Loading in a list of `xyz` coordinates as a "dummy" PDB file
Issue #855
new
Is it possible to load in an arbitrary set of coordinates xyz (an N x 3 array) and treat it like a PDB object for modal analysis? We are interested in modeling macromolecules whose discrete positions have been observed via imaging. These structures are on the nanometer scale, not Angstroms. We dug into Bio3D’s manual but wasn’t able to find an appropriate function that can load in arbitrary coordinates!
An adjacent question is: what is the recommended protocol for modifying force fields, to accommodate structures of different scale (nanometers, not Angstroms)?
Thank you for taking time to read this.
You may need to program a little bit to preprocess the coordinate file for bio3d to recognize. R has generic functions to read any data format. After loading the data into R, you may simply use
as.xyz()to convert it. If you want to embed the coordinates into a PDB object, you need a topology file, such as a PDB, that matches the dimension of the coordinate.
I am not very sure about the second question. Are you talking about the normal mode analysis force field? I would recommend converting the “nanomemter” to “angstrom” and so everything is consistent. You can do it by simply multiplying the coordinate by 10.
Let me know if you still have questions. If so, you may provide an example and see what we can help.