Re: [ccp4bb] dihedral backbone generator
On Mon, 2012-11-12 at 13:47 -0500, Ed Pozharski wrote: > Does anyone know of a tool that would generate a protein molecule > backbone from a set of phi/psi angles? > For the record. Thanks to all who responded. Here is what I found out: 1. MOLEMAN works best. The most cumbersome part is to transfer phi/psi from one structure to another. If anyone is ever interested, I have a bash script that does it in automated manner, all you need to do is to provide the list of residues to be corrected. 2. Other options include TINKER and fortran code by Edward Berry. I couldn't use the second one because it does not do omegas and I have some cis-prolines in the model. TINKER is an awesome MD package from what I can tell. I abandoned it for moleman after concluding that it takes integers values, but I didn't investigate if that is actually true and if it is really a big problem (see below). 3. On the scientific side, it appears that updating phi/psi angles is not enough. Basically, even if I transfer all the angles from one model to another, models match well only in the N-terminal domain. The C-terminal domain which in this case undergoes about 45 degrees closure-type rotation is very much messed up. Perhaps the conclusion is that changes other than phi/psi contribute significantly. Which is, on the second thought, not that surprising. 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
Re: [ccp4bb] dihedral backbone generator
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 21.7110 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 28.5212 9 8 BAD 14 OD1 ASN A 2 1.228 120.881 -44.498 1.00 27.401312 9 BAD 15 ND2 ASN A 2 1.329 116.425 136.488 1.00 30.351312 9 BAD 16 N PHE A 3 1.330 117.436 121.273 1.00 22.0910 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 21.611610 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 ! **
Re: [ccp4bb] dihedral backbone generator
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). The underlying assumption of such a program is that the phi, psi (and omega) angles define the structure, and vice versa. So if you have the before and after structures, you sort of have the answer already- given that change in dihedrals, you will get that change in structure, although I'm not sure if it makes sense to ask whether the strutural chage results from the change in dihedrals or vice versa. I guess you want to keep all dihedrals the same except the half-dozen suspects, and see if you get the same change. dihedrals elsewhere would be expected to change to reoptimize to new contacts and avoid clashes, but maybe the principle change could still be recognized with the rest of the molecule frozen. I have such a code (fortran) that reads a list of phi,psi angles and makes the corresponding backbone (poly gly or polyala I think). Unfortunately it sets all omega angles to exactly 180? (trans), and that by itself may make a significant change in conformation. http://sb20.lbl.gov/berry/for/construct.f written for g77 but gfortran seems to compile. input file format is 1 line for each residue: residue #, phi, psi 1 -49 -26 2 -49 -26 3 -49 -26 4 -49 -26 5 -49 -26 6 -49 -26 7 -49 -26 8 -49 -26 9 -49 -26 10 -49 -26 11 -49 -26 12 -49 -26 o usage: construct < 3-10helix.inp new file is called construct.pdb chain is A EAB 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
[ccp4bb] dihedral backbone generator
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
