Re: [ccp4bb] improper rotation matrix
If you have a copy of MOLEMAN2 lying around, you can use the XYz DIstort command to do exactly this: http://xray.bmc.uu.se/usf/moleman2_man.html#S77 --Gerard On Mon, 12 Mar 2018, Franck Coste wrote: Hi all, I'd like to apply an improper rotation matrix to PDB files but it seems it's not allowed in pdbset. Does anyone know a program where I could do this ? Thanks in advance. Regards, Franck. -- 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] improper rotation matrix
I am struggling to see why one would want to apply an improper rotation, which I thought was defined as rotation plus reflection. Det=-1. Truly bad things happen to ones amino acids. Unless you had the coordinates from a small mol in one chiral arrangement, and wanted it in the other? But in that case just changing the sign of all the atomic coordinates would achieve the same. Adrian Sent from my iPhone > On 12 Mar 2018, at 12:43, Tristan Croll wrote: > > Assuming you have a good reason for this, you can apply any arbitrary > transform fairly straightforwardly in ChimeraX. In the console > (Tools/General/Shell), and assuming your model is the only one loaded: > > m = session.models.list()[0] > import numpy > transform_matrix = numpy.array([[r11, r12, r13, tx], [r21, r22, r23, ty], > [r31, r32, r33, tz]]) > from chimerax.core.geometry import Place > transform = Place(matrix=transform_matrix) > m.atoms.coords = transform.moved(m.atoms.coords) > > ... which could of course be extended into a script to loop over many > models/transforms with a bit more work. > > Hope this helps, > > Tristan > >> On 2018-03-12 10:24, Phil Evans wrote: >> The command ROTATE in pdbset should allow to apply any valid rotation >> matrix, ie determinant = +1.0 >> Anything else will distort the coordinates >>> On 12 Mar 2018, at 10:13, Franck Coste wrote: >>> Hi all, >>> I'd like to apply an improper rotation matrix to PDB files but it seems >>> it's not allowed in pdbset. Does anyone know a program where I could do >>> this ? >>> Thanks in advance. >>> Regards, >>> Franck. >>> -- >>>
Re: [ccp4bb] improper rotation matrix
Assuming you have a good reason for this, you can apply any arbitrary transform fairly straightforwardly in ChimeraX. In the console (Tools/General/Shell), and assuming your model is the only one loaded: m = session.models.list()[0] import numpy transform_matrix = numpy.array([[r11, r12, r13, tx], [r21, r22, r23, ty], [r31, r32, r33, tz]]) from chimerax.core.geometry import Place transform = Place(matrix=transform_matrix) m.atoms.coords = transform.moved(m.atoms.coords) ... which could of course be extended into a script to loop over many models/transforms with a bit more work. Hope this helps, Tristan On 2018-03-12 10:24, Phil Evans wrote: The command ROTATE in pdbset should allow to apply any valid rotation matrix, ie determinant = +1.0 Anything else will distort the coordinates On 12 Mar 2018, at 10:13, Franck Coste wrote: Hi all, I'd like to apply an improper rotation matrix to PDB files but it seems it's not allowed in pdbset. Does anyone know a program where I could do this ? Thanks in advance. Regards, Franck. --
Re: [ccp4bb] improper rotation matrix
Maybe you could turn your distorting matrix into into a fake symmetry operator? On 12 March 2018 at 10:24, Phil Evans wrote: > The command ROTATE in pdbset should allow to apply any valid rotation > matrix, ie determinant = +1.0 > > Anything else will distort the coordinates > > > > On 12 Mar 2018, at 10:13, Franck Coste > wrote: > > > > Hi all, > > > > I'd like to apply an improper rotation matrix to PDB files but it seems > it's not allowed in pdbset. Does anyone know a program where I could do > this ? > > > > Thanks in advance. > > > > Regards, > > > > Franck. > > -- > > >
Re: [ccp4bb] improper rotation matrix
The command ROTATE in pdbset should allow to apply any valid rotation matrix, ie determinant = +1.0 Anything else will distort the coordinates > On 12 Mar 2018, at 10:13, Franck Coste wrote: > > Hi all, > > I'd like to apply an improper rotation matrix to PDB files but it seems it's > not allowed in pdbset. Does anyone know a program where I could do this ? > > Thanks in advance. > > Regards, > > Franck. > -- >
