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@gmail.com> 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 <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