Python Interface to Textal

• File formats used by TEXTAL(TM) are as follows:

  Structure Factors	MTZ
  Electron density map	XPLOR (ASCII)
  Chain and model files	PDB
  Sequence Files	FASTAA

  
  
• The occupancy and bfactor fields in the PDB files output by TEXTAL(TM) are not indicative of the model quality. These fields are used by internal programs to store data pertinent to the programs.
  
  
• The side-chains returned by LOOKUP are not geometrically accurate. RSFIT attempts to correct some of these geometrical inaccuracies.
  
  
• All TEXTAL(TM) programs generate temporary files. These files are named based on the base_name given by the user.
  
  
• At the command line typing the name of any TEXTAL(TM) program will give the usage and help information for that program.

Primitive TEXTAL Scripts

• textal.findmol   This program recenters a skeletonized electron density map over a entire protein macromolecule.
  

  Usage: "textal.findmol [input: trace_PDB] [input: Xplor_map] [input: space_group] [output: reassembled_PDB] [input: neighborhood_radius]"

• textal.capra_scale:   This program scales electron density maps so that they are on a consistent, uniform level.
  

  Usage: "textal.capra_scale [input: XPLOR_map] [output: scaled_XPLOR_map]"

• textal.capra_trace:   This program generates a set of pseudo-atoms, spaced at roughly 0.5Å, along the medial axis of the tubes of density at a given contour level.
  

  Usage: "textal.capra_trace [input: scaled_XPLOR_map] [output: trace_PDB]"

• textal.pdb2feats:   This program calculates feature vectors consisting of 76 numeric values for each trace point.
  

  Usage: "textal.pdb2feats [input: scaled_XPLOR_map] [input: trace_PDB] [output: features]"

• textal.capra_net_predict:   This program uses a neural network to estimate how close a given coordinate is in a map is likely to be to a true C-alpha.
  

  Usage: "textal.capra_net_predict [input: features] [output: distances]"

• textal.capra_chains:   This program constructs C-alpha chains representing the initial backbone of the model. This backbone is comprised of multiple C&alpha chains.
  

  Usage: "textal.capra_chains [input: features] [input: distances] [input: scaled_XPLOR_map] [output: chains_PDB]"

• textal.patch_chains:   This program attempts to connects end of Cα-chains together across breaks where the density might be weaker (slightly below connectivity threshold).
  

  Usage: "textal.patch_chains [input: chains_PDB] [input: scaled_XPLOR_map] [output: patched_chains_PDB]"

• textal.stitch:   This program uses a fragment database to connect C&alpha chain ends (especially loop regions)
  

  Usage: "textal.stitch [options] [input: scaled_XPLOR_map] [input: chains_PDB] [input: trace_PDB] [output: stitched_chains_PDB] [output: filter_chains_PDB]"

• textal.ca_refine:   This program regularizes the backbone by making small adjustments to the inter-CA spacing and 'bond' angles guided by fit to the density.
  

  Usage: "textal.ca_refine [input: chains_PDB] [input: scaled_XPLOR_map] [output: refined_chains_PDB]"

• textal.lookup:   This program performs side-chain modeling by retrieving candidate side-chains that best match the surrounding pattern of density. Lookup usually takes one to two hours to model the side-chains. It is one of the time-consuming steps in TEXTAL(TM) .
  

  Usage: "textal.lookup [input: chains_PDB] [input: scaled_XPLOR_file] [output: initial_model_PDB]"

• textal.rsfit:   This program adjusts the coordinates in a model to better satisfy both geometric constraints, as well as optimizing fit to the density.
  

  Usage: "textal.rsfit [input: model_PDB] [input: scaled_XPLOR_map] [output: final_model_PDB]"

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  High Level Scripts

• textal.fm:   This high level program creates a mask over the entire protein molecule starting from a reflection file (in MTZ format). This program comprises of the primitive functions Read_reflection_file, Findmol, Make_ASU and Make_Centered_Map.
  

  Usage: "textal.fm [input: Reflection_file_mtz]

• textal.capra:   This high level program builds the backbone of a protein model starting from a electron density map. This program comprises of the primitive functions
  • capra_scale
  • capra_trace
  • pdb2feats
  • capra_net_predict
  • capra_chains
  • patch_chains
  • stitch
  • ca_refine
  
  

  Usage: "textal.capra [input_XPLOR_file]"

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  Utilities

• textal.filter_chains:   This program outputs all chains in the input with length greater or equal to a specified length.
  

  Usage: "textal.filter_chains [options] [input: PDB_file] [output: PDB_file]"

• textal.superpose:   This program takes as input 2 chain fragments and returns the rms deviation for the best possible superposition of the 2 given fragments. Usage: "textal.superpose.py [input_CA_fragment1] [input_CA_fragment2] [optional_output_file]"

• textal.trim_chains:   This program takes a pdb and throws out all those chains that do not overlap with some part of a target molecule.
  

  Usage: "textal.trim_chains [options] [input: pdb_to_trim] [input: pdb_template]"

• textal.variance_map:   This program takes as input an electron density map (in XPLOR format) and creates a mask that differentiates between the solvent region and the protein region.
  

  Usage: "textal.variance_map [input_XPLOR_file] [output_XPLOR_file]"

• textal.makemap:   This program creates a electron density map (in XPLOR format) from a set of structure factors.
  

  Usage: "textal.makemap [options] [input: reflection_file] [output: XPLOR_map]"

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