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

[Elaine Meng]

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
>