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
http://pymolwiki.org
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 *
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 at
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 cartoon_tr
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
Dear pymol users,
I try to install pymol in Linux system as following
(1) download pymol-v1.5.0.1.tar.bz2 and decompress it to /opt directory.
(2) go into /opt/pymol/setup directiry and enter the command "setup.sh"
Then I see the install success information:
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 wrote:
> Dear pymol users,
>
> I try to install pymol in Linux system as following
>
> (1) download pymol-v1.5.0.1.tar.bz2 and decompress it to /
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 multip
