Hello I want to know how PyMol does Structural allignment. I am writing a
python script to allign protein structures(from MD simulations) and
eventually calculate RMSD. Please can anyone provide me a source code or a
helping material.Thanx in advance.
Hira Batool
Student of BS-Bioinformatics
Hi Osvaldo,
unfortunately PyMOL doesn't handle to set dihedrals in rings, so you have to
break the ring first. Consider this:
def set_phi(resi, phi, state=1, quiet=1):
x = cmd.index('(first (resi %s and guide)) extend 2 and name C+N+CA' % resi)
try:
a = cmd.get_model(x[2], state)
Hi Syeda,
you have a lot of options in PyMOL to do this. For full-atom RMSD fit on
topologically identical molecules (since it's MD, I guess this is the case),
use the "fit" command:
PyMOL> fit mobile, target
Otherwise, use "align" or "super":
PyMOL> align mobile, target, cycles=0
>From a py
Dear PyMOL users,
After upgrading my notebook to Win7 from XP 'save' function started to function
differently. Before PyMOL would save everything in the directory where I'd
launch it from. Now, by default, it goes to Win32. In some cases I can use
'save as' option and after few clicks get to th
Thanks Thomas,
I tried your solution (adapted to my code) and now everything is working.
def set_phi(res_num, res_name, phi):
if res_num != 0 and res_name != 'PRO':
cmd.set_dihedral('resi %s and name C' % (res_num-1), 'resi %s and
name N' % res_num, 'resi %s and name CA' % res_num, '
Dear all,
I'm getting this error when typing "python setup.py"
Traceback (most recent call last):
File "setup.py", line 327, in
pyogl_extension("pymol.opengl.gl.openglutil_num",
["contrib/pyopengl/openglutil_num.c"]),
File "/usr/lib64/python2.7/distutils/core.py", line 105, in setup
Hi Quyen,
this was an error in setup.py, sorry. Fixed in r4045.
Cheers,
Thomas
On Oct 4, 2013, at 8:43 PM, QT wrote:
> Dear all,
>
> I'm getting this error when typing "python setup.py"
>
> Traceback (most recent call last):
> File "setup.py", line 327, in
> pyogl_extension("pymol.op
