimeraX,<br>
> (3) rendered each model as a surface,<br>
> then (4) tried to color the surfaces as a rainbow, but the last step [step: (4)] only produces red surfaces, not a rainbow.<br>
> rainbow chain palette red:blue<br>
> rainbow polymers palette red:blue<br>
> Steve<br>
> <br>
> On Thu, Feb 14, 2019 at 12:25 PM Elaine Meng <<a href="mailto:meng@cgl.ucsf.edu" target="_blank">meng@cgl.ucsf.edu</a>> wrote:<br>
> Hi Steve,<br>
> Yes, you have to have equal numbers of chains in the two structures on either end of a morph. This is in the “Limitations"<br>
> <<a href="http://rbvi.ucsf.edu/chimerax/docs/user/commands/morph.html" rel="noreferrer" target="_blank">http://rbvi.ucsf.edu/chimerax/docs/user/commands/morph.html</a>><br>
> <<a href="http://rbvi.ucsf.edu/chimerax/docs/user/commands/morph.html#limitations" rel="noreferrer" target="_blank">http://rbvi.ucsf.edu/chimerax/docs/user/commands/morph.html#limitations</a>><br>
> <br>
> You cannot morph only the surfaces; instead you would morph the atomic structures and then show surface for the trajectory as it morphs (in effect, you would just see the surface morphing).<br>
> <br>
> I can’t think of any easy way to gradually change the color of the surface over the trajectory, though. A somewhat tedious way would be to save the trajectory as a multi-model PDB file, then reopen (it would show all the frames at the same time like an NMR ensemble), then “rainbow” with your desired palette, say red->blue, then surface each one, then show each one in trajectory order, hiding the others.<br>
> 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 Feb 14, 2019, at 9:13 AM, Steve Chou <<a href="mailto:stevezchou@gmail.com" target="_blank">stevezchou@gmail.com</a>> wrote:<br>
> > <br>
> > Dear ChimeraX team,<br>
> > 1. Can ChimeraX morph between two surfaces (surfaces generated from two PDBs, not maps)?<br>
> > 2. During morphing, can the color also change gradually from one color (one conformation colored in red) to another color (another conformation colored in blue)?<br>
> > 3. The following command works if #1 has only one chain. <br>
> > morph #2 #1/L frames 10 <br>
> > When there are several chains in #1, ChimeraX stopped with an error (ValueError: models have different number of chains).<br>
> > Thanks in advance!<br>
> > Steve<br>
> > -- <br>
> > Steve Chou<br>
> <br>
> <br>
> <br>
> -- <br>
> Steve Chou<br>
> <br>
> <br>
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</blockquote></div><br clear="all"><br>-- <br><div dir="ltr" class="gmail_signature"><div dir="ltr"><div><div dir="ltr"><div>Steve Chou</div><div><br></div><br></div></div></div></div>