Re: [PyMOL] asymmetric transformation matrices
Hi Thomas, Say, the first system is x and the second y, where y=R(x+s) is the first transformation. Then the reverse transformation follows as y = R(x + s) y = Rx + Rs Rx = y - Rs x = t(R)(y-Rs) Note that that is also equal to: x = t(R)y - s Hope it helps, Tsjerk On Mon, Nov 9, 2009 at 1:09 AM, Thomas Evangelidis te8...@mbg.duth.gr wrote: Dear pymol users, I noticed something strange when superimposing 2 opposite pairs of chains. E.g. DEBUG: template 1BQG_A query 2MUC_A Query Transformation: X2 = +0.86747*(X1+2.29751) + -0.49574*(Y1+60.99794) + -0.04181*(Z1+64.71239) Y2 = -0.49701*(X1+2.29751) + -0.85983*(Y1+60.99794) + -0.11697*(Z1+64.71239) Z2 = +0.02204*(X1+2.29751) + +0.12225*(Y1+60.99794) + -0.99226*(Z1+64.71239) DEBUG: template 2MUC_A query 1BQG_A Query Transformation: X2 = +0.86747*(X1+30.95128) + -0.49701*(Y1+61.15895) + +0.02204*(Z1+56.70381) Y2 = -0.49574*(X1+30.95128) + -0.85983*(Y1+61.15895) + +0.12225*(Z1+56.70381) Z2 = -0.04181*(X1+30.95128) + -0.11697*(Y1+61.15895) + -0.99226*(Z1+56.70381) Although looking at the rotation matrices one is the transpose of the other, the translation vectors are not opposite. Can someone explain that? -- Let Crystal Reports handle the reporting - Free Crystal Reports 2008 30-Day trial. Simplify your report design, integration and deployment - and focus on what you do best, core application coding. Discover what's new with Crystal Reports now. http://p.sf.net/sfu/bobj-july ___ 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 -- Tsjerk A. Wassenaar, Ph.D. Junior UD (post-doc) Biomolecular NMR, Bijvoet Center Utrecht University Padualaan 8 3584 CH Utrecht The Netherlands P: +31-30-2539931 F: +31-30-2537623 -- Let Crystal Reports handle the reporting - Free Crystal Reports 2008 30-Day trial. Simplify your report design, integration and deployment - and focus on what you do best, core application coding. Discover what's new with Crystal Reports now. http://p.sf.net/sfu/bobj-july ___ 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] spectrum
Hi Mark and Sean, On Sat, 07 Nov 2009 10:05:59 -0500 Sean Law magic...@hotmail.com wrote: Sorry for the earlier confusion. I think I found a hackish way of getting a gray spectrum: snip Sean's extensive explanation I know I'm biased, since I wrote the color_b.py script, but I fail to see what is difficult about typing: color_b selectionname, gradient=user, user_rgb=[.2,.2,.2,.5,.5,.5,.8,.8,.8] In order to colour selectionname in a gray spectrum that goes from 20% gray, has a midpoint of 50% gray and ends at 80% gray (where 20% gray is the same as the colour called gray20, i.e. close to black and 80% gray is almost white). Cheers, Rob -- Robert L. Campbell, Ph.D. Senior Research Associate/Adjunct Assistant Professor Botterell Hall Rm 644 Department of Biochemistry, Queen's University, Kingston, ON K7L 3N6 Canada Tel: 613-533-6821Fax: 613-533-2497 robert.campb...@queensu.cahttp://pldserver1.biochem.queensu.ca/~rlc -- Let Crystal Reports handle the reporting - Free Crystal Reports 2008 30-Day trial. Simplify your report design, integration and deployment - and focus on what you do best, core application coding. Discover what's new with Crystal Reports now. http://p.sf.net/sfu/bobj-july ___ 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] asymmetric transformation matrices
As Tsjerk pointed out, there was a mistake in the code. Just for the
record this is the right function:
pdb2entry = { 1ONE: 1ONE_A, 2ONE: 2ONE_A }
# a function to measure Ca distances of oposite pairs of superimpossed
chains (the proteins must have the same aa composition)
def check_for_symmetry(tstruct, qstruct):
# align the pair
cmd.fetch(tstruct)
cmd.extract(pdb2entry[tstruct]+1, tstruct + and chain +
pdb2entry[tstruct][-1:] + and not hetatm)
cmd.fetch(qstruct)
cmd.extract(pdb2entry[qstruct]+1, qstruct + and chain +
pdb2entry[qstruct][-1:] + and not hetatm)
cmd.delete(tstruct)
cmd.delete(qstruct)
print Aligning +pdb2entry[tstruct]+1+ with +pdb2entry[qstruct]+1
cmd.align(pdb2entry[tstruct]+1, pdb2entry[qstruct]+1)
#cmd.do(cealign +pdb2entry[qstruct]+1, +pdb2entry[tstruct]+1)
# align the symmetric pair
cmd.fetch(tstruct)
cmd.extract(pdb2entry[tstruct]+2, tstruct + and chain +
pdb2entry[tstruct][-1:] + and not hetatm)
cmd.fetch(qstruct)
cmd.extract(pdb2entry[qstruct]+2, qstruct + and chain +
pdb2entry[qstruct][-1:] + and not hetatm)
print Aligning +pdb2entry[qstruct]+1+ with +pdb2entry[tstruct]+1
cmd.align(pdb2entry[qstruct]+2, pdb2entry[tstruct]+2)
#cmd.do(cealign +pdb2entry[qstruct]+2, +pdb2entry[tstruct]+2)
# measure distances
pymol.stored.protein_dict = {}
cmd.iterate(pdb2entry[tstruct]+1, stored.protein_dict[(chain,resi)]=1)
Residues = pymol.stored.protein_dict.keys()
Residues.sort()
RMSD = 0
for res in Residues:
chain = res[0]
resi = res[1]
dist1 = cmd.distance('tmp',pdb2entry[tstruct]+1 and chain
+chain+ and resi +resi+ and name ca,pdb2entry[qstruct]+1 and
chain +chain+ and resi +resi+ and name ca)
dist2 = cmd.distance('tmp',pdb2entry[tstruct]+2 and chain
+chain+ and resi +resi+ and name ca,pdb2entry[qstruct]+2 and
chain +chain+ and resi +resi+ and name ca)
print The difference in distance betweem residue IDs ,
resi, is : ,dist1, -,dist2, = ,dist1-dist2
RMSD += (dist1-dist2)**2
RMSD = sqrt(RMSD/len(Residues))
print RMSD of distances between identical residues in 1ONE x
2ONE and this in 2ONE x 1ONE: , RMSD
check_for_symmetry(1ONE, 2ONE)
After this correction the RMSD falls to 2.06853295972e-06, which a
reasonably good number.
--
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[PyMOL] Fwd: asymmetric transformation matrices
Hmm, this should've been replied to the list. The info may be useful to others. Tsjerk -- Forwarded message -- From: Tsjerk Wassenaar tsje...@gmail.com Date: Mon, Nov 9, 2009 at 5:02 PM Subject: Re: [PyMOL] asymmetric transformation matrices To: Thomas Evangelidis te8...@mbg.duth.gr Hi Thomas, You're not doing what you think you're doing. # a function to measure Ca distances of oposite pairs of superimpossed chains (the proteins must have the same aa composition) def check_for_symmetry(tstruct, qstruct): # align the pair cmd.fetch(tstruct) You fetch the first structure, which is placed in state 1 cmd.extract(pdb2entry[tstruct]+1, tstruct + and chain + pdb2entry[tstruct][-1:] + and not hetatm) You extract part of that structure, which is removed from the state cmd.fetch(qstruct) You fetch the other structure, which is also loaded into state 1 cmd.extract(pdb2entry[qstruct]+1, qstruct + and chain + pdb2entry[qstruct][-1:] + and not hetatm) You extract part of that structure print Aligning +pdb2entry[tstruct]+1+ with +pdb2entry[qstruct]+1 cmd.align(pdb2entry[tstruct]+1, pdb2entry[qstruct]+1) #cmd.do(cealign +pdb2entry[qstruct]+1, +pdb2entry[tstruct]+1) # align the symmetric pair cmd.fetch(tstruct) You fetch the first structure again, but this time it's appended to state 2 cmd.extract(pdb2entry[tstruct]+2, tstruct + and chain + pdb2entry[tstruct][-1:] + and not hetatm) You try to extract chain A again. But that is tried on state 1, while that state has no chain A anymore. The object is empty! cmd.fetch(qstruct) Same story for the other object cmd.extract(pdb2entry[qstruct]+2, qstruct + and chain + pdb2entry[qstruct][-1:] + and not hetatm) Empty object... Then in the next part you calculate the RMSD of distances in an empty object (all 0) and the aligned one. That RMSD ends up close to the actual RMSD from the alignment (restricted on CA atoms: 0.280), for obvious reasons. I hope this helps, Tsjerk -- Tsjerk A. Wassenaar, Ph.D. Computational Chemist Medicinal Chemist Neuropharmacologist -- Tsjerk A. Wassenaar, Ph.D. Computational Chemist Medicinal Chemist Neuropharmacologist -- Let Crystal Reports handle the reporting - Free Crystal Reports 2008 30-Day trial. Simplify your report design, integration and deployment - and focus on what you do best, core application coding. Discover what's new with Crystal Reports now. http://p.sf.net/sfu/bobj-july ___ 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] Spectrum
Hi Sean, On Mon, 09 Nov 2009 10:58:53 -0500 Sean Law magic...@hotmail.com wrote: Robert, I would have to agree with you. I've used many of your scripts and have also learned a lot from them and think that the color B script is pretty robust and helpful. Thanks. I could be wrong but I remember the original poster commenting about using the min max settings from the spectrum command and I wonder if that is used to control the min/max of B-factor values to color (so that any values outside of the range of min and max will be colored the extreme min/max color values). Of course, I'm sure it's just as easy to add a couple of lines of extra code into your script to account for that (if it isn't already there). The color_b.py script has options called minimum and maximum just like the spectrum command. These are used to select the range of B-values to colour. So (using PDB code 1dvi as an example) if your actual B-values are between 2 and 55.98 and you set the minimum to 10 and maximum to 50, then use 8 bins (just to get nice numbers here!), by typing: color_b minimum=10, maximum=50, nbins=8 You'll see the following output from the color_b.py script: Minimum and Maximum B-values: 2.0 55.975422 Color select: n. ca and (b15 or b = 15) Color select: n. ca and b15 Color select: n. ca and b20 Color select: n. ca and b25 Color select: n. ca and b30 Color select: n. ca and b35 Color select: n. ca and b40 Color select: n. ca and b45 So yes, anything within the lowest range and below will be in colour 1 and anything within the highest range and above will be in colour 8. Cheers, Rob -- Robert L. Campbell, Ph.D. Senior Research Associate/Adjunct Assistant Professor Botterell Hall Rm 644 Department of Biochemistry, Queen's University, Kingston, ON K7L 3N6 Canada Tel: 613-533-6821Fax: 613-533-2497 robert.campb...@queensu.cahttp://pldserver1.biochem.queensu.ca/~rlc -- Let Crystal Reports handle the reporting - Free Crystal Reports 2008 30-Day trial. Simplify your report design, integration and deployment - and focus on what you do best, core application coding. Discover what's new with Crystal Reports now. http://p.sf.net/sfu/bobj-july ___ 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
