Hi folks,
we are currently facing problems with large VRML files. We have a quite complex
.pse file with several molecules in surface representation. Once we save this
.pse file as VRML it has a size of about 1.2 gigabyte. We could reduce the file
size to about 700mb after combining all
Gzip it and rename the gzipped file with a wrl extension. The VRML standard
specifies that the file can be gzipped and still be readable.
You could also turn down the quality settings for sticks cylinders
cartoons etc.
Good luck!
Darrell
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Another tips is to open the vrml file with 3D modelling
program (for example, Blender) and remove redundant
vertices. It is called Remove Doubles in Blender.
PyMOL tends to define discrete vertices even when their
coordinates are identical.
See http://www.pymolwiki.org/index.php/Blender for
Hi, I am just wondering if there are some useful pymol cgo tutorials
available ? such as how to visualize a 3D triangle object(vertex and
triangle files are known ) in Pymol?
In addition, is the pymol volume visualize (http://pymol.org/volume)
available for educational use ?
Hi Pymol-users,
I'm running a pml-script file to render some images on a remote server, using
pymol 1.4, but I do not get any output at all. And no error message, so it is
hard to troubleshoot, unfortunately.
To reduce the complexity of my script, I have reduced it to basically just
loading
Hi Mike,
I was trying to figure out what to eat today so naturally I started looking
for PDB libraries
with food components. I was looking for garlic related chemicals when I came
across this,
http://molecules.gnu-darwin.org/
which seems to have many pdb files. My question I guess is,
On Mon, Nov 26, 2012 at 8:28 AM, Per Larsson per.lars...@sbc.su.se wrote:
I'm running a pml-script file to render some images on a remote server, using
pymol 1.4, but I do not get any output at all. And no error message, so it is
hard to troubleshoot, unfortunately.
To reduce the complexity
Hi Per,
You'll probably want to use something like this:
# load the file
load http://molecules.gnu-darwin.org/html/00150001_00175000/153919/153919.pdb,
myMolecule
# ray trace and save the image; you need to do this since you're running
# PyMOL headlessly
png ~/foo.png, height=768, width=1024,
Hi Heng,
Hi, I am just wondering if there are some useful pymol cgo tutorials
available ? such as how to visualize a 3D triangle object(vertex and
triangle files are known ) in Pymol?
See https://www.google.com/?q=pymol%20cgo. There is a chapter
subsection on CGOs and also a few scripts the
Dear Thomas
Which version of pymol has python 2.7.
Is it free for academics or I have to purchase license from schrodinger.
Kindly advice.
Many Thanks
Balaji
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Monitor your physical, virtual and cloud infrastructure
I wanted to changed the size of sphere_scale for all atoms in an
object, a selection of Calpha atoms.
I thought I could use the command
set sphere_scale, 5, object_name
this doesnt seem to work and am unclear as to the reason.
thanks
jon
does the command
Dr.
Hi Balaji,
the latest incentive builds (since v1.4, as far as I know) from
Schrödinger are shipped with python 2.7. If you are looking for the
open-source version, Christoph Gohlke has Windows builds with python2.7
as described on the PyMOLWiki:
Hi All,
I recall asking a bunch of questions here about Fuse earlier this year, but
I haven't needed to come back to it until now. Apologies if this has
already been addressed elsewhere.
When I fuse, the two objects are manually attached in a reasonable way,
correct? Does the cartoon
Morphing toward a target .pdb, or end-point analysis and 1) solvent box; or 2)
vacuum?
g...@ohsu.edu
On Nov 26, 2012, at 12:42 PM, Hasan Demirci demirch...@gmail.com wrote:
Dear all,
I am trying to morph two protein-protein complex pdb files.
Everything looks fine but somehow during the
How do I remove myself from the PyMOL users list? I'd like to stop
receiving emails.
Thank you.
M. Hall
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Monitor your physical, virtual and cloud infrastructure from a single
web console. Get in-depth insight into
Hi Mary,
Just a hint for any future lists you might be on: most modern email
lists, including pymol-users, have footers with links to subscription
options. You simply click that to get to a subscription page where you
can unsubscribe.
In this case, I removed you from the list to save you the
Hi Jon,
I'm stumped too, because that's the correct syntax. Can you send me a
copy of your session file?
The only thing I can think of at present is that a selection might need:
set sphere_scale, 5, (selection_name)
Cheers,
-- Jason
On Mon, Nov 26, 2012 at 2:53 PM, Jonathan Grimes
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