Hi Thomas,
If you add "and present" to the selection expression, then you'll only include
atoms which have coordinates in the current state:
select s1, 2hduA & present
I had a quick look at 2hduA and 2r9wA and don't see any non-standard residues,
but a lot of alternate coordinates. Depending
Hi Thomas,
With regard to selections, sometimes a residue has missing atoms or is
non-standard amino acid. In the first case it is matched with another
residue in a second structure during the alignment and then when I try to
fit the two selections of atoms from the two structures I get the follow
Hi Thomas,
In general, the PyMOL API should raise pymol.CmdException if things go wrong.
But in case of cmd.pair_fit() this wasn't happening (see my fix that I pushed
few minutes ago:
https://github.com/schrodinger/pymol-open-source/commit/b26d91c40d20344fef511ea9d6bb664a93f1bb4a
)
cmd.select
Hi Thomas,
This is great! I can even include more atom types in the selection.
Just for the record, is it possible to catch PyMOL exceptions like
"Selector-Error" from within a Python script? Is there any general strategy
to select which exception type to look for? In the past, I was catching
exce
Hi Thomas,
Getting rid of the string length limitations would need some major refactoring.
There is currently no good workaround, other than avoiding such long selections.
In this particular case, the script could use cmd.select_list() instead of
concatenating the index list to a string:
c
Greetings,
I am trying to run focus_alignment command (
https://pymolwiki.org/index.php/Focus_alignment) from within a Python
script with my own custom selection (I include CA+CB atoms instead of only
CA as in the default). Sometimes the selection is very large and PyMOL
cannot hand it:
Selector-
