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

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 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

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On Feb 15, 2019, at 3:20 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 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 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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