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PDBPhantom

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Adrian Quintana edited this page Dec 11, 2017 · 1 revision

PDB Phantom

Purpose

This program allows you to convert a PDB or MMOL file into a Xmipp volume. The conversion can be done in two ways: 1) Using the electron scattering form factors of each atom (this is the default mode); 2) Replacing each atom by a blob.

Electron Form Factor Conversion

Electron form factors are the atom "shapes" seen by the electrons as they travel down the electron microscope. The factors implemented in this program only consider elastic scattering of the traveling electrons. The implementation details of the form factors can be seen at

L.M. Peng, G. Ren, S. L. Dudarev and M. J. Whelan. Robust Parameterization of Elastic and Absorptive Electron Atomic Scattering Factors. Acta Cryst. (1996) A52: 257-276

and

L.M. Peng. Electron atomic scattering factors, Debye-Waller factors and the optical potential for high-energy electron diffraction. J Electron Microscopy (2005) 54(3):199-207.

Blob Conversion

The conversion is carefully performed by replacing all atoms with blobs whose weight and radius are the ones shown in the table below:

Element Radius (Angstroms) Weight
Hydrogen 0.25 1
Carbon 0.70 6
Nitrogen 0.65 7
Oxygen 0.60 8
Phosphorus 1.00 15
Sulfur 1.00 16
Iron 1.40 26
The volume is first sampled at a high sampling rate and then downsampled to the desired sampling rate. The ratio between the desired sampling rate and the high sampling rate is called the downsampling factor M.The downsampling is performed in two steps. The downsampling factor is decomposed as the sum of two components: one that is the largest possible power of 2 and another one that is the rest. The power of two component is downsampled using cubic Bspline pyramid which fulfill the property of producing the low resolution function that is closest in the L2 sense to the original function. Then, the rest of the downsampling is performed by cubic Bspline interpolation which has been shown to be far superior to other interpolation schemes.

Note that this program produces a faithful representation of the PDB file at a given sampling rate but it does not reduce the information content of the output. If you want to filter the output volume to 10 Angstroms, for example, then you must use the xmipp_fourierfilter program. An example is provided below.

Fixed Gaussian conversion

This conversion is thought to convert back from pseudoatoms (see convert_vol2pseudo) to a density volume. The standard deviation of the Gaussians of the pseudoatoms is taken from the PDB header if it is not given through the command line.

Usage


$ pdbphantom ...

Parameters

  • `` Input PDB or MMOL file
  • `` Output rootname. If not provided, the input filename without extensions will be used. Two output files will be created:[output rootname].vol with the output phantom at the desired sampling rate, and`[output rootname]_Fourier_profile.txt`. This second file contains the profile in Fourier space of the atom representing the Hidrogen atom without any sampling. The frequency is continuous and is measured in`1/Angstroms`
  • -sampling_rate [Ts1] =
  • -high_sampling_rate [highTs1/12] = The PDB file is first converted into a volume with a high sampling rate (by default 0.1 Angstroms, take into account that the smallest considered atom is oxygen with a radius of 0.48 Angstroms). Then, it is downsampled to the desired sampling rate (by default, 1 Angstrom, this is the one you should usually manipulate). If the PDB phantom yields a too large volume when sampled at 0.1 Angstroms, the program will abort since it could not allocate all the memory needed. In this case, you have two options: performing the conversion in a computer with more memory; at the expense of aliasing, reduce thehigh_sampling_rate to higher values like 0.2 Angstroms
  • `` Use the blob generation methodology.
  • `` Use the poor Gaussian method.
  • -size [output dim-1] = Dimension of the output volume. It is assumed to be a cube of this dimension and, if the blob option is selected, then it should be a power of 2 because of the pyramid reduction used within the algorithm. If this parameter is not given, then it is automatically computed
  • `` Center the pdb coordinates before converting
  • `` Use the fixed Gaussian method. This sigma is the same one used in the convert_vol2pseudo.
  • -intensityColumn [coloccupancy]= This option is only valid when used with -fixed_Gaussian. Convert_vol2pseudo can write the intensity of each pseudoatom in the "occupancy" column or in the "Bfactor" column. Use this option to tell the program where the intensity is written.

Examples and notes

Converting a PDB file into a Xmipp volume at a sampling rate of 1.6 Angstroms and posterior filtering at 10 Angstroms


$ pdbphantom -i mypdb.pdb -sampling_rate 1.6
$ fourierfilter -i mypdb.vol -sampling 1.6 -low_pass 10 -fourier_mask raised_cosine 0.1

If after filtering you observe rippling in the volume, you can remove it by controlling the shape of the Fourier filter. In particular, you should increase the slope of the raised cosine (always at the expense of attenuating less higher frequencies).

This is the aspect of the volume after conversion:

/1o7d.gif

and this is the aspect of the volume after filtration:

/1o7d_filtered.gif

To plot the Fourier profile, you may use


$ gnuplot
$ gnuplot> plot "mypdb_Fourier_profile.txt" using 1:2 with line

An example of use of pseudoatoms maybe


$ xmipp_convert_vol2pseudo -i DnaBC01_a.vol -o approximation -sigma 1.5 -intensityColumn Bfactor
$ [Deform the approximation.pdb with NMA or whatever]
$ xmipp_convert_pdb2vol -i approximationDeformed.pdb -o DnaBC01_deformed -size 81-fixed_Gaussian

If you want to use a different sigma, then type


$ xmipp_convert_pdb2vol -i approximationDeformed.pdb -o DnaBC01_deformed -size 81-fixed_Gaussian 3 -intensityColumn occupancy

--Main.AlfredoSolano - 29 Jan 2007

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