If you have an old copy of MOLEMAN (not MOLEMAN2!) lying around, this can be
done very easily (ever since it was programmed on Valentine's Day 1993, in
fact - I even remember who my Valentine was :-) - see:
http://xray.bmc.uu.se/usf/moleman_man.html#S13
- READ your original model (PDB file)
- EXPOrt as an internal coordinates file
- then edit the file to modify the torsion angles
- IMPOrt the edited file back into MOLEMAN
- WRITe as a PDB file again
Your molecule will now have the first atom at (0,0,0) and the x-axis along the
first bond etc., so use LSQMAN to superimpose it back onto the starting model
if you like.
You can download source and executables for MOLEMAN, LSQMAN etc. here:
http://xray.bmc.uu.se/markh/usf/
Example: read and export 3CBS - the first few lines of the internal
coordinates file will look like this:
BAD 1 N PRO A 1 0.000 0.000 0.000 1.00 31.62 0 0
0
BAD 2 CA PRO A 1 1.481 0.000 0.000 1.00 31.16 1 0
0
BAD 3 C PRO A 1 1.520 106.499 0.000 1.00 29.86 2 1
0
BAD 4 O PRO A 1 1.233 121.844-171.561 1.00 30.08 3 2
1
BAD 5 CB PRO A 1 2.511 34.402-114.723 1.00 31.63 3 2
1
BAD 6 CG PRO A 1 1.540 94.603 100.767 1.00 32.44 5 3
2
BAD 7 CD PRO A 1 1.535 100.667 -80.739 1.00 31.82 6 5
3
BAD 8 N ASN A 2 1.325 114.622 8.082 1.00 27.88 3 2
1
the torsion of atom 8 is the psi torsion of residue 1 (8 degrees)
BAD 9 CA ASN A 2 1.452 122.416-179.619 1.00 25.61 8 3
2
this torsion is omega of residue 1 (-180)
BAD 10 C ASN A 2 1.528 107.300-118.190 1.00 23.37 9 8
3
this torsion is phi of residue 2 (-118)
BAD 11 O ASN A 2 1.227 119.971 -58.453 1.00 21.71 10 9
8
BAD 12 CB ASN A 2 1.529 109.276 122.858 1.00 27.00 9 8
3
BAD 13 CG ASN A 2 1.510 112.642-171.476 1.00 28.52 12 9
8
BAD 14 OD1 ASN A 2 1.228 120.881 -44.498 1.00 27.40 13 12
9
BAD 15 ND2 ASN A 2 1.329 116.425 136.488 1.00 30.35 13 12
9
BAD 16 N PHE A 3 1.330 117.436 121.273 1.00 22.09 10 9
8
this torsion is psi of residue nr 2 (121)
BAD 17 CA PHE A 3 1.466 120.994 179.948 1.00 21.61 16 10
9
this is omega of residue nr 2 (180)
etc.
--Gerard
On Mon, 12 Nov 2012, Ed Pozharski wrote:
Does anyone know of a tool that would generate a protein molecule
backbone from a set of phi/psi angles?
I actually had written my own code to do this eons ago, but those were
days of Matlab. My actual question is if in a particular protein the
conformational change observed upon substrate binding can be accounted
for by half a dozen residues changing their backbone conformation. I
only expect to do it once, and thus trying to save time and not
translate my old code (looks more like a cipher now).
Cheers,
Ed.
--
After much deep and profound brain things inside my head,
I have decided to thank you for bringing peace to our home.
Julian, King of Lemurs
Best wishes,
--Gerard
******************************************************************
Gerard J. Kleywegt
http://xray.bmc.uu.se/gerard mailto:ger...@xray.bmc.uu.se
******************************************************************
The opinions in this message are fictional. Any similarity
to actual opinions, living or dead, is purely coincidental.
******************************************************************
Little known gastromathematical curiosity: let "z" be the
radius and "a" the thickness of a pizza. Then the volume
of that pizza is equal to pi*z*z*a !
******************************************************************
