distance filters
Issue #701
new
Hi,
I have >1000 PDB from a prediction tool that I want to filter using known NOE's (ie distance restraints between two atoms). Is this utility built into bio3d? Do you have any recommendations on how to utilize bio3d to filter a large dataset of PDB files based on experimental data?
Bio3D does not have a built-in function to filter structures using NOE restraints. But, if you are familiar with R, it shouldn’t be too difficult to write a script to do it.
For dealing with large structural data: Are these structures the same protein? If so, you can concatenate them into one PDB file, each structure as an individual “MODEL” record. Then, you can read it with
pdb <- read.pdb(…, multi=TRUE). All coordinates are saved in the matrixpdb$xyzfor you to easily parse. Alternatively, you can save the structures as a binary trajectory file (e.g., NetCDF, .dcd) using VMD and read them using relevant Bio3D functions.
Hope it helps.