I am wondering how to select molecules in Pymol.
The system I am studying has an amide of interest (oleamide) in oil (At
the moment just dodecane molecules).
I have seen in the manual how to select individual elements, but is it
possible to select either the Nitrogen or oxygen in my oleamide
hi all:
could any one tell me how to get the coordinates for a specific atom in
a particular amino acid using pymol commands
is their a commant with can list the coordinates for each aminoacid in
a protein molecule?? \
kindly clarify, thanking you in advance.
- mohan
Hi Mohan,
You can use iterate_state, which would be the pymol approach:
coords = {}
iterate_state 1,n. ca,coords[i]=(x,y,z)
Or you can take a lower level approach; the python one:
for i in cmd.get_model('n. ca').atom:
print i.coord
cmd.get_model builds you a ChemPy model from a given
Hi Michael,
Have you had a look at 'help selections'?
I am wondering how to select molecules in Pymol.
What exactly do you mean here? The molecule for a certain atom? The
molecule as in 'chain' (if it's a macromolecule), or as in 'residue'
(if it's a ligand/cofactor/solvent)?
The system I am
In newer PyMOLs this is as simple as:
print cmd.get_atom_coords(oneAtom)
where 'oneAtom' is an object or selection of one atom in PyMOL.
For example,
load $TUT/1hpv.pdb
print cmd.get_atom_coords(A/30/CA);
-- Jason
On Mon, Mar 22, 2010 at 9:04 AM, Tsjerk Wassenaar tsje...@gmail.com wrote:
Hi
Of course, you could just use the .pdb file as a text file:
grep CA .pdb | cut -f 2,4,7,8,9
will get you the amino acid number, the amino acid identity, and x,y,z
coordinates for the CA.
Jed
Jason Vertrees wrote:
In newer PyMOLs this is as simple as:
print cmd.get_atom_coords(oneAtom)
2010/3/22 Tatsiana Kirys nus...@mail.ru:
I've installed it. But i have even more errors now:
nus...@linux-3mpg:~/Download/trunk/pymol python setup.py build install
bunch of stuff
/usr/lib/gcc/i586-suse-linux/4.4/../../../../i586-suse-linux/bin/ld: cannot
find -lpng
collect2: ld
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Hi Jed,
On Mon, 22 Mar 2010 10:23:34 -0400 Jed Goldstone jgoldst...@whoi.edu wrote:
Of course, you could just use the .pdb file as a text file:
grep CA .pdb | cut -f 2,4,7,8,9
will get you the amino acid number, the amino acid identity, and x,y,z
coordinates for the CA.
Often this
Of course you're all correct - Thierry Fischmann already emailed me to
correct me :)
I hadn't actually tested anything (mea culpa). I was just trying to
point out for those of us less familiar with python that there were
alternatives to doing this relatively simple thing outside of pymol.
But it is very doable using grep/cut, you'll just have to use the -b
flag that allows you to cut columns:
grep CA .pdb | cut -b 13-26,30-54
Cheers,
Tsjerk
On Mon, Mar 22, 2010 at 3:58 PM, Robert Campbell
robert.campb...@queensu.ca wrote:
Hi Jed,
On Mon, 22 Mar 2010 10:23:34 -0400 Jed
Looks like you don't have the python-devel package. This provides the
header files such as Python.h you need for compiling python modules.
-David
On Fri, Mar 19, 2010 at 5:50 PM, Tatsiana Kirys nus...@mail.ru wrote:
Dear All,
i'm trying to install pymol on suse. i've checked
i dont know why i'm so helpless, but i still got a bunch of messengees:
running build
running build_py
running build_ext
building
The system I am studying has an amide of interest (oleamide) in oil (At
the moment just dodecane molecules).
I have seen in the manual how to select individual elements, but is it
possible to select either the Nitrogen or oxygen in my oleamide
molecules, and then select all atoms which are
thank you for helping. I;ve installed it. But when i run it, is says
OpenGL graphics engine:
GL_VENDOR: Mesa Project
GL_RENDERER: Software Rasterizer
GL_VERSION: 1.4 (2.1 Mesa 7.6)
Traceback (most recent call last):
File /usr/local/lib/python2.6/site-packages/pymol/__init__.py, line
You need to install Python Megawidgets (Pmw)
http://sourceforge.net/projects/pmw/files/Pmw/
-- Jason
2010/3/22 Tatsiana Kirys nus...@mail.ru:
thank you for helping. I;ve installed it. But when i run it, is says
OpenGL graphics engine:
GL_VENDOR: Mesa Project
GL_RENDERER: Software
17th Annual Tcl/Tk Conference (Tcl'2010)
http://www.tcl.tk/community/tcl2010/
October 11 - 15, 2010
Hilton Suites/Conference Center
Chicago/Oakbrook Terrace, Illinois, USA
Important Dates:
Abstracts and proposals due August 1, 2010
Notification to authors August 15, 2010
WIP and BOF
You must install Python megawidgets. Look for pmw on google, download and
follow installation instructions (it is easy). I don't remember if you must
build install again pymol after that or not. This is the last error you
will have!!
By the way, your PC is using MESA libraries. If you are using
yes, thank you very much, it works now!
Mon, 22 Mar 2010 14:49:02 -0400 письмо от Jason Vertrees
jason.vertr...@schrodinger.com:
You need to install Python Megawidgets (Pmw)
http://sourceforge.net/projects/pmw/files/Pmw/
-- Jason
2010/3/22 Tatsiana Kirys nus...@mail.ru:
thank you
THANK YOU, it works
Mon, 22 Mar 2010 17:54:05 +0100 письмо от Hugo Gutierrez de Teran
hugo.te...@usc.es:
You must install Python megawidgets. Look for pmw on google, download and
follow installation instructions (it is easy). I don't remember if you must
build install again pymol
On Mon, Mar 22, 2010 at 4:27 AM, Harry M. Greenblatt
harry.greenbl...@weizmann.ac.il wrote:
BSD
Dear Jason,
I have tried to implement what you suggested, but seeing as I haven't
made a movie in PyMOL in a long time (and was never very expert at it), I
don't seem to have got it working.
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