Warren,
Thanks for the h-bond tip. A related question, I was wondering if PyMOL
can protonate ligands on its own. In other words can it perceive the
atom-type. I have been trying to integrate a perception algorithm
similar to babel with other programs and would like to do it with PyMOL
as well. However I could not find details/examples on the attach
command in the manual (I did not look through the code yet, I am a new
user). So can you please give an example of attach command.
Well, the reason I wanted the parser was some programs like AMBER
(leap) requires different names for linked cysteines. It would be
helpful to get this information from the PDB file since it has it. Also
there is other information in the PDB file which can be useful if
displayed somewhere on the viewer like sequence etc. In other words a
hierarchy window similar to the web-lab viewer. Maybe it does and just
have not figured out how to make it work it.
In any case I think this is a terrific program and although I have just
started using it I am realizing its potential.
Kaushik.
On Friday, September 20, 2002, at 05:24 PM, DeLano, Warren wrote:
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
# 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:war...@sunesis.com
Warren L. DeLano, Ph.D.
-----Original Message-----
From: Kaushik Raha [mailto:kxr...@psu.edu]
Sent: Friday, September 20, 2002 1:36 PM
To: pymol-users@lists.sourceforge.net
Subject: Re: [PyMOL] Disulfide Bonds
A similar question: Does PyMOL have a PDB file parser that can read
disulphide linkages from the file and connect the atoms or one has to
explicitly issue bond commands. Also, can PyMOL display
hydrogen bonds
without the user having to write out a list?
thanks,
Kaushik Raha.
Penn State University.
On Friday, September 20, 2002, at 04:07 PM, DeLano, Warren wrote:
Alex,
If the sulfurs are within disulfide bonding distance,
PyMOL should
connect them by default. If this is not happening, please
send me the
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:war...@sunesis.com
Warren L. DeLano, Ph.D.
-----Original Message-----
From: Alex Morla [mailto:alex...@uic.edu]
Sent: Friday, September 20, 2002 8:48 AM
To: pymol-users@lists.sourceforge.net
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.
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