Michael,
Welcome to PyMOL! I don't think PyMOL is a replacement for SPDV -- the
feature sets are distinct, and you should be able to use both together.
Yes, I think "align" is what you want.
After...
load x.pdb
load y.pdb
This would do an all-matched-atoms alignment:
align x, y
And this wou
Hi there,
I'm switching to pymol from swiss pdb viewer because I simply needed
better quality final images, but one of the coolest features of spdbv
was the 'magic fit' where a single mouse click would superpose overall
alignment of, say, the same protein from two different bacterial
organisms
Jack,
I posted some instructions onto the list a while back, but it's pretty
simple:
# load the PHI map and model
load phimap.phi
load prot.pdb
# show a surface
show surface, prot
# create a color ramp based on the potential
ramp_new ramp, phimap
# now apply that color_ramp to the protein s
Hi,
will PyMol only save images at 72dpi, or can I dial that up somehow?
thanks
Avram Slovic
--
Avram M. Slovic
Biochemistry and Molecular Biophysics
University of Pennsylvania
420 Curie Blvd.
1010 Stellar Chance Bldg.
Philadelphia, PA 19104
L:215-898-3496
Michael,
That's because sheet's aren't flat -- cartoons aren't reality.
set cartoon_flat_sheets, off
set cartoon_smooth_loops, off
In order to force the cartoons to follow the true CA trace.
Cheers,
Warren
--
mailto:war...@delanoscientific.com
Warren L. DeLano, Ph.D.
Principal Scientist
DeLa
Friday, November 7, 2003, 8:50:13 AM, you wrote:
MB> ...I built a model of my protein of interest using 'set
cartoon_fancy_helices,1'...but sidechains of MB>amino acids that
reside on 'strand' regions appear to float in midair and do not
connect to the strand MB>backbone...
On Friday, Novembe
Hi all,
I'm just starting to try out PyMOL (fink package 0.90-2, running
through Apple's X11beta2, on a Lombard G3PB, MacOS 10.2.4).
Its much easier to learn that I thought it would be! Well done Warren,
and codevelopers! One puzzling thing I've noticed: when I build a
model of my protein of i
On Fri, Nov 07, 2003 at 01:52:42PM +, Tom Walsh wrote:
>
> Hi,
>
> I'm trying to start Pymol (version 0.93) in a Python script,
> using the first method described in __init__.py i.e.:
>
> import pymol
>
> pymol.finish_launching()
>
> I've set the PYTHONPATH and PYMOL_PATH variables as req
Hi,
I'm trying to start Pymol (version 0.93) in a Python script,
using the first method described in __init__.py i.e.:
import pymol
pymol.finish_launching()
I've set the PYTHONPATH and PYMOL_PATH variables as required
but I get this error message:
-
Traceback (innermost last):
File "py
