[PyMOL] Structural Allignment in PyMol
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 Biosciences Department COMSATS Institute of Information Technology Islamabad, PAKISTAN-- October Webinars: Code for Performance Free Intel webinars can help you accelerate application performance. Explore tips for MPI, OpenMP, advanced profiling, and more. Get the most from the latest Intel processors and coprocessors. See abstracts and register > http://pubads.g.doubleclick.net/gampad/clk?id=60134791&iu=/4140/ostg.clktrk___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] unable to change phi angle of proline
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).atom[0]
if a.name != "CA":
raise IndexError
except IndexError:
print " missing atoms"
return
if a.resn == "PRO":
bondargs = (x[1], "resi %s and name CD" % resi)
cmd.unbond(*bondargs)
cmd.set_dihedral(x[0], x[1], x[2], x[3], phi, state, quiet)
if a.resn == "PRO":
cmd.bond(*bondargs)
Hope that helps.
Cheers,
Thomas
On Oct 2, 2013, at 8:28 PM, Osvaldo Martin wrote:
> Hi everybody,
>
> I can´t change the phi angle of proline using the function below. It works
> for all other amino acids. If quiet = 0, it prints the value of the variable
> "phi" (i.e. the value that the phi_angle should adopt). The phi angle of
> proline is always around ~11.0
>
> def set_phi(res_num, phi):
> if res_num != 0:
> 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, 'resi %s and name C' %
> res_num, phi, state=1, quiet=1)
>
> Thanks in advance.
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Re: [PyMOL] Structural Allignment in PyMol
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 python script, syntax looks like this:
from pymol import cmd
cmd.fit("mobile", "target")
cmd.align("mobile", "target", cycles=0)
http://pymolwiki.org/index.php/Fit
http://pymolwiki.org/index.php/Rms
http://pymolwiki.org/index.php/Align
http://pymolwiki.org/index.php/Super
Cheers,
Thomas
On Oct 4, 2013, at 5:29 AM, Syeda Hira Batool wrote:
> 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
> Biosciences Department
> COMSATS Institute of Information Technology
> Islamabad, PAKISTAN
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[PyMOL] saving
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 the desired destination. But for, say, 'save whatever.fasta' it doesn't work. My current PyMOL version is 1.5.0.5 32-bit, though the notebook is 64-bit. Unfortunately 64-bit version doesn't work at all on my machine. If you wonder why I'm not using 1.6.0.0 version is because it has issues with APBS. Hope to get some help on the "save" command. Thank you. Vaheh Oganesyan, PhD Antibody development and protein engineering 1 MedImmune Way, Gaithersburg, MD 20878 www.medimmune.com To the extent this electronic communication or any of its attachments contain information that is not in the public domain, such information is considered by MedImmune to be confidential and proprietary. This communication is expected to be read and/or used only by the individual(s) for whom it is intended. If you have received this electronic communication in error, please reply to the sender advising of the error in transmission and delete the original message and any accompanying documents from your system immediately, without copying, reviewing or otherwise using them for any purpose. Thank you for your cooperation. -- October Webinars: Code for Performance Free Intel webinars can help you accelerate application performance. Explore tips for MPI, OpenMP, advanced profiling, and more. Get the most from the latest Intel processors and coprocessors. See abstracts and register > http://pubads.g.doubleclick.net/gampad/clk?id=60134791&iu=/4140/ostg.clktrk ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] unable to change phi angle of proline
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, 'resi %s and name C' %
res_num, phi, state=1, quiet=1)
if res_num != 0 and res_name == 'PRO':
cmd.unbond('resi %s and name N' % res_num, 'resi %s and name CD' %
res_num)
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, 'resi %s and name C' %
res_num, phi, state=1, quiet=1)
cmd.bond('resi %s and name N' % res_num, 'resi %s and name CD' %
res_num
Cheers,
Osvaldo.
On Fri, Oct 4, 2013 at 9:50 AM, Thomas Holder wrote:
> 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).atom[0]
> if a.name != "CA":
> raise IndexError
> except IndexError:
> print " missing atoms"
> return
> if a.resn == "PRO":
> bondargs = (x[1], "resi %s and name CD" % resi)
> cmd.unbond(*bondargs)
> cmd.set_dihedral(x[0], x[1], x[2], x[3], phi, state, quiet)
> if a.resn == "PRO":
> cmd.bond(*bondargs)
>
> Hope that helps.
>
> Cheers,
> Thomas
>
> On Oct 2, 2013, at 8:28 PM, Osvaldo Martin wrote:
> > Hi everybody,
> >
> > I can´t change the phi angle of proline using the function below. It
> works for all other amino acids. If quiet = 0, it prints the value of the
> variable "phi" (i.e. the value that the phi_angle should adopt). The phi
> angle of proline is always around ~11.0
> >
> > def set_phi(res_num, phi):
> > if res_num != 0:
> > 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, 'resi %s and name
> C' % res_num, phi, state=1, quiet=1)
> >
> > Thanks in advance.
>
>
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[PyMOL] Can not compile r4044
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
attrs['script_name'] = os.path.basename(sys.argv[0])
IndexError: list index out of range
How can I resolve this problem?
Best,
Quyen
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Re: [PyMOL] Can not compile r4044
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.opengl.gl.openglutil_num",
> ["contrib/pyopengl/openglutil_num.c"]),
> File "/usr/lib64/python2.7/distutils/core.py", line 105, in setup
> attrs['script_name'] = os.path.basename(sys.argv[0])
> IndexError: list index out of range
>
> How can I resolve this problem?
>
> Best,
> Quyen
--
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