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

[Steve Chou]

By covalent bonds, do you mean that I should add the CONNECT keyword for an
atom pair between a HETATM and an regular ATOM in the PDB?
Steve

On Fri, Feb 15, 2019 at 7:32 PM Elaine Meng <meng at cgl.ucsf.edu> wrote:

> … and now I’m told that currently in ChimeraX, adding pseudobonds wouldn’t
> help anyway, only covalent bonds.  Sorry, the functionality and
> documentation were ported from Chimera (where this pseudobond bond stuff
> did apply), and I was not informed of the difference!
>
> Apologies for the red herring(s),
> Elaine
>
>
> > On Feb 15, 2019, at 4:16 PM, Elaine Meng <meng at cgl.ucsf.edu> wrote:
> >
> > I’m told that the pseudobonds may not be needed if:
> >
> > (A) the two endpoint structures have exactly and only the same atoms
> (with same names, res numbers, chain IDs)
> > -or-
> > (B) the “same true” option is used, when some atoms are different but
> the atoms in question have the same names, res numbers, and chain IDs.
> >
> > That may explain why your Mg was included in the first place if it
> wasn’t pseudobonded to the protein chain.
> >
> > However, that is orthogonal to the problem of poor movement path, which
> as far as I know is not solved.  Sorry about that.
> > Elaine
> >
> >> On Feb 15, 2019, at 3:40 PM, Elaine Meng <meng at cgl.ucsf.edu> wrote:
> >>
> >> Hi Steve,
> >> The problem with the pseudobond file is the blank line.  The reader is
> not very smart.
> >>
> >> The pseudobonds (or distances) were just to have the HET atoms simply
> included in the morph at all, as I understood it and as written here:
> >> <http://rbvi.ucsf.edu/chimerax/docs/user/commands/morph.html#pairing>
> >>
> >> How the HET atoms move along the trajectory is a separate matter, and
> it sounds like they are being handled poorly.  Sorry about the
> limitations.  You could use Help… Report a Bug and attach your session as
> an example for us if these structures are shareable (not private data).
> >>
> >> Elaine
> >>
> >>> On Feb 15, 2019, at 3:20 PM, Steve Chou <stevezchou at gmail.com> wrote:
> >>>
> >>>
> >>> 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
> >>>
> >>
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> >
> >
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>
> --
Steve Chou
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