Hi Adam,
The attached script will create covalent bonds for all polar contacts between
two selections.
Example:
run
https://github.com/Pymol-Scripts/Pymol-script-repo/raw/master/get_raw_distances.py
run bond_hbonds.py
fetch 1nz1, async=0
bond_hbonds resi 1-12, resi 12-22
Hope that helps.
Cheers,
Thomas
'''
(c) 2015, Thomas Holder, Schrodinger LLC
License: BSD-2
'''
from pymol import cmd
try:
get_raw_distances
except NameError:
try:
from psico.querying import get_raw_distances
except ImportError:
print 'please install "psico" or download and run the get_raw_distances script from'
print 'http://pymolwiki.org/index.php/get_raw_distances'
@cmd.extend
def bond_hbonds(sele1, sele2, state=1, quiet=1):
'''
DESCRIPTION
Creates covalent bonds for all polar contacts between sele1 and sele2.
Both selections must be in the same object, PyMOL can't create
cross-object bonds.
USAGE
bond_hbonds sele1, sele2 [, state ]
EXAMPLE
fetch 1nz1, async=0
bond_hbonds resi 1-12, resi 12-22
'''
name = cmd.get_unused_name('hbonds')
cmd.distance(name, sele1, sele2, mode=2, state=state)
distances = get_raw_distances(name, state, '(%s) (%s)' % (sele1, sele2))
for idx1, idx2, dist in distances:
cmd.bond(idx1, idx2)
if not int(quiet):
print ' Created %d bonds' % (len(distances))
cmd.delete(name)
On 23 Jun 2015, at 22:51, H. Adam Steinberg <h.adam.steinb...@gmail.com> wrote:
> Hi all,
>
> If I create a string of double-strand DNA, or take a string of double-strand
> DNA or RNA from a structure, is there any automated way to have the bases
> link, AT, UA, GC, so when I manually sculpt or deform the DNA those bases
> would stay together?
>
> I could go through the structure and manually create physical bonds where the
> hydrogen bonds would be, and I’m guessing that would work, but I’m wondering
> if anyone has a script or is there a function that I am unaware of?
>
> Thanks!
>
> H. Adam Steinberg
> 7904 Bowman Rd
> Lodi, WI 53555
> 608/592-2366
--
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.
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