RE: [PyMOL] Disulfide Bonds

[DeLano, W. <wa...@su...>]

Regarding H-bonds. Funny you should ask -- Hans and I just worked out =
how to do this here at Sunesis...

There isn't a built-in function yet (it is coming), but you can show =
H-bonds between two objects using  atom selections so long as hydrogens =
are present in both molecules.  If you don't have hydrogens, you can use =
h_add on the proteins or provide ligands with valence information and =
then use h_add.

Two examples are below.  For clarity, they draw dashes between the heavy =
atoms and hide the hydrogens.

# EXAMPLE 1: Show hydrogen bonds between protein=20
# and docked ligands (which must have hydrogens)

load target.pdb,prot
load docked_ligs.sdf,lig

# add hydrogens to protein

h_add prot

select don, (elem n,o and (neighbor hydro))
select acc, (elem o or (elem n and not (neighbor hydro)))
dist HBA, (lig and acc),(prot and don), 3.2
dist HBD, (lig and don),(prot and acc), 3.2
delete don
delete acc
hide (hydro)

hide labels,HBA
hide labels,HBD

# EXAMPLE 2
# Show hydrogen bonds between two proteins

load prot1.pdb
load prot2.pdb

h_add prot1
h_add prot2

select don, (elem n,o and (neighbor hydro))
select acc, (elem o or (elem n and not (neighbor hydro)))
dist HBA, (prot1 and acc),(prot2 and don), 3.2
dist HBD, (prot1 and don),(prot2 and acc), 3.2
delete don
delete acc
hide (hydro)

hide labels,HBA
hide labels,HBD

# NOTE: that you could also use this approach between two
# non-overlapping selections within a single object.

As far as SSBOND records go, no PyMOL doesn't currently parse =
these...does it need to?

Warren

--
mailto:wa...@su...
Warren L. DeLano, Ph.D.

> -----Original Message-----
> From: Kaushik Raha [mailto:kx...@ps...]
> Sent: Friday, September 20, 2002 1:36 PM
> To: pym...@li...
> Subject: Re: [PyMOL] Disulfide Bonds
>=20
>=20
> A similar question: Does PyMOL have a PDB file parser that can read=20
> disulphide linkages from the file and connect the atoms or one has to=20
> explicitly issue bond commands. Also, can PyMOL display=20
> hydrogen bonds=20
> without the user having to write out a list?
>=20
> thanks,
>=20
> Kaushik Raha.
> Penn State University.
>=20
> On Friday, September 20, 2002, at 04:07 PM, DeLano, Warren wrote:
>=20
> > Alex,
> >
> > 	If the sulfurs are within disulfide bonding distance,=20
> PyMOL should=20
> > connect them by default.  If this is not happening, please=20
> send me the=20
> > PDB file so I can take a look-see.
> >
> >       Otherwise, you can use the "bond" command to attach them:
> >
> > bond 24/sg,26/sg
> > bond 56/sb,99/sg
> >
> > unpick
> >
> > (unpick will hide the bond baton which gets displayed)
> >
> > Cheers,
> > Warren
> >
> > --
> > mailto:wa...@su...
> > Warren L. DeLano, Ph.D.
> >
> >> -----Original Message-----
> >> From: Alex Morla [mailto:al...@ui...]
> >> Sent: Friday, September 20, 2002 8:48 AM
> >> To: pym...@li...
> >> Subject: [PyMOL] Disulfide Bonds
> >>
> >>
> >> Sorry if this is a novice question, but how do I display the
> >> disulfide bonds
> >> in my models?
> >>
> >> Thanks, and keep up the great work!!
> >>
> >> Alex Morla
> >> Univ. of Illinois, Rockford.
> >>