Hi,
I have 2 monitors running out of an ATI Radeon 8500 on redhat 8.0 using
the summit accelerated Xserver from Xig.com for hardware stereo on one
of the monitors.
I use the dual view function, so 1 big desktop (1 "screen" on 2
monitors)
Very hardware accelerated!
cheers
Dan
On 12 Nov
Warren, I want to be able to use those useful
definations every time I load pymol. I wonder how to
edit the general startup script pymol in order to do
that? By the way, I also want pymol to show distance
when I click two atoms. Thank you.
Eric
> Quoting "Warren L. DeLano"
> :
>
> > Richard,
>
I just tried Summit Xserver, it is definitly a looot fast. But ... in
single head mode. They claim they support Matrox Millennium G450
multihead. In dual view 1600x1200 mode, the pymol won't lanuch, gave out:
GLUT: fatal error in pymol, visual with neccessary capbilities not found.
But in dual vi
Eric,
PyMOL will source startup files in your home directory -- just
put your commands in there:
On Mac/Unix:
$HOME/.pymolrc (for PyMOL commands)
$HOME/.pymolrc.py (for Python code)
On Windows:
%HOMEPATH%\pymolrc(for PyMOL commands)
%HOMEPATH%\pymorc.py (for Python code)
T
Robert Schwarzenbacher, PhD
The Joint Center for Structural Genomics
phone: 858 822 3637
Hi there,
Is there a way to define the clipping planes for only one object in a
scene.
For example I only want to clip the surface while not affecting residues
shown in stick.
Or alternatively is there a w
Is it possible to get pymol to calculate surface area for a defined
object? For instance, can it calculate surface area occupied by arginines.
Thanks,
Joel
Joel M. Harp
Vanderbilt University
To calculate surface area for a defined object from the PyMOL command
line type:
print cmd.get_area("obj")
where obj is the name of your object.
for arginines:
create ARG, resn ARG
print cmd.get_area("ARG")
Kaushik.
On Wednesday, November 12, 2003, at 05:10 PM, Harp, Joel M wrote:
Is it
Joel,
Yes, PyMOL does have this capability, but it is immature and not
routinely validated.
The basic concepts are:
1) "get_area selection" command will return the effective surface area
of the dots that you would see from "show dots, selection". This is a
discrete approximation -- not an ex
Close, but it depends on whether you want the surface area of the
residues alone, or in the context of the molecule.
load protein.pdb
get_area resn arg
will be less than
create arg_object, resn arg
get_area arg_object
This is because the first example will give you only the exposed area of
Hi Warren,
I found out that it is possible to write out AMBER style atom name
formats with hydrogens added using the Chempy which is pretty neat.
However it seems like this does not recognize the N-terminal residue
for adding hydrogens. Is that still the case? I am still using PyMOL
088 (I w
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