Hi Santrupti,
In Chemoinformatics "heavy atoms" are all non-hydrogen atoms. In
crystallography, "heavy atoms" could mean the atoms used for experimental
phasing, like selenium.
I hope these examples answer your questions:
# non-hydrogen RMSD
align prot1 & not hydro, prot2 & not hydro, cycles=0
# SE atom RMSD
align prot1 & elem SE, prot2 & elem SE, cycles=0
# backbone RMSD
align prot1 & name N+C+CA+O, prot2 & name N+C+CA+O, cycles=0
# pairwise RMSD for a lot of structures, using Python API
python
import itertools
models = cmd.get_object_list()
for m1, m2 in itertools.combinations(models, 2):
s1 = m1 + " & name N+C+CA+O"
s2 = m2 + " & name N+C+CA+O"
a = cmd.align(s1, s2, cycles=0)
print("Backbone RMSD for {} and {}: {}".format(m1, m2, a[0]))
python end
Please also read https://pymolwiki.org/index.php/Align
Cheers,
Thomas
> On Aug 30, 2018, at 10:42 PM, Santrupti Nerli <sne...@ucsc.edu> wrote:
>
> Hi,
>
> I want to calculate pairwise RMSD for heavy atoms and backbone atoms.
>
> I see that for backbone, I can use name n+c+ca+o. But, do the same atoms also
> represent heavy atoms?
>
> What are the differences between backbone and heavy atoms? How to compute
> pairwise RMSD for a lot of structures? Can I use align here?
>
> Thank you very much.
--
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.
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