Hi,
I've done this by rendering two images (actually 4 to get stereo). One without
the CGOs and one with them. Then I overlaid them with photoshop and changed the
trasnparency of the CGO containing layer. I just used triangles and it looked
rather nice.
~Lari~
Hi,
does anyone know what file type to save text as (in OS X) for a .pml
file? I can't get PyMol to recognize RTF, etc...
thanks
Avram Slovic
Hi
I am trying to combine a scene with annotations spanning several lines.
So far something like
scene new, store, message=Line1\nLine2
would produce some nice coloration effects but not a newline character.
I was able to use the api function to do the trick
mesg=line1\nline2
Carsten,
Hmm...
Unfortunately, the PyMOL command language currently provide any way of
expressing a newline character, so you will need to use the API form of
the scene command. Note that it is perfectly legal to use that form in
a .pml file as follows, without an intervening variable:
I have a logitech MX700 Cordless Optical Mouse that claims to be a 3-
button mouse, but I can never get it to produce the results provided
for 3-button viewing or editing by PyMOL. Perhaps I do not have it
configured correctly (I cannot find a clue in the instructions or in
simple
Hi
I have installed version 0.98 on my new dual processor machine running
windows XP. Pymol runs fine, but when trying to load a large PDB file
(~4Mb), the program crashes and I get a runtime error:
This application has requested the Runtime to terminate it in an
unusual way
Does anyone have
Hi,
I've just realized that through the mutagenesis wizard you can
view/select different conformations for a sidechain. I've been playing
around, and it seems that the conformations are selected according to a
backbone-independent rotamer library. Am I correct? Which library has
been used?
It looks like a CGO (compiled graphics object) behind the molecule, then
rendered using pov-ray, probably a script floating around to do this
somewhere on the internets.
Corinne Zeitler wrote:
Hi,
I was wondering if anyone knows how to produce the type of image in
Pymol that is on the Pymol
I use a cheap microsoft optical (or basic optical) usb mouse on linux,
so it should work on your macosx.
If you want something more configurable under macosx and don't want to
destroy the Appleness of your computer with an MS mouse then this
might work for you
Hi Corinne, Sabuj,
You're right with regards to the CGO. An example script (written by
Gareth Stockwell) can be found at
http://md.chem.rug.nl/~tsjerk/Scripts/walls.py. With regards to the
raytracing, don't be fooled, I'd say this was Pymol's internal
raytracer :)
Hope it helps,
Tsjerk
On
Xavier,
PyMOL 0.99beta09 and earlier use a crude backbone-independent rotamer
library.
However, current development versions (PyMOL 0.99beta10 on up) now
provide both the Dunbrack backbone-dependent and backbone-independent
rotamers.
Cheers,
Warren
--
Warren L. DeLano, Ph.D.
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