On Feb 15, 2019, at 3:02 PM, Steve Chou  wrote:

Hi Elaine,

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

#2/A:13@NE2  #2/A:704@O
#2/A:13@NE2  #2/A:502@MG
#2/A:13@NE2  #2/A:501@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@NE2  #1/A:704@O
distance #1/A:13@NE2  #1/A:502@MG
distance #1/A:13@NE2  #1/A:501@PB

distance #2/A:13@NE2  #2/A:704@O
distance #2/A:13@NE2  #2/A:502@MG
distance #2/A:13@NE2  #2/A:501@PB
=============================

I was able to see the distance labels in the two structure. 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@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@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@NE2    #1/A:502@MG
> ===============================
> All the best,
> Steve
> 
> On Thu, Feb 14, 2019 at 7:43 PM Elaine Meng <meng@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@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

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