Rongjin,
PyMOL can certainly color surfaces by atom color and other properties.
show surface
color green, elem c
color violet, elem n+o
But Grasp's hydrophobicity function may be doing something more
sophisticated then that...
Cheers,
Warren
> -Original Message-
> From: pymo
Morri has a good point:
The standalone pymol-0_xx-bin-linux-libc6-i386.tgz binary builds
should be capable of running on virtually any current x86-based Linux
system: RH, SUSE, Debian, Fedora, or whatever.
So, if you're having trouble with compilation or use of
distribution-spec
Matt,
Try:
set selection_width, 6
set selection_width, 7
set selection_width, 8
Cheers,
Warren
> -Original Message-
> From: pymol-users-ad...@lists.sourceforge.net
> [mailto:pymol-users-ad...@lists.sourceforge.net] On Behalf Of
> Matthew Zimmerman
> Sent: Thurs
Hi Michael,
I downloaded pymol-0_93-bin-linux-libc6-i386.tgz to my Debian machine.
When I run this copy rather than the .deb version I am able to ray trace
lines without a crash.
Best,
Morri
On Thu, 19 Feb 2004, Michael Banck wrote:
> On Thu, Feb 19, 2004 at 08:22:14AM +0100, Thomas Siegmund w
Alex
try typing:
dss
this will assign secondary structure to your PDB and then the cartoon
will show you the sheets and helices you desire.
Scott
On Feb 19, 2004, at 1:44 PM, ALEX DAJKOVIC wrote:
dear all,
i am new to pymol and i have a question about cartoons.
i saw the demo of cartoon r
Hello --
So I've installed PyMOL onto a new system, and I'm having trouble with
the little pink indicators that pop up when you make a selection. On
this machine they appear to about a single pixel wide, which on a
1280x1024 resolution screen makes them practically invisible! I've tried
pokin
dear all,
i am new to pymol and i have a question about cartoons.
i saw the demo of cartoon ribbons and really liked it, but i haven't
been able to get my protein displayed that way. when i give the command
"cartoon automatic" all i get is a simple line that apparently traces
the backbone of my
John,
Welcome to PyMOL!
> I wish to do the equivalent to the following molscript
> command "line position res-atom A97 OE1 to position res-atom M200 MN;"
dist my_line, a/97/OE1, M/200/MN
hide labels
Also note that PyMOL can draw hydrogen-bonds automatically using its limited
chemical int
Dan,
I think it's fair to say that PyMOL's currently molecular building
capabilities are at the stage of a technology
demonstration/proof-of-concept, but very little effort has yet been expended
toward making them useful for real work.
Part of that is because we don't yet have a
I have searched the manual and forum and cannot find how to draw a hydrogen bond
between two specific atoms.
I wish to do the equivalent to the following molscript command
"line position res-atom A97 OE1 to position res-atom M200 MN;"
which draws a line between two atoms A97 OE1 and Mn200. So no
Hello everyone,
I'm trying to build some model proteins for a diagram showing a protein
unfolding over several steps. I'm using the build function in the 0.95beta10
release. The main problem is that I can't control the angle of the protein
chain, so the chain just goes off in one direction on
* Tsjerk Wassenaar [2004-02-19 04:30] wrote:
>
> Hi Guys,
>
> I seem to have some trouble rendering with povray. The render starts and
> finishes fine, and the image is created, but Pymol crashes with a
> segmentation fault as soon as the rendering is done. The image is not
> loaded to the vi
Michael,
* Michael Banck [2004-02-19 12:24] wrote:
> On Thu, Feb 19, 2004 at 08:22:14AM +0100, Thomas Siegmund wrote:
> > For me PyMol on SuSE 8.2 crashed always when raytracing a line element.
>
> That seems to be identical to Debian Bug #229080
> (http://bugs.debian.org/229080)
>
> > The sto
Hi Guys,
I seem to have some trouble rendering with povray. The render starts and
finishes fine, and the image is created, but Pymol crashes with a
segmentation fault as soon as the rendering is done. The image is not
loaded to the viewer. I'm using povray 3.5 with Pymol 0.93 on a laptop
(Int
On Thu, Feb 19, 2004 at 08:22:14AM +0100, Thomas Siegmund wrote:
> For me PyMol on SuSE 8.2 crashed always when raytracing a line element.
That seems to be identical to Debian Bug #229080
(http://bugs.debian.org/229080)
> The stock compiler on SuSE 8.2 is gcc 3.3 20030226 (prerelease). I
> got
Beware of sweeping statements - I work with nucleic acids (mostly
bound to proteins) and I am continually irritated by the use of * in
nucleic acid names, and I think I qualify as anyone.
Now that the ASCII code has settled down somewhat, " ' " could take
it's rightful place in PDB files,
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