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

Sat Feb 16 07:45:12 PST 2019

Hi Steve,
First of all, if the atoms in question (ion, water) are already included in your morph trajectory, there is no need to do anything. This (pseudo)bonding stuff is merely to have them included the trajectory rather than omitted, and mainly applies to morphing in Chimera rather than ChimeraX. 

I think you told me that those atoms are already included in your morph trajectory, so none of the rest of this message is relevant to your situation.

A poor path of movement is a separate issue that may not be solved.  

If those atoms are NOT included.
There isn’t a good way to add covalent bonds in ChimeraX currently.  That was just a statement that covalent ligands like glycosylations or retinal in rhodopsin would be included under certain circumstances.  You would instead use “same true” morph option and make sure that all atoms to be included in the morph have the same atom names, chain IDs and residue numbers.

If they don’t already have identical naming etc. it is generally hard to do for the protein part.  One idea to avoid that is two stages:

- morph the protein, write trajectory as PDB multiple files
- take first and last morph trajectory structures and edit in the Mg, water, with same atom names, chain ID, residue numbers in their starting and ending positions
- morph starting from those two structures

Again, none of this solves the “path of movement” problem.  For that, you could try messing with the morphing parameters, but it is possible that won’t help.
<http://rbvi.ucsf.edu/chimerax/docs/user/commands/morph.html#morph-parameters>

Elaine

> On Feb 15, 2019, at 7:29 PM, Steve Chou <stevezchou at gmail.com> wrote:
> 
> 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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