Re: [PyMOL] Building of the Carbon lattice
Hi James,
just calculate the coordinates and write them out in PDB format, quite
simple task. Try the attached script.
Cheers,
Thomas
James Starlight wrote, On 01/04/13 09:14:
Hi Mike,
Chimera can build such lattices by means of it's build structure
module. On other hand I want to build such 2D lattices
http://imageshack.us/photo/my-images/543/lattice.png/
made from SP3 carbons as the nodes via some automatic script to
obtain lattices with desired dimensions.
James
--
Thomas Holder
PyMOL Developer
Schrödinger Contractor
from numpy import array
s = 'HETATM %4d C03 UNK 1%8.3f%8.3f%8.3f 0.00 0.00 C '
c = array([[ 0.064, 2.851, -1.085 ],
[ 0.260, 1.969, 0.159 ]])
x_shift = array([ 1.67441517, -0.91605961, 1.66504574])
y_shift = array([-0.69477826, -0.40578592, 2.40198410])
out = open('lattice.pdb', 'w')
i = 0
for x in range(10):
for y in range(10):
for v in (c + (x-y/2) * x_shift + y * y_shift):
i += 1
print out, s % (i, v[0], v[1], v[2])
out.close()
try:
from pymol import cmd
cmd.load('lattice.pdb')
except ImportError:
print 'Please load lattice.pdb with PyMOL'
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Re: [PyMOL] Regarding electrostatic potential mapping
Hi Soumya, can you send me (off-list) the map file and pdb file? Cheers, Thomas Soumya Lipsa Rath wrote, On 12/29/12 13:41: Dear Users, I am trying to calculate the electrostatic potential of my protein using Delphi software. However, when I load it to pymol, I see the red colour at the centre and blue in the rest of the part even if I vary the scale. It appears to me as if it is coloring based on the distance from the centre. These are the steps after loading it to pymol: 1) load myfile.pdb 2) load myfile.phi, map 3) ramp_new e_lvl, map, 4) set surface_color, e_lvl, myfile I have attached the Delphi log file for reference also. I would really appreciate any help in this regard. Thanks, Soumya -- Thomas Holder PyMOL Developer Schrödinger Contractor -- Master HTML5, CSS3, ASP.NET, MVC, AJAX, Knockout.js, Web API and much more. Get web development skills now with LearnDevNow - 350+ hours of step-by-step video tutorials by Microsoft MVPs and experts. SALE $99.99 this month only -- learn more at: http://p.sf.net/sfu/learnmore_122812 ___ 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] Building of the Carbon lattice
Where do you get the x_shift and y_shift values? I ended up writing a program to take bond lengths and directions relative to select coord systems to generate periodic or almost periodic things. Right now polyenes but extensible. Is there some program that does this easily? This allows me to write a simple TcL script and reorient the whole molecule by changing one parameter . I don't currently have a way to include library items, like say a methyl group, and I was debating about doing this in python but I wanted to have easy access to lapack etc for later extensions. Thanks. Date: Fri, 4 Jan 2013 11:13:39 +0100 From: spel...@users.sourceforge.net To: jmsstarli...@gmail.com CC: pymol-users@lists.sourceforge.net Subject: Re: [PyMOL] Building of the Carbon lattice Hi James, just calculate the coordinates and write them out in PDB format, quite simple task. Try the attached script. Cheers, Thomas James Starlight wrote, On 01/04/13 09:14: Hi Mike, Chimera can build such lattices by means of it's build structure module. On other hand I want to build such 2D lattices http://imageshack.us/photo/my-images/543/lattice.png/ made from SP3 carbons as the nodes via some automatic script to obtain lattices with desired dimensions. James -- Thomas Holder PyMOL Developer Schrödinger Contractor -- Master HTML5, CSS3, ASP.NET, MVC, AJAX, Knockout.js, Web API and much more. Get web development skills now with LearnDevNow - 350+ hours of step-by-step video tutorials by Microsoft MVPs and experts. SALE $99.99 this month only -- learn more at: http://p.sf.net/sfu/learnmore_122812 ___ 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 -- Master HTML5, CSS3, ASP.NET, MVC, AJAX, Knockout.js, Web API and much more. Get web development skills now with LearnDevNow - 350+ hours of step-by-step video tutorials by Microsoft MVPs and experts. SALE $99.99 this month only -- learn more at: http://p.sf.net/sfu/learnmore_122812 ___ 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] Building of the Carbon lattice
Hi Mike, I simply measured x_shift and y_shift from a cyclohexane fragment. Use the graphical Builder or the fragment command to load stuff from the fragment library. PyMOL fragment cyclohexane Cheers, Thomas Mike Marchywka wrote, On 01/04/13 15:44: Where do you get the x_shift and y_shift values? I ended up writing a program to take bond lengths and directions relative to select coord systems to generate periodic or almost periodic things. Right now polyenes but extensible. Is there some program that does this easily? This allows me to write a simple TcL script and reorient the whole molecule by changing one parameter . I don't currently have a way to include library items, like say a methyl group, and I was debating about doing this in python but I wanted to have easy access to lapack etc for later extensions. Thanks. -- Thomas Holder PyMOL Developer Schrödinger Contractor -- Master HTML5, CSS3, ASP.NET, MVC, AJAX, Knockout.js, Web API and much more. Get web development skills now with LearnDevNow - 350+ hours of step-by-step video tutorials by Microsoft MVPs and experts. SALE $99.99 this month only -- learn more at: http://p.sf.net/sfu/learnmore_122812 ___ 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] Building of the Carbon lattice
well, my point was just that they seem to be orientation sensitive although I didn't look at entire script in any detail and that if you wanted to re-orient the fragment you would have to recalculate these. Nothing difficult but just easier if there was a script that said something like put this thing here with this orientation wrt some prior fragment ( no absolute directions at this point. ) Date: Fri, 4 Jan 2013 15:52:13 +0100 From: spel...@users.sourceforge.net To: marchy...@hotmail.com CC: pymol-users@lists.sourceforge.net Subject: Re: [PyMOL] Building of the Carbon lattice Hi Mike, I simply measured x_shift and y_shift from a cyclohexane fragment. Use the graphical Builder or the fragment command to load stuff from the fragment library. PyMOL fragment cyclohexane Cheers, Thomas Mike Marchywka wrote, On 01/04/13 15:44: Where do you get the x_shift and y_shift values? I ended up writing a program to take bond lengths and directions relative to select coord systems to generate periodic or almost periodic things. Right now polyenes but extensible. Is there some program that does this easily? This allows me to write a simple TcL script and reorient the whole molecule by changing one parameter . I don't currently have a way to include library items, like say a methyl group, and I was debating about doing this in python but I wanted to have easy access to lapack etc for later extensions. Thanks. -- Thomas Holder PyMOL Developer Schrödinger Contractor -- Master HTML5, CSS3, ASP.NET, MVC, AJAX, Knockout.js, Web API and much more. Get web development skills now with LearnDevNow - 350+ hours of step-by-step video tutorials by Microsoft MVPs and experts. SALE $99.99 this month only -- learn more at: http://p.sf.net/sfu/learnmore_122812 ___ 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
