If a model is modified, the "rebuild" command does not always update the
surface. For example,
show lines, theProtein and not elem H
show surface
show lines, elem H
rebuild
The surface does not change. But if I now,
hide surface
show surface
t
Hello,
Take the following scenario. I have two cube files, the first one holds some
values of a function (electron localization function),
while in the second cube for each value in the first cube file i can have
either one of the numbers from 0 to 6.
After loading the first cube file in Pymol, I c
Jakob,
Try,
rotate [xAxis, yAxis, zAxis], someAngle, yourSelection
For example:
# grab a protein
fetch 1cll, async=0
# zoom & color
zoom i. 20-25
color blue, i. 20-25
# rotate some selected atoms
rotate [0.25, 0.4, 0], -12.5, i. 20-25
Cheers,
-- Jason
On Mon, Jun 28, 2010 at 11:14 AM, Jakob
Prija,
Electrostatics can be done through the APBS plugin
(http://pymolwiki.org/index.php/APBS). Michael Lerner has done a
fantastic job on that.
There are many scripts online that will help you calculate the solvent
accessible surface area (for various features), but for any loaded
object you c
Greetings,
First, after a reading a recent post that piqued my interest, I
implemented a script that will draw a plane through backbone atoms.
This could be useful to anyone wanting to see or teach the planarity
of the main chain atom. The script and example images are here:
http://pymolwiki.org/
Hello
I want to calculate electrostatic potential and solvant accessible area of
protein.
How can I do the above mentioned calculations using Pymol.
Please guide me using tutorials.
Thank you
--
Prija Ponnan
--
This SF.n
Hi Lies,
here a few among many options:
http://www.salilab.org/modeller/
http://swissmodel.expasy.org/
http://modbase.compbio.ucsf.edu/modbase-cgi/index.cgi
On Mon, Jun 28, 2010 at 06:15, Lies Van Nieuwenhove
wrote:
> Dear Sir, Ms,
>
> I don't know enough about bio-informatics but I need a
Dear Sir, Ms,
I don't know enough about bio-informatics but I need a molecular model and
pdb file for 2 proteins. I only have the protein sequence and a protein that
can be used for homology modelling.
Could you tell me if and how I can do this in pymol?
Thank you,
Sincerely yours,
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thanks, how can I flip a selection of atoms around an arbitrary axis?
2010/6/28 Edward A. Berry
> Jakob Nielsen wrote:
> > Dear Pymol users,
> > I would like to modify a protein pdb file with a "crankshaft" flip,
> > which is the anti-correlated double change: psi(i-1) += delta and phi(i)
> > -=
thanks for your help, it is difficult for me to imagine the effect of this
operation, but I have read a few places that this should be the effect, but
I might be wrong. Anyway, what I want is using two consecutive C-alphas as
"flexible hinges" rotating the peptide plane between this two C-alphas
ar
Jakob Nielsen wrote:
> Dear Pymol users,
> I would like to modify a protein pdb file with a "crankshaft" flip,
> which is the anti-correlated double change: psi(i-1) += delta and phi(i)
> -= delta. Such a change should leave the protein coordinates unchanged
> effecting only atoms in residues i-1 a
Dear Jakob,
On Mon, 28 Jun 2010 15:32:59 +0200 Jakob Nielsen
wrote:
> I would like to modify a protein pdb file with a "crankshaft" flip, which
> is the anti-correlated double change: psi(i-1) += delta and phi(i) -= delta.
> Such a change should leave the protein coordinates unchanged effecting
Dear Pymol users,
I would like to modify a protein pdb file with a "crankshaft" flip, which
is the anti-correlated double change: psi(i-1) += delta and phi(i) -= delta.
Such a change should leave the protein coordinates unchanged effecting only
atoms in residues i-1 and i. However implementation i
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