define angle between groups of atom 'planes' for refinement restraint?
Hi all I was wondering if there was language in the monomer restraint libraries (.cif) or a custom phenix.refine geometry restraint a that defines an angle between two planes, where each plane is a group of coplanar atoms. Thanks! F --------------------------------------------- Francis E. Reyes M.Sc. 215 UCB University of Colorado at Boulder
Hi Francis, I'm not sure it exists (unless someone added it recently). However, you can do this using distance restraints (custom bonds). You just need to figure out bonds between which atoms to create so they mimic the angle restraint you are interested in. Pavel
Hi all
I was wondering if there was language in the monomer restraint libraries (.cif) or a custom phenix.refine geometry restraint a that defines an angle between two planes, where each plane is a group of coplanar atoms.
Thanks!
F
Francis
If you have the two planar groups you just need to define a torsion
with the first three atoms in plan-1 and the last three atoms in
plan-2. Ensure there are no conflicting torsions or chirals. I'd be
happy to take a look at you files once you've tried to edit it to your
specs. I'd used REEL to edit the file.
Cheers
Nigel
NB. Any files sent to me will be held in strictest confidence.
On Thu, Nov 10, 2011 at 7:46 AM, Francis E Reyes
Hi all
I was wondering if there was language in the monomer restraint libraries (.cif) or a custom phenix.refine geometry restraint a that defines an angle between two planes, where each plane is a group of coplanar atoms.
Thanks!
F
--------------------------------------------- Francis E. Reyes M.Sc. 215 UCB University of Colorado at Boulder
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Nope.
Maybe you can do it by restraining distances between pairs of atoms?
1st plane: A - B - C - D - E
2nd plane: V - W - X - Y - Z
Distance restraints: A-V, B-W, C-X, D-Y, E-Z
In combination with other restraints this may do what you want.
Ralf
On Thu, Nov 10, 2011 at 7:46 AM, Francis E Reyes wrote: Hi all I was wondering if there was language in the monomer restraint libraries
(.cif) or a custom phenix.refine geometry restraint a that defines an
angle between two planes, where each plane is a group of coplanar atoms. Thanks! F ---------------------------------------------
Francis E. Reyes M.Sc.
215 UCB
University of Colorado at Boulder _______________________________________________
phenixbb mailing list
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It's not what you are asking for her, but just to point out (FYI) that if you want to _measure_ the angle between planes from coordinates, (or other things like distance from defined planes etc), there's an old program in CCP4 called geomcalc which has flexible options for defining such things Phil On 10 Nov 2011, at 15:46, Francis E Reyes wrote:
Hi all
I was wondering if there was language in the monomer restraint libraries (.cif) or a custom phenix.refine geometry restraint a that defines an angle between two planes, where each plane is a group of coplanar atoms.
Thanks!
F
--------------------------------------------- Francis E. Reyes M.Sc. 215 UCB University of Colorado at Boulder
_______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb
participants (5)
-
Francis E Reyes -
Nigel Moriarty -
Pavel Afonine -
Phil Evans -
Ralf Grosse-Kunstleve