Dear PyMOL-Users:
Today's questions regarding alignment RMS values suggest to me that I
should re-emphasize what PyMOL is and is not good for:
Please everyone keep in mind that PyMOL is intended to be just a
"molecular graphics" program, to be used for displaying, comparing, and
manipulating mole
Warren,
before I write something incorrect into Methods section, do you think
the overall RMSD returned by align command is a valid criterion to
select which structure of the family is most similar?
Tom
> Tom,
>
> Apologies for the confusion, but there really isn't any way to
> measure ove
Tom,
Apologies for the confusion, but there really isn't any way to measure overall
structural similarity in PyMOL other than pair_fit, but you have to do the work
of explicitly stating which pairs are to be aligned.
The pair_fit selections don't have to be identical, but they do have to
co
Hi Warren,
Now I am more confused. I used align command to measure the overall
RMSD between homologous structures. Apparently align is not
appropriate if not sufficient sequence similarity is present. I later
came across CEalign plugin, which does structure-based
superimposition. This comm
Thank you Adnreas.
I'm straggling with cealign now. When I run it in batch mode I get
"Selector-Error: Invalid selection name" for certain structures, which
in fact are very close homologs, whereas the number of RMSD values I
get varies (sometimes 3, 5, etc). Here's the code:
query_template
Hey Thomas,
if you want to use align anyway, make sure to use the quite=0 option.
The "quiet" option (if present) is set to zero by default for parsed
PyMOL commands, but is not set for Python API calls.
align
is nearly equal to
cmd.align(quiet=0)
Thus, if you want to get rmsd output, include qu
