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
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
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 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] Building of the Carbon lattice
What does Chimera do? I finally wrote my own c++ tool that let's a TcL script specify a molecule's layout in terms of relevance like bond length and angle. I decided it was worth the effort since I didn't want to look around much for existing stuff and would eventually add my own stuff for analysis. The real decision was to learn python or just use TcL. I guess if I was looking for a tool to generate from a script I'd probably prefer python. Thanks. > Date: Fri, 28 Dec 2012 05:42:27 -0800 > From: jmsstarli...@gmail.com > To: pymol-users@lists.sourceforge.net > Subject: Re: [PyMOL] Building of the Carbon lattice > > Hi Tsjerk! > > This is the example of such lattice which I've built using Chimera! > http://imageshack.us/photo/my-images/543/lattice.png/ > > this is simple model of the Carbon-contained lattice without hydrogens. > So I'd like to build such lattices from different atoms as nodes > defining only atom type as well as number of nodes. > > Also I'd like to simulate this model using PBC so it seems that big > dimensions of such lattice doesn't matter, doesn’t it ? ( It will be > simpler to build smaller symmetric model ) > > James > > -- > 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
[PyMOL] Building of the Carbon lattice
Dear PyMol users! I'd like to build simple 2D lattice model consisted of the Carbon atoms connected by the single bonds. Could you provide me with some script which can build such lattices of the desired dimensions ? Thanks for help James -- Master Visual Studio, SharePoint, SQL, ASP.NET, C# 2012, HTML5, CSS, MVC, Windows 8 Apps, JavaScript and much more. Keep your skills current with LearnDevNow - 3,200 step-by-step video tutorials by Microsoft MVPs and experts. ON SALE this month only -- learn more at: http://p.sf.net/sfu/learnmore_122712 ___ 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
