On Mon, Mar 22, 2010 at 4:27 AM, Harry M. Greenblatt
wrote:
> BS"D
> 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. Here is what I did, on my Ma
THANK YOU, it works
Mon, 22 Mar 2010 17:54:05 +0100 письмо от Hugo Gutierrez de Teran
:
> 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.
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
:
> You need to install Python Megawidgets (Pmw)
>
> http://sourceforge.net/projects/pmw/files/Pmw/
>
> -- Jason
>
> 2010/3/22 Tatsiana Kirys :
> >
> > thank you for helping. I;ve installed it. B
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 need to install Python Megawidgets (Pmw)
http://sourceforge.net/projects/pmw/files/Pmw/
-- Jason
2010/3/22 Tatsiana Kirys :
>
> 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
>
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 43
>> 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 whi
This error:
creating /usr/local/lib/python2.6
error: could not create '/usr/local/lib/python2.6': Permission denied
Means that you must run the compilation command as root (or with su
privileges)
The command:
python setup.py build install
Can be decomposed into:
python setup.py build (this part ha
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
> 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 wrote:
> >
> >
> > Dear All,
> >
> > i'm trying to install pymol on suse. i've checked t
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
wrote:
> Hi Jed,
>
> On Mon, 22 Mar 2010 10:23:34 -0400 Jed Goldstone wrote:
>
>> Of
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.
Apol
Hi Jed,
On Mon, 22 Mar 2010 10:23:34 -0400 Jed Goldstone 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 will work, but
--
Download Intel® Parallel Studio Eval
Try the new software tools for yourself. Speed compiling, find bugs
proactively, and fine-tune applications for parallel performance.
See why Intel Parallel Studio got high marks dur
2010/3/22 Tatsiana Kirys :
> 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 returned 1
Assuming there are separate residues for each molecule, do they have a
residue name defined? So you can do something like "select r. OLE"?
-David
On Mon, Mar 22, 2010 at 7:56 AM, Michael Doig wrote:
> I am wondering how to select molecules in Pymol.
>
> The system I am studying has an amide of
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
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 wrote:
> Hi Mohan,
>
> You
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 a
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 selecti
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
---
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
mo
23 matches
Mail list logo
