Assign distance between every atom and an axis or plane to an attribute
Hi, I would like to iterate over all atoms in a model, measure the distance between each atom and a predefined axis or plane in the session, and assign the distance to an attribute associated with the atom. For bonus points I would like to do the same for two models (the same protein in different conformations), and then calculate the difference in this distance for matched pairs of atoms. The first part of this - iterating over every atom - I know how to do, more or less, in the scripting interface (I am assuming there is no way to do this kind of "iterate/run command/ assign command output to attribute" operation in the attribute calculator). But how do I measure the distance between an atom and a selected plane/axis, and then assign it to an attribute that I can use for example in Render by Attribute? I can see how to measure the distance between pairs of atoms, but not between atoms and a plane or axis. Cheers, Oli
Hi Oli, If the object (centroid, axis, or plane) was created with Axes/Planes/Centroids or the “define” command, you can specify it by identifier in the “distance” command, for example: distance c1 c2 - measure the distance between centroid c1 and centroid c2 distance signed p2 :313.a@o - measure the signed distance between plane p2 and atom O in residue 313 of chain A <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/distance.html> I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco On Feb 24, 2016, at 5:21 AM, Oliver Clarke <olibclarke@gmail.com> wrote:
Hi,
I would like to iterate over all atoms in a model, measure the distance between each atom and a predefined axis or plane in the session, and assign the distance to an attribute associated with the atom. For bonus points I would like to do the same for two models (the same protein in different conformations), and then calculate the difference in this distance for matched pairs of atoms.
The first part of this - iterating over every atom - I know how to do, more or less, in the scripting interface (I am assuming there is no way to do this kind of "iterate/run command/ assign command output to attribute" operation in the attribute calculator).
But how do I measure the distance between an atom and a selected plane/axis, and then assign it to an attribute that I can use for example in Render by Attribute? I can see how to measure the distance between pairs of atoms, but not between atoms and a plane or axis.
Cheers, Oli _______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
This will assign attributes such as “dist_p1”, “dist_p2”, “dist_c1" etc. to every atom for every axis/plane/centroid in your session: from StructMeasure.Geometry import geomManager from chimera import openModels, Molecule for item in geomManager.items: for m in openModels.list(modelTypes=[Molecule]): for a, d in zip(m.atoms, item.pointDistances([a.xformCoord() for a in atoms])): setattr(a, “dist_” + item.id, d) For the bonus point part, if the atoms of your conformers are in the same respective order in their input files, then their m.atoms will be in the same order in Chimera. So, if the models are ‘m1’ and ‘m2’: for a1, a2 in zip(m1.atoms, m2.atoms): a1.diff_p1 = a2.diff_p1 = a1.dist_p1 - a2.dist_p1 —Eric Eric Pettersen UCSF Computer Graphics Lab
On Feb 24, 2016, at 5:21 AM, Oliver Clarke <olibclarke@gmail.com> wrote:
Hi,
I would like to iterate over all atoms in a model, measure the distance between each atom and a predefined axis or plane in the session, and assign the distance to an attribute associated with the atom. For bonus points I would like to do the same for two models (the same protein in different conformations), and then calculate the difference in this distance for matched pairs of atoms.
The first part of this - iterating over every atom - I know how to do, more or less, in the scripting interface (I am assuming there is no way to do this kind of "iterate/run command/ assign command output to attribute" operation in the attribute calculator).
But how do I measure the distance between an atom and a selected plane/axis, and then assign it to an attribute that I can use for example in Render by Attribute? I can see how to measure the distance between pairs of atoms, but not between atoms and a plane or axis.
Cheers, Oli _______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
participants (3)
-
Elaine Meng -
Eric Pettersen -
Oliver Clarke