>1. Alignment and Translations/Rotations (Joshua L. Adelman)
> rotation of the protein). Ideally what I want to do is do a single
> alignment of the last frame of the first sequence with the first frame
> of the second sequence (they should be nearly identical structures)
> and
> then get the
> Is there a way for me to define a plane of atoms say 4 Nitrogens in a
> heme complex and then determine how far out-of-plane the Fe atom is? If
so
> either in Pymol or another program I'd love to know the secret.
Hello Kristl,
have you tried to just individually add up the x, y, and z coordina
>1. color by b-factor (Smita Bhatia)
> --__--__--
> Message: 1
> Date: Thu, 25 Sep 2003 18:49:51 -0400 (EDT)
> From: Smita Bhatia
> To: pymol-users@lists.sourceforge.net
> Subject: [PyMOL] color by b-factor
> Hello all,
> I have colored and rendered a pdb file in pymol according to the
> b-
Dear PyMol community,
During analyzing the water structure of a protein I was wondering if PyMol
is capable to select buried water molecules. Since the surface waters occupy
clefts it would be nice to see if there is a regular distribution inside of
the protein as well.
So is it possible to make
Hello fellows,
this is not a real question since I found a workaround but I would like to
know wether this is a bug in PyMOL or just the result of the Python
selection algorithm.
Well, the problem was arising by playing around with Mr. DeLanos example
script to produce the contact surface of two
Hello PyMol fellows,
I was trying to put two different electron density figures side by side
using the method described by Warren Delano some time ago.
In short terms (e.g.):
origin molecule-1
rotate y,60,molecule-1
origin molecule-2
rotate y,-60, molecule-2
1. It seems to work only for rot
Dear PyMol user,
I've seen a cover illustration made using PyMol (Nucl. Acid. Res. february
issue 2003) and was exicited to see that is it possible to show missed residues
in a curved (!) dotted line manner. How one can achieve this? So far I thought
the way is to bridge the two ends of missed pro
Dear PyMol users,
I'm looking for a way to create a hemisphere of given xyz coordinates and a
specified radius. It seems to me a job for a CGO object. So maybe somebody
has been created such a object already and would like to share the details.
Thanks,
Bartholomeus
Dear PyMol users,
1.
I'm puzzled with a coloring problem while coloring a protein molecule
accordingly to its secondary structure by using 'discrete color' option:
If there are a helix and/or strand adjacent together (e.g. helix from 1-10
and sheet from 11-20) the small pseudo-loop region between
Hello subscribers out there!
Robert Campbell and Warren Delano gave some useful hints to cgo label
orientation a few days ago. But so far, I didn't succed yet to get the
labels in plane of the molecule. It was barely possible to rotate and
translate the cgo label [cmd.rotate/translate, thanks to R
Hello there!
I followed mailing list instructions to create cgo based labels via a python
script. Unfortunately, the labels are not in plane but more like
perpendicular. So is there a way to alter the orientation of such cgo
labels. I think one could apply pymol's "set_view" matrix to the labels t
Dear all!
I've encountered several questions while playing aroung with PyMOL. Maybe
there is someone who could provide some help?
1. dash options
It seems that all the "dash" settings (e.g. "dash_length", "dash_with",
"dash_radius") are global modifiers and cannot be assigned to specific
interac
to be a global modifier since an local assigment (set ...=0,
"residues xyz") does not work.
Thank you!
Greetings,
Bartholomeus Kuettner
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