Dear Pymolers.
I am playing around with creating a pdf file with 3 D graphics.
I am saving in *idtf* format, which I convert to *u3d, *and then include in
pdf through latex.
I can do this on windows, but I can't compile IDTFConverter *on linux 64.*
I have made this progress
On 04/03/13 12:21, Troels Emtekær Linnet wrote:
Dear Pymolers.
I am playing around with creating a pdf file with 3 D graphics.
I am saving in *idtf* format, which I convert to *u3d, *and then include
in pdf through latex.
I can do this on windows, but I can't compile IDTFConverter *on
Hello everybody,
I have done several MD simulations with the Martini force field of systems that
contain a small protein and surfactant with GROMACS. It is possible to show
with pymol the secondary structure of the protein with a cartoon representation
and the detergent molecules with beads
Hi Stephane,
You don't have phi/psi angles, so determining secondary structure is a
bit problematic. What you can do is draw a trace through the backbone
beads and set the secondary structure representation explicitly.
You'll have to make sure to exclude connections between chains.
set
Thank you for your help Thomas,
Using your settings I get a lot of partial surfaces
Showing the surface around the Pocket selection like this:
show surface, protein within 0.5 of pocket_selection
worked well but I still see a piece of surface that I really don't want to
show up. I guess I can
Hi Yarrow -
If you add br. to the show surface command, you will get more continuous
surfaces, as the selection will be made by residue instead of by atom.
show surface, br. protein within 0.5 of pocket_selection
If you don't want to show the surface from a particular residue (e.g. if it's
Hi Yeping,
Check out
http://www.pymolwiki.org/index.php/Linux_Install#Compile_and_install.
Cheers,
-- Jason
On Mon, Mar 4, 2013 at 8:17 PM, yp sun sunyep...@yahoo.com.cn wrote:
Dear pymol users,
I try to install pymol in Linux system as following
(1) download pymol-v1.5.0.1.tar.bz2 and
Greetings,
Please also investigate the following settings:
# needs a real atom selection
surface_carve_selection
# distance from the above selection to cull surfaces
surface_carve_cutoff
I looked at your data and there is a small problem. You have a few points
where one atom is mapped to
