Xmipp

xmipp_volume_from_pdb (v3.0)

Usage

Covert a PDB file to a volume.

Parameters

-i <pdb_file>
File to process
-o <fn_root>
Root name for output
--sampling <Ts=1>
Sampling rate (Angstroms/pixel)
--high_sampling_rate <highTs=0.08333333>
Sampling rate before downsampling
--size <output_dim=-1>
Final size in pixels (must be a power of 2, if blobs are used)
--centerPDB
Center PDB with the center of mass
--blobs
Use blobs instead of scattering factors
--poor_Gaussian
Use a simple Gaussian adapted to each atom
--fixed_Gaussian <std=-1>
Use a fixed Gausian for each atom with this standard deviation If not given, the standard deviation is taken from the PDB file
--intensityColumn <intensity_type=occupancy>
Where to write the intensity in the PDB file
where <intensity_type> can be:
  • occupancy
  • Bfactor Valid values: occupancy, Bfactor

Examples and notes

Sample at 1.6A and limit the frequency to 10A
   xmipp_volume_from_pdb -i 1o7d.pdb --sampling 1.6
   xmipp_transform_filter -i 1o7d.vol -o 1o7dFiltered.vol --fourier low_pass 10 raised_cosine 0.05 --sampling 1.6

User's comments

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