[chimerax-users] Fwd: [Chimera-users] Can ChimeraX morph between two surfaces?

[Steve Chou]

Hi Elaine,
(1) I tried to read the pseudobonds from a file (.pb) ,
=========================
#1/A:13 at NE2  #1/A:704 at O
#1/A:13 at NE2  #1/A:502 at MG
#1/A:13 at NE2  #1/A:501 at PB

#2/A:13 at NE2  #2/A:704 at O
#2/A:13 at NE2  #2/A:502 at MG
#2/A:13 at NE2  #2/A:501 at PB
=========================
the program reported an error.
=============================

ValueError: not enough values to unpack (expected 2, got 0)
File
"/opt/UCSF/ChimeraX-daily/lib/python3.7/site-packages/chimerax/read_pbonds/readpbonds.py",
line 27, in read_pseudobond_file
aspec1, aspec2 = line.split()[:2]
See log for complete Python traceback.
=============================

(2) Then I tried to add distances on the ChimeraX terminal
=============================
distance #1/A:13 at NE2  #1/A:704 at O
distance #1/A:13 at NE2  #1/A:502 at MG
distance #1/A:13 at NE2  #1/A:501 at PB

distance #2/A:13 at NE2  #2/A:704 at O
distance #2/A:13 at NE2  #2/A:502 at MG
distance #2/A:13 at NE2  #2/A:501 at PB
=============================
I was able to see the distance labels in the two structures. And I saw an
new model (name: distances; ID:3) show up in the "Models" panels. Then I
ran morphing again. The Mg and water molecules moved, but still didn't move
together with the protein.
Steve

On Fri, Feb 15, 2019 at 11:31 AM Elaine Meng <meng at cgl.ucsf.edu> wrote:

> Hi Steve,
> Yes, if those are the correct specifiers for atoms in your structure.
> You'd make a plain text file with name *.pb with lines like that and open
> it.
>
> You don’t have to read in pseudobonds from a file, however.  If not too
> many, probably easier just to add distance monitors.
> <http://rbvi.ucsf.edu/chimerax/docs/user/commands/distance.html>
> <http://rbvi.ucsf.edu/chimerax/docs/user/selection.html#context>
>
> Elaine
>
> > On Feb 14, 2019, at 9:49 PM, Steve Chou <stevezchou at gmail.com> wrote:
> >
> > Hi Elaine,
> > Thanks for your detailed explanation!
> > What's the format of the pseudobond file? Should it look like this?
> > ===============================
> > #1/A:13 at NE2    #1/A:502 at MG
> > ===============================
> > All the best,
> > Steve
> >
> > On Thu, Feb 14, 2019 at 7:43 PM Elaine Meng <meng at cgl.ucsf.edu> wrote:
> > Hi Steve,
> > Actually I’m surprised the Mg and water were included (even if present
> at both ends) because I thought they had to be tethered by a bond or
> pseudobond (like a distance measurement) to the biopolymer chain, as
> described here under “Atoms in Common”:
> >
> > <http://rbvi.ucsf.edu/chimerax/docs/user/commands/morph.html#pairing>
> >
> > For the case where composition changes, you could add in a fake Mg ion
> and water to the structure that’s missing them, but you’d have to decide
> where to put them.  Also it was my understanding that they had to be
> tethered to the biopolymer chain (e.g. add distance measurement, which can
> then be hidden), but maybe that requirement has changed, or the Mg does
> already have a metal-coordination pseudobond to the biopolymer.
> >
> > Or if you don’t care if the Mg or water move during the morph, you could
> just display those atoms from the original model (that was input to
> morphing) even though they are not present in the trajectory.
> > Elaine
> > -----
> > Elaine C. Meng, Ph.D.
> > UCSF Chimera(X) team
> > Department of Pharmaceutical Chemistry
> > University of California, San Francisco
> >
> > > On Feb 14, 2019, at 12:51 PM, Steve Chou <stevezchou at gmail.com> wrote:
> > >
> > > Thanks, Elaine!
> > > You command "rainbow structures" works beautifully.
> > > There is "a Mg ion" and "a water molecule" in the two conformations.
> > > (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.
> > > (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.
> > > Is there a way to morph the specific components properly?
> > > Steve
> > >
> >
> >
> >
> >
> > _______________________________________________
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>

-- 
Steve Chou


-- 
Steve Chou
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